[1] "ofn"        "-oTTHCA-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/THCA-TP/19775590/THCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THCA-TP/19782153/transformed.cor.cli.txt"

nPatients in clinical file=503, in cluster file=499, common to both=499
[1] "Reduce the number of clustering variables from 107 to 96."
[1]  96 499
[1] "AMP PEAK  1(1P36.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE 
                             5                            494 
  AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE 
                             5                            494 
[1] "AMP PEAK  2(1P32.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE 
                            5                           494 
  AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE 
                            5                           494 
[1] "AMP PEAK  3(1P31.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE 
                            5                           494 
  AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE 
                            5                           494 
[1] "AMP PEAK  4(1Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE 
                           29                           470 
  AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE 
                           29                           470 
[1] "AMP PEAK  5(1Q43) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE 
                         29                         470 
  AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE 
                         29                         470 
[1] "AMP PEAK  6(2P16.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE 
                            3                           496 
  AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE 
                            3                           496 
[1] "AMP PEAK  8(2Q37.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(2Q37.2) MUTATED AMP PEAK  8(2Q37.2) WILD-TYPE 
                            3                           496 
  AMP PEAK  8(2Q37.2) MUTATED AMP PEAK  8(2Q37.2) WILD-TYPE 
                            3                           496 
[1] "AMP PEAK  9(3P22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(3P22.3) MUTATED AMP PEAK  9(3P22.3) WILD-TYPE 
                            4                           495 
  AMP PEAK  9(3P22.3) MUTATED AMP PEAK  9(3P22.3) WILD-TYPE 
                            4                           495 
[1] "AMP PEAK 10(3P14.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE 
                            5                           494 
  AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE 
                            5                           494 
[1] "AMP PEAK 11(4P16.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(4P16.1) MUTATED AMP PEAK 11(4P16.1) WILD-TYPE 
                            7                           492 
  AMP PEAK 11(4P16.1) MUTATED AMP PEAK 11(4P16.1) WILD-TYPE 
                            7                           492 
[1] "AMP PEAK 12(4Q28.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(4Q28.2) MUTATED AMP PEAK 12(4Q28.2) WILD-TYPE 
                            6                           493 
  AMP PEAK 12(4Q28.2) MUTATED AMP PEAK 12(4Q28.2) WILD-TYPE 
                            6                           493 
[1] "AMP PEAK 13(4Q31.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(4Q31.21) MUTATED AMP PEAK 13(4Q31.21) WILD-TYPE 
                            10                            489 
  AMP PEAK 13(4Q31.21) MUTATED AMP PEAK 13(4Q31.21) WILD-TYPE 
                            10                            489 
[1] "AMP PEAK 14(4Q32.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(4Q32.3) MUTATED AMP PEAK 14(4Q32.3) WILD-TYPE 
                            7                           492 
  AMP PEAK 14(4Q32.3) MUTATED AMP PEAK 14(4Q32.3) WILD-TYPE 
                            7                           492 
[1] "AMP PEAK 15(5P14.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(5P14.3) MUTATED AMP PEAK 15(5P14.3) WILD-TYPE 
                           23                           476 
  AMP PEAK 15(5P14.3) MUTATED AMP PEAK 15(5P14.3) WILD-TYPE 
                           23                           476 
[1] "AMP PEAK 16(5Q21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(5Q21.1) MUTATED AMP PEAK 16(5Q21.1) WILD-TYPE 
                           23                           476 
  AMP PEAK 16(5Q21.1) MUTATED AMP PEAK 16(5Q21.1) WILD-TYPE 
                           23                           476 
[1] "AMP PEAK 17(5Q21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(5Q21.1) MUTATED AMP PEAK 17(5Q21.1) WILD-TYPE 
                           20                           479 
  AMP PEAK 17(5Q21.1) MUTATED AMP PEAK 17(5Q21.1) WILD-TYPE 
                           20                           479 
[1] "AMP PEAK 18(5Q33.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(5Q33.1) MUTATED AMP PEAK 18(5Q33.1) WILD-TYPE 
                           21                           478 
  AMP PEAK 18(5Q33.1) MUTATED AMP PEAK 18(5Q33.1) WILD-TYPE 
                           21                           478 
[1] "AMP PEAK 19(5Q35.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(5Q35.2) MUTATED AMP PEAK 19(5Q35.2) WILD-TYPE 
                           20                           479 
  AMP PEAK 19(5Q35.2) MUTATED AMP PEAK 19(5Q35.2) WILD-TYPE 
                           20                           479 
[1] "AMP PEAK 20(6P22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(6P22.3) MUTATED AMP PEAK 20(6P22.3) WILD-TYPE 
                            3                           496 
  AMP PEAK 20(6P22.3) MUTATED AMP PEAK 20(6P22.3) WILD-TYPE 
                            3                           496 
[1] "AMP PEAK 21(6P22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(6P22.2) MUTATED AMP PEAK 21(6P22.2) WILD-TYPE 
                            4                           495 
  AMP PEAK 21(6P22.2) MUTATED AMP PEAK 21(6P22.2) WILD-TYPE 
                            4                           495 
[1] "AMP PEAK 22(6P21.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(6P21.31) MUTATED AMP PEAK 22(6P21.31) WILD-TYPE 
                             3                            496 
  AMP PEAK 22(6P21.31) MUTATED AMP PEAK 22(6P21.31) WILD-TYPE 
                             3                            496 
[1] "AMP PEAK 23(6P21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(6P21.2) MUTATED AMP PEAK 23(6P21.2) WILD-TYPE 
                            4                           495 
  AMP PEAK 23(6P21.2) MUTATED AMP PEAK 23(6P21.2) WILD-TYPE 
                            4                           495 
[1] "AMP PEAK 24(6P12.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(6P12.2) MUTATED AMP PEAK 24(6P12.2) WILD-TYPE 
                            3                           496 
  AMP PEAK 24(6P12.2) MUTATED AMP PEAK 24(6P12.2) WILD-TYPE 
                            3                           496 
[1] "AMP PEAK 25(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(6Q12) MUTATED AMP PEAK 25(6Q12) WILD-TYPE 
                          3                         496 
  AMP PEAK 25(6Q12) MUTATED AMP PEAK 25(6Q12) WILD-TYPE 
                          3                         496 
[1] "AMP PEAK 26(6Q27) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(6Q27) MUTATED AMP PEAK 26(6Q27) WILD-TYPE 
                          4                         495 
  AMP PEAK 26(6Q27) MUTATED AMP PEAK 26(6Q27) WILD-TYPE 
                          4                         495 
[1] "AMP PEAK 27(7Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(7Q11.21) MUTATED AMP PEAK 27(7Q11.21) WILD-TYPE 
                            20                            479 
  AMP PEAK 27(7Q11.21) MUTATED AMP PEAK 27(7Q11.21) WILD-TYPE 
                            20                            479 
[1] "AMP PEAK 28(7Q21.11) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(7Q21.11) MUTATED AMP PEAK 28(7Q21.11) WILD-TYPE 
                            21                            478 
  AMP PEAK 28(7Q21.11) MUTATED AMP PEAK 28(7Q21.11) WILD-TYPE 
                            21                            478 
[1] "AMP PEAK 29(7Q31.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(7Q31.1) MUTATED AMP PEAK 29(7Q31.1) WILD-TYPE 
                           22                           477 
  AMP PEAK 29(7Q31.1) MUTATED AMP PEAK 29(7Q31.1) WILD-TYPE 
                           22                           477 
[1] "AMP PEAK 30(7Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 30(7Q34) MUTATED AMP PEAK 30(7Q34) WILD-TYPE 
                         22                         477 
  AMP PEAK 30(7Q34) MUTATED AMP PEAK 30(7Q34) WILD-TYPE 
                         22                         477 
[1] "AMP PEAK 31(9Q22.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 31(9Q22.31) MUTATED AMP PEAK 31(9Q22.31) WILD-TYPE 
                             6                            493 
  AMP PEAK 31(9Q22.31) MUTATED AMP PEAK 31(9Q22.31) WILD-TYPE 
                             6                            493 
[1] "AMP PEAK 32(9Q31.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 32(9Q31.1) MUTATED AMP PEAK 32(9Q31.1) WILD-TYPE 
                            6                           493 
  AMP PEAK 32(9Q31.1) MUTATED AMP PEAK 32(9Q31.1) WILD-TYPE 
                            6                           493 
[1] "AMP PEAK 33(9Q34.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 33(9Q34.3) MUTATED AMP PEAK 33(9Q34.3) WILD-TYPE 
                            7                           492 
  AMP PEAK 33(9Q34.3) MUTATED AMP PEAK 33(9Q34.3) WILD-TYPE 
                            7                           492 
[1] "AMP PEAK 34(10Q24.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 34(10Q24.2) MUTATED AMP PEAK 34(10Q24.2) WILD-TYPE 
                             3                            496 
  AMP PEAK 34(10Q24.2) MUTATED AMP PEAK 34(10Q24.2) WILD-TYPE 
                             3                            496 
[1] "AMP PEAK 35(10Q25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 35(10Q25.1) MUTATED AMP PEAK 35(10Q25.1) WILD-TYPE 
                             4                            495 
  AMP PEAK 35(10Q25.1) MUTATED AMP PEAK 35(10Q25.1) WILD-TYPE 
                             4                            495 
[1] "AMP PEAK 36(11P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 36(11P13) MUTATED AMP PEAK 36(11P13) WILD-TYPE 
                           8                          491 
  AMP PEAK 36(11P13) MUTATED AMP PEAK 36(11P13) WILD-TYPE 
                           8                          491 
[1] "AMP PEAK 37(12P11.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 37(12P11.1) MUTATED AMP PEAK 37(12P11.1) WILD-TYPE 
                            16                            483 
  AMP PEAK 37(12P11.1) MUTATED AMP PEAK 37(12P11.1) WILD-TYPE 
                            16                            483 
[1] "AMP PEAK 38(12Q21.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 38(12Q21.31) MUTATED AMP PEAK 38(12Q21.31) WILD-TYPE 
                             17                             482 
  AMP PEAK 38(12Q21.31) MUTATED AMP PEAK 38(12Q21.31) WILD-TYPE 
                             17                             482 
[1] "AMP PEAK 39(12Q23.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 39(12Q23.1) MUTATED AMP PEAK 39(12Q23.1) WILD-TYPE 
                            17                            482 
  AMP PEAK 39(12Q23.1) MUTATED AMP PEAK 39(12Q23.1) WILD-TYPE 
                            17                            482 
[1] "AMP PEAK 40(13Q14.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 40(13Q14.2) MUTATED AMP PEAK 40(13Q14.2) WILD-TYPE 
                             6                            493 
  AMP PEAK 40(13Q14.2) MUTATED AMP PEAK 40(13Q14.2) WILD-TYPE 
                             6                            493 
[1] "AMP PEAK 41(13Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 41(13Q34) MUTATED AMP PEAK 41(13Q34) WILD-TYPE 
                           7                          492 
  AMP PEAK 41(13Q34) MUTATED AMP PEAK 41(13Q34) WILD-TYPE 
                           7                          492 
[1] "AMP PEAK 42(14Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 42(14Q12) MUTATED AMP PEAK 42(14Q12) WILD-TYPE 
                          13                          486 
  AMP PEAK 42(14Q12) MUTATED AMP PEAK 42(14Q12) WILD-TYPE 
                          13                          486 
[1] "AMP PEAK 43(14Q32.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 43(14Q32.31) MUTATED AMP PEAK 43(14Q32.31) WILD-TYPE 
                             13                             486 
  AMP PEAK 43(14Q32.31) MUTATED AMP PEAK 43(14Q32.31) WILD-TYPE 
                             13                             486 
[1] "AMP PEAK 46(18Q12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 46(18Q12.1) MUTATED AMP PEAK 46(18Q12.1) WILD-TYPE 
                             7                            492 
  AMP PEAK 46(18Q12.1) MUTATED AMP PEAK 46(18Q12.1) WILD-TYPE 
                             7                            492 
[1] "AMP PEAK 47(18Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 47(18Q22.1) MUTATED AMP PEAK 47(18Q22.1) WILD-TYPE 
                             7                            492 
  AMP PEAK 47(18Q22.1) MUTATED AMP PEAK 47(18Q22.1) WILD-TYPE 
                             7                            492 
[1] "AMP PEAK 48(18Q22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 48(18Q22.3) MUTATED AMP PEAK 48(18Q22.3) WILD-TYPE 
                             8                            491 
  AMP PEAK 48(18Q22.3) MUTATED AMP PEAK 48(18Q22.3) WILD-TYPE 
                             8                            491 
[1] "AMP PEAK 49(19P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 49(19P13.3) MUTATED AMP PEAK 49(19P13.3) WILD-TYPE 
                             8                            491 
  AMP PEAK 49(19P13.3) MUTATED AMP PEAK 49(19P13.3) WILD-TYPE 
                             8                            491 
[1] "AMP PEAK 50(20P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 50(20P13) MUTATED AMP PEAK 50(20P13) WILD-TYPE 
                          14                          485 
  AMP PEAK 50(20P13) MUTATED AMP PEAK 50(20P13) WILD-TYPE 
                          14                          485 
[1] "AMP PEAK 51(20Q13.11) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 51(20Q13.11) MUTATED AMP PEAK 51(20Q13.11) WILD-TYPE 
                             14                             485 
  AMP PEAK 51(20Q13.11) MUTATED AMP PEAK 51(20Q13.11) WILD-TYPE 
                             14                             485 
[1] "AMP PEAK 52(20Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 52(20Q13.2) MUTATED AMP PEAK 52(20Q13.2) WILD-TYPE 
                            14                            485 
  AMP PEAK 52(20Q13.2) MUTATED AMP PEAK 52(20Q13.2) WILD-TYPE 
                            14                            485 
[1] "AMP PEAK 53(20Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 53(20Q13.2) MUTATED AMP PEAK 53(20Q13.2) WILD-TYPE 
                            13                            486 
  AMP PEAK 53(20Q13.2) MUTATED AMP PEAK 53(20Q13.2) WILD-TYPE 
                            13                            486 
[1] "AMP PEAK 54(21Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 54(21Q21.3) MUTATED AMP PEAK 54(21Q21.3) WILD-TYPE 
                             6                            493 
  AMP PEAK 54(21Q21.3) MUTATED AMP PEAK 54(21Q21.3) WILD-TYPE 
                             6                            493 
[1] "AMP PEAK 55(22Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 55(22Q11.21) MUTATED AMP PEAK 55(22Q11.21) WILD-TYPE 
                              7                             492 
  AMP PEAK 55(22Q11.21) MUTATED AMP PEAK 55(22Q11.21) WILD-TYPE 
                              7                             492 
[1] "AMP PEAK 56(XP22.12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 56(XP22.12) MUTATED AMP PEAK 56(XP22.12) WILD-TYPE 
                            10                            489 
  AMP PEAK 56(XP22.12) MUTATED AMP PEAK 56(XP22.12) WILD-TYPE 
                            10                            489 
[1] "AMP PEAK 57(XP11.4) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 57(XP11.4) MUTATED AMP PEAK 57(XP11.4) WILD-TYPE 
                            9                           490 
  AMP PEAK 57(XP11.4) MUTATED AMP PEAK 57(XP11.4) WILD-TYPE 
                            9                           490 
[1] "AMP PEAK 58(XP11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 58(XP11.22) MUTATED AMP PEAK 58(XP11.22) WILD-TYPE 
                             8                            491 
  AMP PEAK 58(XP11.22) MUTATED AMP PEAK 58(XP11.22) WILD-TYPE 
                             8                            491 
[1] "AMP PEAK 59(XP11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 59(XP11.21) MUTATED AMP PEAK 59(XP11.21) WILD-TYPE 
                             9                            490 
  AMP PEAK 59(XP11.21) MUTATED AMP PEAK 59(XP11.21) WILD-TYPE 
                             9                            490 
[1] "AMP PEAK 60(XQ21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 60(XQ21.2) MUTATED AMP PEAK 60(XQ21.2) WILD-TYPE 
                            9                           490 
  AMP PEAK 60(XQ21.2) MUTATED AMP PEAK 60(XQ21.2) WILD-TYPE 
                            9                           490 
[1] "AMP PEAK 61(XQ22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 61(XQ22.3) MUTATED AMP PEAK 61(XQ22.3) WILD-TYPE 
                           15                           484 
  AMP PEAK 61(XQ22.3) MUTATED AMP PEAK 61(XQ22.3) WILD-TYPE 
                           15                           484 
[1] "AMP PEAK 62(XQ23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 62(XQ23) MUTATED AMP PEAK 62(XQ23) WILD-TYPE 
                          9                         490 
  AMP PEAK 62(XQ23) MUTATED AMP PEAK 62(XQ23) WILD-TYPE 
                          9                         490 
[1] "AMP PEAK 63(XQ24) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 63(XQ24) MUTATED AMP PEAK 63(XQ24) WILD-TYPE 
                          9                         490 
  AMP PEAK 63(XQ24) MUTATED AMP PEAK 63(XQ24) WILD-TYPE 
                          9                         490 
[1] "AMP PEAK 64(XQ24) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 64(XQ24) MUTATED AMP PEAK 64(XQ24) WILD-TYPE 
                          9                         490 
  AMP PEAK 64(XQ24) MUTATED AMP PEAK 64(XQ24) WILD-TYPE 
                          9                         490 
[1] "AMP PEAK 65(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 65(XQ28) MUTATED AMP PEAK 65(XQ28) WILD-TYPE 
                         10                         489 
  AMP PEAK 65(XQ28) MUTATED AMP PEAK 65(XQ28) WILD-TYPE 
                         10                         489 
[1] "DEL PEAK  1(1Q24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE 
                            3                           496 
  DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE 
                            3                           496 
[1] "DEL PEAK  2(1Q42.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE 
                             5                            494 
  DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE 
                             5                            494 
[1] "DEL PEAK  3(2P23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE 
                           12                           487 
  DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE 
                           12                           487 
[1] "DEL PEAK  4(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           10                           489 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           10                           489 
[1] "DEL PEAK  5(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           13                           486 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           13                           486 
[1] "DEL PEAK  7(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                            5                           494 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                            5                           494 
[1] "DEL PEAK  8(5P15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE 
                            4                           495 
  DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE 
                            4                           495 
[1] "DEL PEAK 11(6Q22.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                             7                            492 
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                             7                            492 
[1] "DEL PEAK 13(7Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE 
                          4                         495 
  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE 
                          4                         495 
[1] "DEL PEAK 14(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE 
                            4                           495 
  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE 
                            4                           495 
[1] "DEL PEAK 15(8P22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE 
                          4                         495 
  DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE 
                          4                         495 
[1] "DEL PEAK 16(8P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE 
                          4                         495 
  DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE 
                          4                         495 
[1] "DEL PEAK 17(8Q24.22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE 
                             7                            492 
  DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE 
                             7                            492 
[1] "DEL PEAK 18(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                           20                           479 
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                           20                           479 
[1] "DEL PEAK 19(9Q22.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE 
                            27                            472 
  DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE 
                            27                            472 
[1] "DEL PEAK 20(10P12.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE 
                              7                             492 
  DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE 
                              7                             492 
[1] "DEL PEAK 21(10Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE 
                            12                            487 
  DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE 
                            12                            487 
[1] "DEL PEAK 22(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE 
                             12                             487 
  DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE 
                             12                             487 
[1] "DEL PEAK 23(11P15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE 
                             7                            492 
  DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE 
                             7                            492 
[1] "DEL PEAK 24(13Q12.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE 
                             18                             481 
  DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE 
                             18                             481 
[1] "DEL PEAK 25(13Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE 
                            19                            480 
  DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE 
                            19                            480 
[1] "DEL PEAK 27(15Q25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE 
                             9                            490 
  DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE 
                             9                            490 
[1] "DEL PEAK 29(16Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE 
                             6                            493 
  DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE 
                             6                            493 
[1] "DEL PEAK 30(17P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE 
                             8                            491 
  DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE 
                             8                            491 
[1] "DEL PEAK 31(18Q12.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE 
                             4                            495 
  DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE 
                             4                            495 
[1] "DEL PEAK 32(19P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE 
                             7                            492 
  DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE 
                             7                            492 
[1] "DEL PEAK 33(19P13.12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE 
                              8                             491 
  DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE 
                              8                             491 
[1] "DEL PEAK 36(21Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE 
                             9                            490 
  DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE 
                             9                            490 
[1] "DEL PEAK 37(22Q12.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE 
                            90                            409 
  DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE 
                            90                            409 
[1] "DEL PEAK 38(22Q13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE 
                            89                            410 
  DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE 
                            89                            410 
[1] "DEL PEAK 39(22Q13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE 
                            89                            410 
  DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE 
                            89                            410 
[1] "DEL PEAK 40(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE 
                             90                             409 
  DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE 
                             90                             409 
[1] "DEL PEAK 41(XQ23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE 
                          4                         495 
  DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE 
                          4                         495 
[1] "DEL PEAK 42(XQ22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE 
                            4                           495 
  DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE 
                            4                           495 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "HISTOLOGICAL_TYPE"                   
[14] "RADIATION_EXPOSURE"                  
[15] "EXTRATHYROIDAL_EXTENSION"            
[16] "RESIDUAL_TUMOR"                      
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "MULTIFOCALITY"                       
[19] "TUMOR_SIZE"                          
[20] "RACE"                                
[21] "ETHNICITY"                           

Input Data has 21 rows and 499 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=73,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=16,	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=430,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RADIATION_EXPOSURE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'EXTRATHYROIDAL_EXTENSION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'MULTIFOCALITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'TUMOR_SIZE':	nDistinctValues=61,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 499 columns, 1 survival variables, and 16 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"           "PATHOLOGIC_STAGE"        
 [3] "PATHOLOGY_T_STAGE"        "PATHOLOGY_N_STAGE"       
 [5] "PATHOLOGY_M_STAGE"        "GENDER"                  
 [7] "RADIATION_THERAPY"        "HISTOLOGICAL_TYPE"       
 [9] "RADIATION_EXPOSURE"       "EXTRATHYROIDAL_EXTENSION"
[11] "RESIDUAL_TUMOR"           "NUMBER_OF_LYMPH_NODES"   
[13] "MULTIFOCALITY"            "TUMOR_SIZE"              
[15] "RACE"                     "ETHNICITY"               
YEARS_TO_BIRTH, nv=73, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
142 165 167  23 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
142 165 167  23 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
142 165 167  23 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
142 165 167  23 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=4, binary=FALSE, numeric=FALSE
RADIATION_EXPOSURE, nv=2, binary=FALSE, numeric=FALSE
EXTRATHYROIDAL_EXTENSION, nv=4, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=28, binary=FALSE, numeric=TRUE
MULTIFOCALITY, nv=2, binary=FALSE, numeric=FALSE
TUMOR_SIZE, nv=61, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1P36.32) MUTATION ANALYSIS
D1V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  1(1P36.32) MUTATED     5   0
  AMP PEAK  1(1P36.32) WILD-TYPE 476  16
  AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE 
                             5                            492 
  AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE 
                             0                             16 
$`AMP PEAK  1(1P36.32) MUTATED`
TCGA-EL-A3GP TCGA-EL-A4JX TCGA-ET-A3BT TCGA-FY-A3NM TCGA-L6-A4EU 
       49.51        45.96        87.62         0.99         9.50 

$`AMP PEAK  1(1P36.32) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
       30.58        35.41        27.45        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74         6.77        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        36.33        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       35.87        40.96        36.99        20.22        30.61        42.54 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20        23.21        21.27        20.48        24.82        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ 
       21.01        18.97         7.76        35.67         3.12        36.43 
TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       24.76        17.23        27.62        30.87        21.34        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        80.52        63.19        52.44        39.95        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04         0.72 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
        0.26         3.02        25.45        30.61         0.16         0.23 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        33.50         0.39         0.39        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS 
       26.73       155.54        97.74       158.83         7.66        45.53 
TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY 
       60.95       157.15        37.94        57.01       106.62         4.18 
TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 
       79.50       139.86        98.53        69.57        57.11       108.36 
TCGA-EL-A3GO TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       64.87        50.24       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       150.48       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        89.56        78.97        51.78 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        47.38        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JZ 
       60.16         7.07        59.44        57.47        34.72        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       47.84        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       78.61        57.01        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       32.32        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       22.52        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33         0.49         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
      106.09       107.41       108.46        84.89       123.32       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       95.34        94.13        55.10        98.20        28.24        50.40 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
       79.10        76.64         5.79        77.82        75.42        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
       52.47       116.78        94.59        84.85        80.58        66.84 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       43.73        62.83       166.62        24.72        43.99        46.26 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
       44.38        40.21        37.48        33.17        31.40        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       71.44        31.59        79.69        24.69        68.22       117.40 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77       112.80        39.95        33.63        81.83       106.36 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD 
       85.15        85.68        78.77        71.08         4.11         1.05 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       13.28         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       17.82         7.82        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08         0.30         0.76        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       15.16         6.58        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83        31.10         8.22        25.64        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       21.83        36.10        32.45        30.21        23.93        12.89 

  AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE 
                          0.99                           0.16 
  AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE 
                         87.62                         169.32 
  AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE 
                         45.96                          30.61 
[1] "1.0 - 87.6 (46.0)"  "0.2 - 169.3 (30.6)"
[1] "hr="     "9100000"
D1V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK  1(1P36.32) MUTATED         1        0         3        0         1
  AMP PEAK  1(1P36.32) WILD-TYPE     281       50       108        2        45
                                vv
clus                             STAGE IVC
  AMP PEAK  1(1P36.32) MUTATED           0
  AMP PEAK  1(1P36.32) WILD-TYPE         6
D1V3, multiclass
           clus
vv          AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE
  STAGE I                              1                            281
  STAGE II                             0                             50
  STAGE III                            3                            108
  STAGE IV                             0                              2
  STAGE IVA                            1                             45
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK  1(1P36.32) MUTATED     0   1   4   0
  AMP PEAK  1(1P36.32) WILD-TYPE 142 164 163  23
D1V4, multiclass
    clus
vv   AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE
  T1                            0                            142
  T2                            1                            164
  T3                            4                            163
  T4                            0                             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"
D1V5, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.32) MUTATED     2   3
  AMP PEAK  1(1P36.32) WILD-TYPE 223 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.32) MUTATED      2    3
  AMP PEAK  1(1P36.32) WILD-TYPE  223  221
   clus
vv  AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE
  0                            2                            223
  1                            3                            221
[1] 2 2
[1] FALSE
D1V6, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.32) MUTATED     2   0
  AMP PEAK  1(1P36.32) WILD-TYPE 276   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.32) MUTATED      2    0
  AMP PEAK  1(1P36.32) WILD-TYPE  276    9
   clus
vv  AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE
  0                            2                            276
  1                            0                              9
[1] 2 2
[1] FALSE
D1V7, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.32) MUTATED     4   1
  AMP PEAK  1(1P36.32) WILD-TYPE 361 133
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.32) MUTATED      4    1
  AMP PEAK  1(1P36.32) WILD-TYPE  361  133
        clus
vv       AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE
  FEMALE                            4                            361
  MALE                              1                            133
[1] 2 2
[1] FALSE
D1V8, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.32) MUTATED     2   2
  AMP PEAK  1(1P36.32) WILD-TYPE 183 288
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.32) MUTATED      2    2
  AMP PEAK  1(1P36.32) WILD-TYPE  183  288
     clus
vv    AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE
  NO                             2                            183
  YES                            2                            288
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK  1(1P36.32) MUTATED                0
  AMP PEAK  1(1P36.32) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK  1(1P36.32) MUTATED                                               3
  AMP PEAK  1(1P36.32) WILD-TYPE                                           352
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK  1(1P36.32) MUTATED                                                                        0
  AMP PEAK  1(1P36.32) WILD-TYPE                                                                    100
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK  1(1P36.32) MUTATED                                                                     2
  AMP PEAK  1(1P36.32) WILD-TYPE                                                                  34
D1V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK  1(1P36.32) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            0
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               2
                                                                        clus
vv                                                                       AMP PEAK  1(1P36.32) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            100
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                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"
D1V10, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.32) MUTATED     4   1
  AMP PEAK  1(1P36.32) WILD-TYPE 416  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.32) MUTATED      4    1
  AMP PEAK  1(1P36.32) WILD-TYPE  416   16
     clus
vv    AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE
  NO                             4                            416
  YES                            1                             16
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK  1(1P36.32) MUTATED              3                       0    2
  AMP PEAK  1(1P36.32) WILD-TYPE          129                      18  328
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK  1(1P36.32) MUTATED                     0
  AMP PEAK  1(1P36.32) WILD-TYPE                   1
D1V11, multiclass
                         clus
vv                        AMP PEAK  1(1P36.32) MUTATED
  MINIMAL (T3)                                       3
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               2
  VERY ADVANCED (T4B)                                0
                         clus
vv                        AMP PEAK  1(1P36.32) WILD-TYPE
  MINIMAL (T3)                                       129
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               328
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  1(1P36.32) MUTATED     4   1   0   0
  AMP PEAK  1(1P36.32) WILD-TYPE 379  50   4  30
D1V12, multiclass
    clus
vv   AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE
  R0                            4                            379
  R1                            1                             50
  R2                            0                              4
  RX                            0                             30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V13, continuous
D1V14, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.32) MUTATED     2   3
  AMP PEAK  1(1P36.32) WILD-TYPE 223 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.32) MUTATED      2    3
  AMP PEAK  1(1P36.32) WILD-TYPE  223  261
            clus
vv           AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE
  MULTIFOCAL                            2                            223
  UNIFOCAL                              3                            261
[1] 2 2
[1] FALSE
D1V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  1(1P36.32) MUTATED                                  0     0
  AMP PEAK  1(1P36.32) WILD-TYPE                                1    52
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1P36.32) MUTATED                           3     2
  AMP PEAK  1(1P36.32) WILD-TYPE                        24   326
D1V16, multiclass
                                  clus
vv                                 AMP PEAK  1(1P36.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                       2
                                  clus
vv                                 AMP PEAK  1(1P36.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        52
  BLACK OR AFRICAN AMERICAN                                    24
  WHITE                                                       326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V17, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.32) MUTATED     0   5
  AMP PEAK  1(1P36.32) WILD-TYPE  38 354
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.32) MUTATED      0    5
  AMP PEAK  1(1P36.32) WILD-TYPE   38  354
                        clus
vv                       AMP PEAK  1(1P36.32) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            5
                        clus
vv                       AMP PEAK  1(1P36.32) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            354
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(1P32.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(1P32.3) MUTATED     5   0
  AMP PEAK  2(1P32.3) WILD-TYPE 476  16
  AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE 
                            5                           492 
  AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE 
                            0                            16 
$`AMP PEAK  2(1P32.3) MUTATED`
TCGA-DO-A2HM TCGA-EM-A3O8 TCGA-ET-A3BT TCGA-ET-A40Q TCGA-FY-A3NM 
        2.33         0.49        87.62        46.26         0.99 

$`AMP PEAK  2(1P32.3) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
       30.58        35.41        27.45        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74         6.77        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        36.33        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       35.87        40.96        36.99        20.22        30.61        42.54 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20        23.21        21.27        20.48        24.82        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ 
       21.01        18.97         7.76        35.67         3.12        36.43 
TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       24.76        17.23        27.62        30.87        21.34        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       35.38        54.90        21.53        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        30.61         0.16         0.23        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        33.50         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        69.57        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       49.51        50.24       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       150.48       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        89.56        78.97        51.78 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        47.38        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       60.16         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        47.84        43.59        24.30        27.06        23.90 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J 
       19.46        78.61        57.01        54.08        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P 
       15.75        10.45        14.53        10.65        44.19        41.29 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        47.57        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        32.32        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        29.72        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O9 TCGA-EM-A3OA 
       15.02        14.50        15.06         7.33         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
      106.09       107.41       108.46        84.89       123.32       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       95.34        94.13        55.10        98.20        28.24        50.40 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
       79.10        76.64         5.79        77.82        75.42        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
       52.47       116.78        94.59        84.85        80.58        66.84 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40R 
       43.73        62.83       166.62        24.72        43.99        44.38 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       40.21        37.48        33.17        31.40        73.74        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
      112.80        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        13.28 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10       116.09         1.25        20.42        17.82 
TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
        7.82        19.56        13.91        16.27        15.68        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08         0.30         0.76        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58        22.49        19.04         1.35        21.60         1.68 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46         2.99        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        18.51        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
       31.10         8.22        25.64        17.23        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
      113.85        26.70        43.69        18.64        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       84.72        35.28        33.24        33.40        40.37        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        9.50        36.10        32.45        30.21        23.93        12.89 

  AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE 
                         0.49                          0.16 
  AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE 
                        87.62                        169.32 
  AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE 
                         2.33                         30.61 
[1] "0.5 - 87.6 (2.3)"   "0.2 - 169.3 (30.6)"
[1] "hr="     "3300000"
D2V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK  2(1P32.3) MUTATED         2        0         1        0         2
  AMP PEAK  2(1P32.3) WILD-TYPE     280       50       110        2        44
                               vv
clus                            STAGE IVC
  AMP PEAK  2(1P32.3) MUTATED           0
  AMP PEAK  2(1P32.3) WILD-TYPE         6
D2V3, multiclass
           clus
vv          AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE
  STAGE I                             2                           280
  STAGE II                            0                            50
  STAGE III                           1                           110
  STAGE IV                            0                             2
  STAGE IVA                           2                            44
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  2(1P32.3) MUTATED     2   1   2   0
  AMP PEAK  2(1P32.3) WILD-TYPE 140 164 165  23
D2V4, multiclass
    clus
vv   AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE
  T1                           2                           140
  T2                           1                           164
  T3                           2                           165
  T4                           0                            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"
D2V5, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P32.3) MUTATED     2   3
  AMP PEAK  2(1P32.3) WILD-TYPE 223 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P32.3) MUTATED      2    3
  AMP PEAK  2(1P32.3) WILD-TYPE  223  221
   clus
vv  AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE
  0                           2                           223
  1                           3                           221
[1] 2 2
[1] FALSE
D2V6, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P32.3) MUTATED     0   0
  AMP PEAK  2(1P32.3) WILD-TYPE 278   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P32.3) MUTATED      0    0
  AMP PEAK  2(1P32.3) WILD-TYPE  278    9
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P32.3) MUTATED     3   2
  AMP PEAK  2(1P32.3) WILD-TYPE 362 132
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P32.3) MUTATED      3    2
  AMP PEAK  2(1P32.3) WILD-TYPE  362  132
        clus
vv       AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE
  FEMALE                           3                           362
  MALE                             2                           132
[1] 2 2
[1] FALSE
D2V8, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P32.3) MUTATED     1   2
  AMP PEAK  2(1P32.3) WILD-TYPE 184 288
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P32.3) MUTATED      1    2
  AMP PEAK  2(1P32.3) WILD-TYPE  184  288
     clus
vv    AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE
  NO                            1                           184
  YES                           2                           288
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK  2(1P32.3) MUTATED                0
  AMP PEAK  2(1P32.3) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK  2(1P32.3) MUTATED                                               2
  AMP PEAK  2(1P32.3) WILD-TYPE                                           353
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK  2(1P32.3) MUTATED                                                                        1
  AMP PEAK  2(1P32.3) WILD-TYPE                                                                     99
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK  2(1P32.3) MUTATED                                                                     2
  AMP PEAK  2(1P32.3) WILD-TYPE                                                                  34
D2V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK  2(1P32.3) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              2
                                                                        clus
vv                                                                       AMP PEAK  2(1P32.3) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            99
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               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"
D2V10, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P32.3) MUTATED     2   2
  AMP PEAK  2(1P32.3) WILD-TYPE 418  15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P32.3) MUTATED      2    2
  AMP PEAK  2(1P32.3) WILD-TYPE  418   15
     clus
vv    AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE
  NO                            2                           418
  YES                           2                            15
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK  2(1P32.3) MUTATED              2                       0    3
  AMP PEAK  2(1P32.3) WILD-TYPE          130                      18  327
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK  2(1P32.3) MUTATED                     0
  AMP PEAK  2(1P32.3) WILD-TYPE                   1
D2V11, multiclass
                         clus
vv                        AMP PEAK  2(1P32.3) MUTATED
  MINIMAL (T3)                                      2
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              3
  VERY ADVANCED (T4B)                               0
                         clus
vv                        AMP PEAK  2(1P32.3) WILD-TYPE
  MINIMAL (T3)                                      130
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              327
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  2(1P32.3) MUTATED     4   0   0   1
  AMP PEAK  2(1P32.3) WILD-TYPE 379  51   4  29
D2V12, multiclass
    clus
vv   AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE
  R0                           4                           379
  R1                           0                            51
  R2                           0                             4
  RX                           1                            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"
D2V13, continuous
D2V14, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P32.3) MUTATED     3   2
  AMP PEAK  2(1P32.3) WILD-TYPE 222 262
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P32.3) MUTATED      3    2
  AMP PEAK  2(1P32.3) WILD-TYPE  222  262
            clus
vv           AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE
  MULTIFOCAL                           3                           222
  UNIFOCAL                             2                           262
[1] 2 2
[1] FALSE
D2V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  2(1P32.3) MUTATED                                  0     0
  AMP PEAK  2(1P32.3) WILD-TYPE                                1    52
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1P32.3) MUTATED                           0     4
  AMP PEAK  2(1P32.3) WILD-TYPE                        27   324
D2V16, multiclass
                                  clus
vv                                 AMP PEAK  2(1P32.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      4
                                  clus
vv                                 AMP PEAK  2(1P32.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       52
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V17, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P32.3) MUTATED     0   4
  AMP PEAK  2(1P32.3) WILD-TYPE  38 355
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P32.3) MUTATED      0    4
  AMP PEAK  2(1P32.3) WILD-TYPE   38  355
                        clus
vv                       AMP PEAK  2(1P32.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           4
                        clus
vv                       AMP PEAK  2(1P32.3) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           355
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(1P31.1) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  3(1P31.1) MUTATED     5   0
  AMP PEAK  3(1P31.1) WILD-TYPE 476  16
  AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE 
                            5                           492 
  AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE 
                            0                            16 
$`AMP PEAK  3(1P31.1) MUTATED`
TCGA-DJ-A2PW TCGA-DO-A2HM TCGA-EM-A4FR TCGA-ET-A3BT TCGA-FY-A3NM 
       34.85         2.33        21.53        87.62         0.99 

$`AMP PEAK  3(1P31.1) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
       30.58        35.41        27.45        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       31.99        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       54.90        21.53        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        52.44        39.95        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       47.84        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       78.61        57.01        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       32.32        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       22.52        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33         0.49         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       22.45        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
      107.41       108.46        84.89       123.32       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       94.13        55.10        98.20        28.24        50.40        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
       76.64         5.79        77.82        75.42        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       62.83       166.62        24.72        43.99        46.26        44.38 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       40.21        37.48        33.17        31.40        73.74        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
      112.80        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        13.28 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10       116.09         1.25        20.42        17.82 
TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
        7.82        19.56        13.91        16.27        15.68        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08         0.30         0.76        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58        22.49        19.04         1.35        21.60         1.68 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46         2.99        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        18.51        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
       31.10         8.22        25.64        17.23        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
      113.85        26.70        43.69        18.64        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       84.72        35.28        33.24        33.40        40.37        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        9.50        36.10        32.45        30.21        23.93        12.89 

  AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE 
                         0.99                          0.16 
  AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE 
                        87.62                        169.32 
  AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE 
                        21.53                         30.61 
[1] "1.0 - 87.6 (21.5)"  "0.2 - 169.3 (30.6)"
[1] "hr="     "3300000"
D3V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK  3(1P31.1) MUTATED         1        0         2        0         2
  AMP PEAK  3(1P31.1) WILD-TYPE     281       50       109        2        44
                               vv
clus                            STAGE IVC
  AMP PEAK  3(1P31.1) MUTATED           0
  AMP PEAK  3(1P31.1) WILD-TYPE         6
D3V3, multiclass
           clus
vv          AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE
  STAGE I                             1                           281
  STAGE II                            0                            50
  STAGE III                           2                           109
  STAGE IV                            0                             2
  STAGE IVA                           2                            44
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  3(1P31.1) MUTATED     1   1   3   0
  AMP PEAK  3(1P31.1) WILD-TYPE 141 164 164  23
D3V4, multiclass
    clus
vv   AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE
  T1                           1                           141
  T2                           1                           164
  T3                           3                           164
  T4                           0                            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"
D3V5, binary
                               cls
clus                              0   1
  AMP PEAK  3(1P31.1) MUTATED     1   4
  AMP PEAK  3(1P31.1) WILD-TYPE 224 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1P31.1) MUTATED      1    4
  AMP PEAK  3(1P31.1) WILD-TYPE  224  220
   clus
vv  AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE
  0                           1                           224
  1                           4                           220
[1] 2 2
[1] FALSE
D3V6, binary
                               cls
clus                              0   1
  AMP PEAK  3(1P31.1) MUTATED     1   0
  AMP PEAK  3(1P31.1) WILD-TYPE 277   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1P31.1) MUTATED      1    0
  AMP PEAK  3(1P31.1) WILD-TYPE  277    9
   clus
vv  AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE
  0                           1                           277
  1                           0                             9
[1] 2 2
[1] FALSE
D3V7, binary
                               cls
clus                              0   1
  AMP PEAK  3(1P31.1) MUTATED     2   3
  AMP PEAK  3(1P31.1) WILD-TYPE 363 131
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1P31.1) MUTATED      2    3
  AMP PEAK  3(1P31.1) WILD-TYPE  363  131
        clus
vv       AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE
  FEMALE                           2                           363
  MALE                             3                           131
[1] 2 2
[1] FALSE
D3V8, binary
                               cls
clus                              0   1
  AMP PEAK  3(1P31.1) MUTATED     0   3
  AMP PEAK  3(1P31.1) WILD-TYPE 185 287
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1P31.1) MUTATED      0    3
  AMP PEAK  3(1P31.1) WILD-TYPE  185  287
     clus
vv    AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE
  NO                            0                           185
  YES                           3                           287
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK  3(1P31.1) MUTATED                1
  AMP PEAK  3(1P31.1) WILD-TYPE              7
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK  3(1P31.1) MUTATED                                               3
  AMP PEAK  3(1P31.1) WILD-TYPE                                           352
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK  3(1P31.1) MUTATED                                                                        0
  AMP PEAK  3(1P31.1) WILD-TYPE                                                                    100
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK  3(1P31.1) MUTATED                                                                     1
  AMP PEAK  3(1P31.1) WILD-TYPE                                                                  35
D3V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK  3(1P31.1) MUTATED
  OTHER  SPECIFY                                                                                   1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           0
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              1
                                                                        clus
vv                                                                       AMP PEAK  3(1P31.1) WILD-TYPE
  OTHER  SPECIFY                                                                                     7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           100
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, binary
                               cls
clus                              0   1
  AMP PEAK  3(1P31.1) MUTATED     3   1
  AMP PEAK  3(1P31.1) WILD-TYPE 417  16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1P31.1) MUTATED      3    1
  AMP PEAK  3(1P31.1) WILD-TYPE  417   16
     clus
vv    AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE
  NO                            3                           417
  YES                           1                            16
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK  3(1P31.1) MUTATED              1                       0    4
  AMP PEAK  3(1P31.1) WILD-TYPE          131                      18  326
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK  3(1P31.1) MUTATED                     0
  AMP PEAK  3(1P31.1) WILD-TYPE                   1
D3V11, multiclass
                         clus
vv                        AMP PEAK  3(1P31.1) MUTATED
  MINIMAL (T3)                                      1
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              4
  VERY ADVANCED (T4B)                               0
                         clus
vv                        AMP PEAK  3(1P31.1) WILD-TYPE
  MINIMAL (T3)                                      131
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              326
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  3(1P31.1) MUTATED     4   0   0   1
  AMP PEAK  3(1P31.1) WILD-TYPE 379  51   4  29
D3V12, multiclass
    clus
vv   AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE
  R0                           4                           379
  R1                           0                            51
  R2                           0                             4
  RX                           1                            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"
D3V13, continuous
D3V14, binary
                               cls
clus                              0   1
  AMP PEAK  3(1P31.1) MUTATED     3   2
  AMP PEAK  3(1P31.1) WILD-TYPE 222 262
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1P31.1) MUTATED      3    2
  AMP PEAK  3(1P31.1) WILD-TYPE  222  262
            clus
vv           AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE
  MULTIFOCAL                           3                           222
  UNIFOCAL                             2                           262
[1] 2 2
[1] FALSE
D3V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  3(1P31.1) MUTATED                                  0     0
  AMP PEAK  3(1P31.1) WILD-TYPE                                1    52
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(1P31.1) MUTATED                           0     4
  AMP PEAK  3(1P31.1) WILD-TYPE                        27   324
D3V16, multiclass
                                  clus
vv                                 AMP PEAK  3(1P31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      4
                                  clus
vv                                 AMP PEAK  3(1P31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       52
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V17, binary
                               cls
clus                              0   1
  AMP PEAK  3(1P31.1) MUTATED     0   4
  AMP PEAK  3(1P31.1) WILD-TYPE  38 355
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1P31.1) MUTATED      0    4
  AMP PEAK  3(1P31.1) WILD-TYPE   38  355
                        clus
vv                       AMP PEAK  3(1P31.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           4
                        clus
vv                       AMP PEAK  3(1P31.1) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           355
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(1Q31.2) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(1Q31.2) MUTATED    26   2
  AMP PEAK  4(1Q31.2) WILD-TYPE 455  14
  AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE 
                           28                           469 
  AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE 
                            2                            14 
$`AMP PEAK  4(1Q31.2) MUTATED`
TCGA-4C-A93U TCGA-BJ-A192 TCGA-BJ-A290 TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
        4.24        44.35        30.21        11.57        30.02        25.12 
TCGA-DJ-A13U TCGA-DO-A2HM TCGA-EL-A3GP TCGA-EL-A3GU TCGA-EL-A3H5 TCGA-EL-A3MZ 
       23.38         2.33        49.51       136.01        83.57        52.50 
TCGA-EL-A3T9 TCGA-EL-A3ZO TCGA-EL-A4JX TCGA-EM-A3O3 TCGA-ET-A39P TCGA-ET-A3BT 
        5.72        47.38        45.96        14.50        95.34        87.62 
TCGA-FE-A231 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A40L TCGA-H2-A26U TCGA-IM-A3EB 
       31.59         0.99        19.56         6.58        17.00        48.92 
TCGA-IM-A3U2 TCGA-J8-A3O1 TCGA-KS-A4IB TCGA-L6-A4EU 
       18.51        27.19        84.72         9.50 

$`AMP PEAK  4(1Q31.2) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        49.78        16.34        14.73        41.33 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73        25.48        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A28R 
       42.08        51.39        41.52        20.58         4.83        42.15 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04        35.54        32.45        11.31        30.97        11.08 
TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 
       22.88        18.38        16.57        20.48        18.97         7.04 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.01        13.94        36.39        23.31        18.64         7.99 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
       10.88        21.01         3.45        23.84        28.44        15.45 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
       21.63        23.18        19.43        23.47        12.66        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.66        35.84        21.63        50.17        37.64        15.85 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       18.54        18.84        30.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       56.19        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       54.90        21.53        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        52.44        39.95        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GQ 
       98.53        69.57        57.11       108.36        64.87        50.24 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY 
      115.10        65.39        50.37        50.20       147.75       101.13 
TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H7 
      139.99        49.32        33.50        43.36        49.71       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3N2 TCGA-EL-A3N3 
      150.48       108.66        57.63        17.52        29.65       147.42 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
      107.47        66.90        82.82        89.56        78.97        51.78 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       62.30        36.03        53.06        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JZ TCGA-EL-A4K0 
        7.07        59.44        57.47        34.72        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       34.39        30.51        53.36        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       43.59        24.30        27.06        23.90        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        48.49        18.05        19.79        19.46        78.61 
TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       57.01        54.08        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       14.53        10.65        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
       17.88        13.18        23.51         6.05         2.99        12.30 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       48.46        13.15        22.16        40.34        19.73        32.32 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       33.96        17.59        17.46        17.29        14.60        22.52 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O6 
       12.07        17.49        17.39        16.18        15.02        15.06 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33         0.49         9.24        13.91        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       29.95        29.85        13.51        12.79        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
       21.34         5.33        26.37        26.37        22.45        21.53 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       60.49        24.46        13.68        81.93        81.70        77.56 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       70.42        56.58        60.20        63.39        65.29        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       63.45        88.41        58.75        37.25        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       83.34         2.66        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39R TCGA-ET-A39S 
      108.46        84.89       123.32       100.57        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       98.20        28.24        50.40        79.10        76.64         5.79 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       77.82        75.42        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A232 TCGA-FE-A233 
       33.17        31.40        73.74        71.44        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       117.40        66.77       112.80        39.95        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.11         1.05        13.28         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3R6 TCGA-FY-A3R7 
        1.25        20.42        17.82         7.82        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       17.36        15.16        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
        1.68        12.53        21.67        12.46         2.99        20.05 
TCGA-H2-A422 TCGA-IM-A3ED TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       18.61        47.41        16.90        21.83        31.10         8.22 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       25.64        17.23        43.17        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY 
       24.69        22.29         5.75         2.47         2.60         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       18.64        32.45        87.39        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       40.37        21.83        36.10        32.45        30.21        23.93 
TCGA-QD-A8IV 
       12.89 

  AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE 
                         0.99                          0.16 
  AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE 
                       136.01                        169.32 
  AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE 
                       28.605                        30.870 
[1] "1.0 - 136.0 (28.6)" "0.2 - 169.3 (30.9)"
[1] "hr=" "2.7"
D4V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK  4(1Q31.2) MUTATED         7        0        12        1         9
  AMP PEAK  4(1Q31.2) WILD-TYPE     275       50        99        1        37
                               vv
clus                            STAGE IVC
  AMP PEAK  4(1Q31.2) MUTATED           0
  AMP PEAK  4(1Q31.2) WILD-TYPE         6
D4V3, multiclass
           clus
vv          AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE
  STAGE I                             7                           275
  STAGE II                            0                            50
  STAGE III                          12                            99
  STAGE IV                            1                             1
  STAGE IVA                           9                            37
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  4(1Q31.2) MUTATED     2   4  18   5
  AMP PEAK  4(1Q31.2) WILD-TYPE 140 161 149  18
D4V4, multiclass
    clus
vv   AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE
  T1                           2                           140
  T2                           4                           161
  T3                          18                           149
  T4                           5                            18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
                               cls
clus                              0   1
  AMP PEAK  4(1Q31.2) MUTATED     5  22
  AMP PEAK  4(1Q31.2) WILD-TYPE 220 202
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(1Q31.2) MUTATED      5   22
  AMP PEAK  4(1Q31.2) WILD-TYPE  220  202
   clus
vv  AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE
  0                           5                           220
  1                          22                           202
[1] 2 2
[1] FALSE
D4V6, binary
                               cls
clus                              0   1
  AMP PEAK  4(1Q31.2) MUTATED    14   0
  AMP PEAK  4(1Q31.2) WILD-TYPE 264   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(1Q31.2) MUTATED     14    0
  AMP PEAK  4(1Q31.2) WILD-TYPE  264    9
   clus
vv  AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE
  0                          14                           264
  1                           0                             9
[1] 2 2
[1] FALSE
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(1Q31.2) MUTATED    20   9
  AMP PEAK  4(1Q31.2) WILD-TYPE 345 125
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(1Q31.2) MUTATED     20    9
  AMP PEAK  4(1Q31.2) WILD-TYPE  345  125
        clus
vv       AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE
  FEMALE                          20                           345
  MALE                             9                           125
[1] 2 2
[1] FALSE
D4V8, binary
                               cls
clus                              0   1
  AMP PEAK  4(1Q31.2) MUTATED     8  17
  AMP PEAK  4(1Q31.2) WILD-TYPE 177 273
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(1Q31.2) MUTATED      8   17
  AMP PEAK  4(1Q31.2) WILD-TYPE  177  273
     clus
vv    AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE
  NO                            8                           177
  YES                          17                           273
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK  4(1Q31.2) MUTATED                0
  AMP PEAK  4(1Q31.2) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK  4(1Q31.2) MUTATED                                              25
  AMP PEAK  4(1Q31.2) WILD-TYPE                                           330
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK  4(1Q31.2) MUTATED                                                                        0
  AMP PEAK  4(1Q31.2) WILD-TYPE                                                                    100
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK  4(1Q31.2) MUTATED                                                                     4
  AMP PEAK  4(1Q31.2) WILD-TYPE                                                                  32
D4V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK  4(1Q31.2) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   25
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           0
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              4
                                                                        clus
vv                                                                       AMP PEAK  4(1Q31.2) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    330
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           100
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               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"
D4V10, binary
                               cls
clus                              0   1
  AMP PEAK  4(1Q31.2) MUTATED    26   1
  AMP PEAK  4(1Q31.2) WILD-TYPE 394  16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(1Q31.2) MUTATED     26    1
  AMP PEAK  4(1Q31.2) WILD-TYPE  394   16
     clus
vv    AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE
  NO                           26                           394
  YES                           1                            16
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK  4(1Q31.2) MUTATED             14                       4   10
  AMP PEAK  4(1Q31.2) WILD-TYPE          118                      14  320
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK  4(1Q31.2) MUTATED                     1
  AMP PEAK  4(1Q31.2) WILD-TYPE                   0
D4V11, multiclass
                         clus
vv                        AMP PEAK  4(1Q31.2) MUTATED
  MINIMAL (T3)                                     14
  MODERATE/ADVANCED (T4A)                           4
  NONE                                             10
  VERY ADVANCED (T4B)                               1
                         clus
vv                        AMP PEAK  4(1Q31.2) WILD-TYPE
  MINIMAL (T3)                                      118
  MODERATE/ADVANCED (T4A)                            14
  NONE                                              320
  VERY ADVANCED (T4B)                                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  4(1Q31.2) MUTATED    17   6   0   4
  AMP PEAK  4(1Q31.2) WILD-TYPE 366  45   4  26
D4V12, multiclass
    clus
vv   AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE
  R0                          17                           366
  R1                           6                            45
  R2                           0                             4
  RX                           4                            26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V13, continuous
D4V14, binary
                               cls
clus                              0   1
  AMP PEAK  4(1Q31.2) MUTATED     9  20
  AMP PEAK  4(1Q31.2) WILD-TYPE 216 244
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(1Q31.2) MUTATED      9   20
  AMP PEAK  4(1Q31.2) WILD-TYPE  216  244
            clus
vv           AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE
  MULTIFOCAL                           9                           216
  UNIFOCAL                            20                           244
[1] 2 2
[1] FALSE
D4V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  4(1Q31.2) MUTATED                                  1     1
  AMP PEAK  4(1Q31.2) WILD-TYPE                                0    51
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(1Q31.2) MUTATED                           5    21
  AMP PEAK  4(1Q31.2) WILD-TYPE                        22   307
D4V16, multiclass
                                  clus
vv                                 AMP PEAK  4(1Q31.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  5
  WHITE                                                     21
                                  clus
vv                                 AMP PEAK  4(1Q31.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       51
  BLACK OR AFRICAN AMERICAN                                   22
  WHITE                                                      307
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V17, binary
                               cls
clus                              0   1
  AMP PEAK  4(1Q31.2) MUTATED     6  20
  AMP PEAK  4(1Q31.2) WILD-TYPE  32 339
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(1Q31.2) MUTATED      6   20
  AMP PEAK  4(1Q31.2) WILD-TYPE   32  339
                        clus
vv                       AMP PEAK  4(1Q31.2) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                          20
                        clus
vv                       AMP PEAK  4(1Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                32
  NOT HISPANIC OR LATINO                           339
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(1Q43) MUTATION ANALYSIS
D5V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  5(1Q43) MUTATED    25   3
  AMP PEAK  5(1Q43) WILD-TYPE 456  13
  AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE 
                         28                         469 
  AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE 
                          3                          13 
$`AMP PEAK  5(1Q43) MUTATED`
TCGA-4C-A93U TCGA-BJ-A290 TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DJ-A13U 
        4.24        30.21        11.57        30.02        25.12        23.38 
TCGA-DJ-A1QE TCGA-DO-A2HM TCGA-EL-A3GP TCGA-EL-A3GU TCGA-EL-A3H5 TCGA-EL-A3MX 
      135.91         2.33        49.51       136.01        83.57        57.63 
TCGA-EL-A3MZ TCGA-EL-A3T9 TCGA-EL-A3ZO TCGA-EL-A4JX TCGA-EM-A3O3 TCGA-ET-A39P 
       52.50         5.72        47.38        45.96        14.50        95.34 
TCGA-ET-A3BT TCGA-FE-A231 TCGA-FY-A3NM TCGA-FY-A40L TCGA-H2-A26U TCGA-IM-A3EB 
       87.62        31.59         0.99         6.58        17.00        48.92 
TCGA-IM-A3U2 TCGA-J8-A3O1 TCGA-KS-A4IB TCGA-L6-A4EU 
       18.51        27.19        84.72         9.50 

$`AMP PEAK  5(1Q43) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        49.78        16.34        14.73        41.33 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73        25.48        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       42.08        51.39        41.52        20.58         4.83        44.35 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
       42.15        21.04        35.54        32.45        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       11.08        22.88        18.38        16.57        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        7.99        10.88        21.01         3.45        23.84        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
       15.45        21.63        23.18        19.43        23.47        12.66 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
       12.43        12.66        35.84        21.63        50.17        37.64 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A69J TCGA-DE-A69K 
       15.85        18.54        18.84        30.12        14.70        14.27 
TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
        2.76         9.96        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
        8.71        56.19        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       54.90        21.53        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        52.44        39.95        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GQ 
       98.53        69.57        57.11       108.36        64.87        50.24 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY 
      115.10        65.39        50.37        50.20       147.75       101.13 
TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H7 
      139.99        49.32        33.50        43.36        49.71       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MY TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
      150.48       108.66        17.52        29.65       147.42       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       36.03        53.06        65.49        61.22        60.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       59.44        57.47        34.72        37.94        31.04        34.39 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        53.36        44.15        41.13        47.84        43.59 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       24.30        27.06        23.90        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
       48.49        18.05        19.79        19.46        78.61        57.01 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       54.08        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.65        44.19        41.29        14.24        47.57        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       13.18        23.51         6.05         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        40.34        19.73        32.32        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ 
       17.59        17.46        17.29        14.60        22.52        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        33.07        13.38         8.35        29.72 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        47.38        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O7 
       17.49        17.39        16.18        15.02        15.06         7.33 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
        0.49         9.24        13.91        38.66        38.86        29.95 
TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       29.85        13.51        12.79        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        5.33        26.37        26.37        22.45        21.53        60.49 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       24.46        13.68        81.93        81.70        77.56        70.42 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       56.58        60.20        63.39        65.29        18.38        63.45 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       88.41        58.75        37.25        52.60        54.35        83.34 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89       123.32       100.57        94.13        55.10        98.20 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BU 
       28.24        50.40        79.10        76.64         5.79        77.82 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       75.42        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       31.40        73.74        71.44        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      117.40        66.77       112.80        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        1.05        13.28         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       20.42        17.82         7.82        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       17.36        15.16        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
        1.68        12.53        21.67        12.46         2.99        20.05 
TCGA-H2-A422 TCGA-IM-A3ED TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       18.61        47.41        16.90        21.83        31.10         8.22 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       25.64        17.23        43.17        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY 
       24.69        22.29         5.75         2.47         2.60         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       18.64        32.45        87.39        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       40.37        21.83        36.10        32.45        30.21        23.93 
TCGA-QD-A8IV 
       12.89 

  AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE 
                       0.99                        0.16 
  AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE 
                     136.01                      169.32 
  AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE 
                     30.115                      30.610 
[1] "1.0 - 136.0 (30.1)" "0.2 - 169.3 (30.6)"
[1] "hr=" "3.6"
D5V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK  5(1Q43) MUTATED         6        0        12        1         9
  AMP PEAK  5(1Q43) WILD-TYPE     276       50        99        1        37
                             vv
clus                          STAGE IVC
  AMP PEAK  5(1Q43) MUTATED           1
  AMP PEAK  5(1Q43) WILD-TYPE         5
D5V3, multiclass
           clus
vv          AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE
  STAGE I                           6                         276
  STAGE II                          0                          50
  STAGE III                        12                          99
  STAGE IV                          1                           1
  STAGE IVA                         9                          37
  STAGE IVC                         1                           5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK  5(1Q43) MUTATED     2   3  18   6
  AMP PEAK  5(1Q43) WILD-TYPE 140 162 149  17
D5V4, multiclass
    clus
vv   AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE
  T1                         2                         140
  T2                         3                         162
  T3                        18                         149
  T4                         6                          17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
                             cls
clus                            0   1
  AMP PEAK  5(1Q43) MUTATED     6  22
  AMP PEAK  5(1Q43) WILD-TYPE 219 202
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(1Q43) MUTATED      6   22
  AMP PEAK  5(1Q43) WILD-TYPE  219  202
   clus
vv  AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE
  0                         6                         219
  1                        22                         202
[1] 2 2
[1] FALSE
D5V6, binary
                             cls
clus                            0   1
  AMP PEAK  5(1Q43) MUTATED    14   1
  AMP PEAK  5(1Q43) WILD-TYPE 264   8
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(1Q43) MUTATED     14    1
  AMP PEAK  5(1Q43) WILD-TYPE  264    8
   clus
vv  AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE
  0                        14                         264
  1                         1                           8
[1] 2 2
[1] FALSE
D5V7, binary
                             cls
clus                            0   1
  AMP PEAK  5(1Q43) MUTATED    21   8
  AMP PEAK  5(1Q43) WILD-TYPE 344 126
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(1Q43) MUTATED     21    8
  AMP PEAK  5(1Q43) WILD-TYPE  344  126
        clus
vv       AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE
  FEMALE                        21                         344
  MALE                           8                         126
[1] 2 2
[1] FALSE
D5V8, binary
                             cls
clus                            0   1
  AMP PEAK  5(1Q43) MUTATED     8  17
  AMP PEAK  5(1Q43) WILD-TYPE 177 273
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(1Q43) MUTATED      8   17
  AMP PEAK  5(1Q43) WILD-TYPE  177  273
     clus
vv    AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE
  NO                          8                         177
  YES                        17                         273
[1] 2 2
[1] FALSE
                             vv
clus                          OTHER  SPECIFY
  AMP PEAK  5(1Q43) MUTATED                0
  AMP PEAK  5(1Q43) WILD-TYPE              8
                             vv
clus                          THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK  5(1Q43) MUTATED                                              25
  AMP PEAK  5(1Q43) WILD-TYPE                                           330
                             vv
clus                          THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK  5(1Q43) MUTATED                                                                        0
  AMP PEAK  5(1Q43) WILD-TYPE                                                                    100
                             vv
clus                          THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK  5(1Q43) MUTATED                                                                     4
  AMP PEAK  5(1Q43) WILD-TYPE                                                                  32
D5V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK  5(1Q43) MUTATED
  OTHER  SPECIFY                                                                                 0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                 25
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                         0
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                            4
                                                                        clus
vv                                                                       AMP PEAK  5(1Q43) WILD-TYPE
  OTHER  SPECIFY                                                                                   8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  330
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                         100
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                             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"
D5V10, binary
                             cls
clus                            0   1
  AMP PEAK  5(1Q43) MUTATED    26   1
  AMP PEAK  5(1Q43) WILD-TYPE 394  16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(1Q43) MUTATED     26    1
  AMP PEAK  5(1Q43) WILD-TYPE  394   16
     clus
vv    AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE
  NO                         26                         394
  YES                         1                          16
[1] 2 2
[1] FALSE
                             vv
clus                          MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK  5(1Q43) MUTATED             14                       4   10
  AMP PEAK  5(1Q43) WILD-TYPE          118                      14  320
                             vv
clus                          VERY ADVANCED (T4B)
  AMP PEAK  5(1Q43) MUTATED                     1
  AMP PEAK  5(1Q43) WILD-TYPE                   0
D5V11, multiclass
                         clus
vv                        AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE
  MINIMAL (T3)                                   14                         118
  MODERATE/ADVANCED (T4A)                         4                          14
  NONE                                           10                         320
  VERY ADVANCED (T4B)                             1                           0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  5(1Q43) MUTATED    17   6   0   4
  AMP PEAK  5(1Q43) WILD-TYPE 366  45   4  26
D5V12, multiclass
    clus
vv   AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE
  R0                        17                         366
  R1                         6                          45
  R2                         0                           4
  RX                         4                          26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V13, continuous
D5V14, binary
                             cls
clus                            0   1
  AMP PEAK  5(1Q43) MUTATED     8  21
  AMP PEAK  5(1Q43) WILD-TYPE 217 243
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(1Q43) MUTATED      8   21
  AMP PEAK  5(1Q43) WILD-TYPE  217  243
            clus
vv           AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE
  MULTIFOCAL                         8                         217
  UNIFOCAL                          21                         243
[1] 2 2
[1] FALSE
D5V15, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  5(1Q43) MUTATED                                  1     1
  AMP PEAK  5(1Q43) WILD-TYPE                                0    51
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(1Q43) MUTATED                           5    21
  AMP PEAK  5(1Q43) WILD-TYPE                        22   307
D5V16, multiclass
                                  clus
vv                                 AMP PEAK  5(1Q43) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    1
  BLACK OR AFRICAN AMERICAN                                5
  WHITE                                                   21
                                  clus
vv                                 AMP PEAK  5(1Q43) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     51
  BLACK OR AFRICAN AMERICAN                                 22
  WHITE                                                    307
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V17, binary
                             cls
clus                            0   1
  AMP PEAK  5(1Q43) MUTATED     5  21
  AMP PEAK  5(1Q43) WILD-TYPE  33 338
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(1Q43) MUTATED      5   21
  AMP PEAK  5(1Q43) WILD-TYPE   33  338
                        clus
vv                       AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE
  HISPANIC OR LATINO                             5                          33
  NOT HISPANIC OR LATINO                        21                         338
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(2P16.1) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  6(2P16.1) MUTATED     3   0
  AMP PEAK  6(2P16.1) WILD-TYPE 478  16
  AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE 
                            3                           494 
  AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE 
                            0                            16 
$`AMP PEAK  6(2P16.1) MUTATED`
TCGA-DJ-A4UQ TCGA-ET-A2MZ TCGA-ET-A39N 
       33.04        37.25       123.32 

$`AMP PEAK  6(2P16.1) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
       30.58        35.41        27.45        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74         6.77        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        36.33        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       35.87        40.96        36.99        20.22        30.61        42.54 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20        23.21        21.27        20.48        24.82        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ 
       21.01        18.97         7.76        35.67         3.12        36.43 
TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UR 
       24.76        17.23        27.62        30.87        21.34        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        30.61         0.16         0.23        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        33.50         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        69.57        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       49.51        50.24       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       150.48       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        89.56        78.97        51.78 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        47.38        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       60.16         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        47.84        43.59        24.30        27.06        23.90 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J 
       19.46        78.61        57.01        54.08        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P 
       15.75        10.45        14.53        10.65        44.19        41.29 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        47.57        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        32.32        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        29.72        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 
       15.02        14.50        15.06         7.33         0.49         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       13.91        38.66        38.86        29.95        29.85        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        84.59        29.33        21.34         5.33        26.37 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
       26.37        22.45        21.53        60.49        24.46        13.68 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       81.93        81.70        77.56        70.42        56.58        60.20 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       63.39        65.29        18.38        63.45        88.41        58.75 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
      106.09       107.41       108.46        84.89       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       94.13        55.10        98.20        28.24        50.40        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
       76.64         5.79        87.62        77.82        75.42        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
       52.47       116.78        94.59        84.85        80.58        66.84 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       43.73        62.83       166.62        24.72        43.99        46.26 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
       44.38        40.21        37.48        33.17        31.40        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       71.44        31.59        79.69        24.69        68.22       117.40 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77       112.80        39.95        33.63        81.83       106.36 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD 
       85.15        85.68        78.77        71.08         4.11         1.05 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       13.28         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       17.82         7.82         0.99        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83        31.10         8.22        25.64        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       23.93        12.89 

  AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE 
                        33.04                          0.16 
  AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE 
                       123.32                        169.32 
  AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE 
                       37.250                        30.595 
[1] "33.0 - 123.3 (37.2)" "0.2 - 169.3 (30.6)" 
[1] "hr="     "9100000"
D6V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK  6(2P16.1) MUTATED         2        0         0        0         1
  AMP PEAK  6(2P16.1) WILD-TYPE     280       50       111        2        45
                               vv
clus                            STAGE IVC
  AMP PEAK  6(2P16.1) MUTATED           0
  AMP PEAK  6(2P16.1) WILD-TYPE         6
D6V3, multiclass
           clus
vv          AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE
  STAGE I                             2                           280
  STAGE II                            0                            50
  STAGE III                           0                           111
  STAGE IV                            0                             2
  STAGE IVA                           1                            45
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  6(2P16.1) MUTATED     1   0   2   0
  AMP PEAK  6(2P16.1) WILD-TYPE 141 165 165  23
D6V4, multiclass
    clus
vv   AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE
  T1                           1                           141
  T2                           0                           165
  T3                           2                           165
  T4                           0                            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"
D6V5, binary
                               cls
clus                              0   1
  AMP PEAK  6(2P16.1) MUTATED     1   1
  AMP PEAK  6(2P16.1) WILD-TYPE 224 223
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(2P16.1) MUTATED      1    1
  AMP PEAK  6(2P16.1) WILD-TYPE  224  223
   clus
vv  AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE
  0                           1                           224
  1                           1                           223
[1] 2 2
[1] FALSE
D6V6, binary
                               cls
clus                              0   1
  AMP PEAK  6(2P16.1) MUTATED     1   0
  AMP PEAK  6(2P16.1) WILD-TYPE 277   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(2P16.1) MUTATED      1    0
  AMP PEAK  6(2P16.1) WILD-TYPE  277    9
   clus
vv  AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE
  0                           1                           277
  1                           0                             9
[1] 2 2
[1] FALSE
D6V7, binary
                               cls
clus                              0   1
  AMP PEAK  6(2P16.1) MUTATED     1   2
  AMP PEAK  6(2P16.1) WILD-TYPE 364 132
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(2P16.1) MUTATED      1    2
  AMP PEAK  6(2P16.1) WILD-TYPE  364  132
        clus
vv       AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE
  FEMALE                           1                           364
  MALE                             2                           132
[1] 2 2
[1] FALSE
D6V8, binary
                               cls
clus                              0   1
  AMP PEAK  6(2P16.1) MUTATED     1   2
  AMP PEAK  6(2P16.1) WILD-TYPE 184 288
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(2P16.1) MUTATED      1    2
  AMP PEAK  6(2P16.1) WILD-TYPE  184  288
     clus
vv    AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE
  NO                            1                           184
  YES                           2                           288
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK  6(2P16.1) MUTATED                1
  AMP PEAK  6(2P16.1) WILD-TYPE              7
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK  6(2P16.1) MUTATED                                               2
  AMP PEAK  6(2P16.1) WILD-TYPE                                           353
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK  6(2P16.1) MUTATED                                                                        0
  AMP PEAK  6(2P16.1) WILD-TYPE                                                                    100
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK  6(2P16.1) MUTATED                                                                     0
  AMP PEAK  6(2P16.1) WILD-TYPE                                                                  36
D6V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK  6(2P16.1) MUTATED
  OTHER  SPECIFY                                                                                   1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           0
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       AMP PEAK  6(2P16.1) WILD-TYPE
  OTHER  SPECIFY                                                                                     7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           100
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, binary
                               cls
clus                              0   1
  AMP PEAK  6(2P16.1) MUTATED     3   0
  AMP PEAK  6(2P16.1) WILD-TYPE 417  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(2P16.1) MUTATED      3    0
  AMP PEAK  6(2P16.1) WILD-TYPE  417   17
     clus
vv    AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE
  NO                            3                           417
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK  6(2P16.1) MUTATED              1                       0    2
  AMP PEAK  6(2P16.1) WILD-TYPE          131                      18  328
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK  6(2P16.1) MUTATED                     0
  AMP PEAK  6(2P16.1) WILD-TYPE                   1
D6V11, multiclass
                         clus
vv                        AMP PEAK  6(2P16.1) MUTATED
  MINIMAL (T3)                                      1
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              2
  VERY ADVANCED (T4B)                               0
                         clus
vv                        AMP PEAK  6(2P16.1) WILD-TYPE
  MINIMAL (T3)                                      131
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              328
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  6(2P16.1) MUTATED     2   0   0   1
  AMP PEAK  6(2P16.1) WILD-TYPE 381  51   4  29
D6V12, multiclass
    clus
vv   AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE
  R0                           2                           381
  R1                           0                            51
  R2                           0                             4
  RX                           1                            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"
D6V13, continuous
[1] "Remove cluster labels:"      "AMP PEAK  6(2P16.1) MUTATED"
clus
  AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE 
                            2                           383 
                   TCGA-4C-A93U                    TCGA-BJ-A0Z0 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A0Z3                    TCGA-BJ-A0Z9 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A0ZA                    TCGA-BJ-A0ZB 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A0ZH                    TCGA-BJ-A0ZJ 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A18Y                    TCGA-BJ-A18Z 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A190                    TCGA-BJ-A191 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A28R                    TCGA-BJ-A28T 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A28W                    TCGA-BJ-A28X 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A28Z                    TCGA-BJ-A290 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A291                    TCGA-BJ-A2N8 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A2N9                    TCGA-BJ-A2NA 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A3EZ                    TCGA-BJ-A3PR 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A3PU                    TCGA-BJ-A45C 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A45D                    TCGA-BJ-A45E 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A45G                    TCGA-BJ-A45I 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A45J                    TCGA-BJ-A45K 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A4O8                    TCGA-BJ-A4O9 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-CE-A13K                    TCGA-CE-A3MD 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-CE-A483                    TCGA-CE-A484 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-CE-A485                    TCGA-DE-A0XZ 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DE-A0Y2                    TCGA-DE-A0Y3 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DE-A3KN                    TCGA-DE-A4M8 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DE-A4MA                    TCGA-DE-A4MB 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DE-A4MC                    TCGA-DE-A4MD 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DE-A69K                    TCGA-DE-A7U5 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A13M                    TCGA-DJ-A13O 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A13R                    TCGA-DJ-A13T 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A13V                    TCGA-DJ-A13W 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A13X                    TCGA-DJ-A1QG 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A1QH                    TCGA-DJ-A1QM 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A2PO                    TCGA-DJ-A2PP 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A2PQ                    TCGA-DJ-A2PR 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A2PS                    TCGA-DJ-A2PT 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A2PU                    TCGA-DJ-A2PV 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A2PW                    TCGA-DJ-A2PX 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A2PY                    TCGA-DJ-A2PZ 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A2Q0                    TCGA-DJ-A2Q1 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A2Q2                    TCGA-DJ-A2Q3 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A2Q4                    TCGA-DJ-A2Q5 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A2Q6                    TCGA-DJ-A2Q7 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A2Q8                    TCGA-DJ-A2Q9 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A2QA                    TCGA-DJ-A2QB 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A3UK                    TCGA-DJ-A3UM 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A3UN                    TCGA-DJ-A3UO 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A3UP                    TCGA-DJ-A3UQ 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A3UR                    TCGA-DJ-A3UU 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A3UW                    TCGA-DJ-A3UX 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A3UZ                    TCGA-DJ-A3V0 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A3V2                    TCGA-DJ-A3V3 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A3V4                    TCGA-DJ-A3V5 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A3V7                    TCGA-DJ-A3V8 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A3V9                    TCGA-DJ-A3VA 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A3VB                    TCGA-DJ-A3VD 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A3VF                    TCGA-DJ-A3VG 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A3VI                    TCGA-DJ-A3VJ 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A3VK                    TCGA-DJ-A3VL 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A4UL                    TCGA-DJ-A4UP 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A4UR                    TCGA-DJ-A4UW 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A4V2                    TCGA-DJ-A4V5 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DO-A1K0                    TCGA-DO-A2HM 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-E3-A3DY                    TCGA-E3-A3DZ 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-E3-A3E0                    TCGA-E3-A3E1 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-E3-A3E2                    TCGA-E3-A3E3 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-E3-A3E5                    TCGA-E8-A242 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-E8-A2EA                    TCGA-E8-A414 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-E8-A415                    TCGA-E8-A417 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-E8-A419                    TCGA-E8-A433 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-E8-A436                    TCGA-E8-A438 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-E8-A44K                    TCGA-EL-A3CM 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A3CN                    TCGA-EL-A3CO 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A3CR                    TCGA-EL-A3CS 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A3CT                    TCGA-EL-A3CU 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A3CV                    TCGA-EL-A3CW 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A3CX                    TCGA-EL-A3CY 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A3CZ                    TCGA-EL-A3D0 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A3D1                    TCGA-EL-A3D4 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A3D5                    TCGA-EL-A3D6 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A3GO                    TCGA-EL-A3GP 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A3GQ                    TCGA-EL-A3GS 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A3GU                    TCGA-EL-A3GV 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A3GX                    TCGA-EL-A3H3 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A3H4                    TCGA-EL-A3H5 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A3H7                    TCGA-EL-A3H8 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A3MW                    TCGA-EL-A3MX 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A3MZ                    TCGA-EL-A3N2 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A3T0                    TCGA-EL-A3T1 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A3T2                    TCGA-EL-A3TB 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A3ZH                    TCGA-EL-A3ZK 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A3ZL                    TCGA-EL-A3ZM 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A3ZN                    TCGA-EL-A3ZO 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A3ZP                    TCGA-EL-A3ZS 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A4JV                    TCGA-EL-A4JW 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A4JX                    TCGA-EL-A4JZ 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A4K0                    TCGA-EL-A4K1 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A4K2                    TCGA-EL-A4K4 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A4K6                    TCGA-EL-A4K7 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A4KD                    TCGA-EL-A4KG 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A4KI                    TCGA-EM-A1CS 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A1CT                    TCGA-EM-A1CU 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A1CV                    TCGA-EM-A1CW 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A1YC                    TCGA-EM-A1YD 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A1YE                    TCGA-EM-A22I 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A22J                    TCGA-EM-A22K 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A22L                    TCGA-EM-A22M 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A22N                    TCGA-EM-A22O 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A22P                    TCGA-EM-A22Q 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A2CK                    TCGA-EM-A2CN 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A2CP                    TCGA-EM-A2CQ 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A2CT                    TCGA-EM-A2CU 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A2OV                    TCGA-EM-A2OX 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A2OY                    TCGA-EM-A2OZ 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A2P0                    TCGA-EM-A2P1 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A2P2                    TCGA-EM-A3AJ 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A3AK                    TCGA-EM-A3AL 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A3AN                    TCGA-EM-A3AO 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A3AQ                    TCGA-EM-A3AR 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A3FJ                    TCGA-EM-A3FK 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A3FM                    TCGA-EM-A3FN 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A3FO                    TCGA-EM-A3FP 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A3FQ                    TCGA-EM-A3FR 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A3O3                    TCGA-EM-A3O8 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A3O9                    TCGA-EM-A3OA 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A3OB                    TCGA-EM-A3ST 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A3SU                    TCGA-EM-A3SX 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A3SZ                    TCGA-EM-A4FF 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A4FM                    TCGA-EM-A4FN 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A4FO                    TCGA-EM-A4FQ 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A4FR                    TCGA-EM-A4FV 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A4G1                    TCGA-ET-A25G 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-ET-A25I                    TCGA-ET-A25J 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-ET-A25K                    TCGA-ET-A25L 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-ET-A25M                    TCGA-ET-A25N 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-ET-A25O                    TCGA-ET-A25P 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-ET-A2MX                    TCGA-ET-A2N0 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-ET-A2N1                    TCGA-ET-A2N4 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-ET-A39K                    TCGA-ET-A39L 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-ET-A39O                    TCGA-ET-A39P 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-ET-A39R                    TCGA-ET-A39S 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-ET-A39T                    TCGA-ET-A3BO 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-ET-A3BP                    TCGA-ET-A3BQ 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-ET-A3BS                    TCGA-ET-A3BT 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-ET-A3BU                    TCGA-ET-A3BV 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-ET-A3BX                    TCGA-ET-A3DQ 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-ET-A3DR                    TCGA-ET-A3DS 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-ET-A3DT                    TCGA-ET-A3DU 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-ET-A3DV                    TCGA-ET-A3DW 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-ET-A40P                    TCGA-ET-A40Q 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-ET-A40R                    TCGA-ET-A40S 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-ET-A40T                    TCGA-ET-A4KN 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-FE-A22Z                    TCGA-FE-A230 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-FE-A231                    TCGA-FE-A232 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-FE-A233                    TCGA-FE-A234 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-FE-A235                    TCGA-FE-A236 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-FE-A237                    TCGA-FE-A238 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-FE-A239                    TCGA-FE-A23A 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-FE-A3PB                    TCGA-FE-A3PC 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-FE-A3PD                    TCGA-FK-A3S3 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-FK-A3SB                    TCGA-FK-A3SE 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-FK-A3SG                    TCGA-FK-A3SH 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-FK-A4UB                    TCGA-FY-A2QD 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-FY-A3I4                    TCGA-FY-A3I5 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-FY-A3NM                    TCGA-FY-A3NN 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-FY-A3ON                    TCGA-FY-A3R6 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-FY-A3R7                    TCGA-FY-A3R9 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-FY-A3TY                    TCGA-FY-A3W9 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-FY-A3YR                    TCGA-FY-A40K 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-FY-A40L                    TCGA-FY-A40M 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-FY-A40N                    TCGA-FY-A4B3 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-FY-A4B4                    TCGA-GE-A2C6 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-H2-A26U                    TCGA-H2-A2K9 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-H2-A3RH                    TCGA-H2-A3RI 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-H2-A421                    TCGA-H2-A422 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-IM-A3EB                    TCGA-IM-A3ED 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-IM-A3U2                    TCGA-IM-A3U3 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-IM-A41Y                    TCGA-IM-A41Z 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-IM-A420                    TCGA-IM-A4EB 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-J8-A3NZ                    TCGA-J8-A3O0 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-J8-A3O1                    TCGA-J8-A3O2 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-J8-A3YD                    TCGA-J8-A3YE 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-J8-A3YF                    TCGA-J8-A3YG 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-J8-A3YH                    TCGA-J8-A42S 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-J8-A4HW                    TCGA-J8-A4HY 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-KS-A41F                    TCGA-KS-A41I 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-KS-A41J                    TCGA-KS-A41L 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-KS-A4I1                    TCGA-KS-A4I3 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-KS-A4I5                    TCGA-KS-A4I7 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-KS-A4I9                    TCGA-KS-A4IB 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-KS-A4IC                    TCGA-KS-A4ID 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-L6-A4EP                    TCGA-L6-A4EQ 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-L6-A4EU                    TCGA-MK-A4N6 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-MK-A4N7                    TCGA-MK-A4N9 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-QD-A8IV 
"AMP PEAK  6(2P16.1) WILD-TYPE" 
D6V14, binary
                               cls
clus                              0   1
  AMP PEAK  6(2P16.1) MUTATED     1   2
  AMP PEAK  6(2P16.1) WILD-TYPE 224 262
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(2P16.1) MUTATED      1    2
  AMP PEAK  6(2P16.1) WILD-TYPE  224  262
            clus
vv           AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE
  MULTIFOCAL                           1                           224
  UNIFOCAL                             2                           262
[1] 2 2
[1] FALSE
D6V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  6(2P16.1) MUTATED                                  0     1
  AMP PEAK  6(2P16.1) WILD-TYPE                                1    51
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(2P16.1) MUTATED                           0     2
  AMP PEAK  6(2P16.1) WILD-TYPE                        27   326
D6V16, multiclass
                                  clus
vv                                 AMP PEAK  6(2P16.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      2
                                  clus
vv                                 AMP PEAK  6(2P16.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       51
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V17, binary
                               cls
clus                              0   1
  AMP PEAK  6(2P16.1) MUTATED     0   3
  AMP PEAK  6(2P16.1) WILD-TYPE  38 356
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(2P16.1) MUTATED      0    3
  AMP PEAK  6(2P16.1) WILD-TYPE   38  356
                        clus
vv                       AMP PEAK  6(2P16.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           3
                        clus
vv                       AMP PEAK  6(2P16.1) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           356
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  8(2Q37.2) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  8(2Q37.2) MUTATED     3   0
  AMP PEAK  8(2Q37.2) WILD-TYPE 478  16
  AMP PEAK  8(2Q37.2) MUTATED AMP PEAK  8(2Q37.2) WILD-TYPE 
                            3                           494 
  AMP PEAK  8(2Q37.2) MUTATED AMP PEAK  8(2Q37.2) WILD-TYPE 
                            0                            16 
$`AMP PEAK  8(2Q37.2) MUTATED`
TCGA-BJ-A290 TCGA-DJ-A13M TCGA-FK-A3SD 
       30.21        48.79         1.05 

$`AMP PEAK  8(2Q37.2) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       30.97        11.08        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       38.17       169.32        18.58         8.71        56.19        23.38 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       43.17        52.37         8.32        11.01       135.91        30.61 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       44.98        42.51        14.96        17.59         6.02        42.58 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
       47.41        17.56        10.09         7.82        30.58        35.41 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       27.45        26.20        38.83        33.96        31.99        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       28.96         8.78         8.42        34.36        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24        33.93        37.48        36.46        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        33.53        35.18        15.88        36.92        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       32.42        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        17.69        59.57        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        42.54        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL 
        7.76        35.67         3.12        36.43        24.76        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        21.34        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        52.44        39.95        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       47.84        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       78.61        57.01        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       32.32        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       22.52        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33         0.49         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
      106.09       107.41       108.46        84.89       123.32       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       95.34        94.13        55.10        98.20        28.24        50.40 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
       79.10        76.64         5.79        87.62        77.82        75.42 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
       46.65        52.47       116.78        94.59        84.85        80.58 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
       66.84        43.73        62.83       166.62        24.72        43.99 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
       46.26        44.38        40.21        37.48        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      117.40        66.77       112.80        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       13.28         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       17.82         7.82         0.99        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83        31.10         8.22        25.64        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       23.93        12.89 

  AMP PEAK  8(2Q37.2) MUTATED AMP PEAK  8(2Q37.2) WILD-TYPE 
                         1.05                          0.16 
  AMP PEAK  8(2Q37.2) MUTATED AMP PEAK  8(2Q37.2) WILD-TYPE 
                        48.79                        169.32 
  AMP PEAK  8(2Q37.2) MUTATED AMP PEAK  8(2Q37.2) WILD-TYPE 
                        30.21                         30.61 
[1] "1.1 - 48.8 (30.2)"  "0.2 - 169.3 (30.6)"
[1] "hr="     "1200000"
D7V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK  8(2Q37.2) MUTATED         2        0         1        0         0
  AMP PEAK  8(2Q37.2) WILD-TYPE     280       50       110        2        46
                               vv
clus                            STAGE IVC
  AMP PEAK  8(2Q37.2) MUTATED           0
  AMP PEAK  8(2Q37.2) WILD-TYPE         6
D7V3, multiclass
           clus
vv          AMP PEAK  8(2Q37.2) MUTATED AMP PEAK  8(2Q37.2) WILD-TYPE
  STAGE I                             2                           280
  STAGE II                            0                            50
  STAGE III                           1                           110
  STAGE IV                            0                             2
  STAGE IVA                           0                            46
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  8(2Q37.2) MUTATED     2   0   1   0
  AMP PEAK  8(2Q37.2) WILD-TYPE 140 165 166  23
D7V4, multiclass
    clus
vv   AMP PEAK  8(2Q37.2) MUTATED AMP PEAK  8(2Q37.2) WILD-TYPE
  T1                           2                           140
  T2                           0                           165
  T3                           1                           166
  T4                           0                            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"
D7V5, binary
                               cls
clus                              0   1
  AMP PEAK  8(2Q37.2) MUTATED     2   1
  AMP PEAK  8(2Q37.2) WILD-TYPE 223 223
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(2Q37.2) MUTATED      2    1
  AMP PEAK  8(2Q37.2) WILD-TYPE  223  223
   clus
vv  AMP PEAK  8(2Q37.2) MUTATED AMP PEAK  8(2Q37.2) WILD-TYPE
  0                           2                           223
  1                           1                           223
[1] 2 2
[1] FALSE
D7V6, binary
                               cls
clus                              0   1
  AMP PEAK  8(2Q37.2) MUTATED     3   0
  AMP PEAK  8(2Q37.2) WILD-TYPE 275   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(2Q37.2) MUTATED      3    0
  AMP PEAK  8(2Q37.2) WILD-TYPE  275    9
   clus
vv  AMP PEAK  8(2Q37.2) MUTATED AMP PEAK  8(2Q37.2) WILD-TYPE
  0                           3                           275
  1                           0                             9
[1] 2 2
[1] FALSE
D7V7, binary
                               cls
clus                              0   1
  AMP PEAK  8(2Q37.2) MUTATED     2   1
  AMP PEAK  8(2Q37.2) WILD-TYPE 363 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(2Q37.2) MUTATED      2    1
  AMP PEAK  8(2Q37.2) WILD-TYPE  363  133
        clus
vv       AMP PEAK  8(2Q37.2) MUTATED AMP PEAK  8(2Q37.2) WILD-TYPE
  FEMALE                           2                           363
  MALE                             1                           133
[1] 2 2
[1] FALSE
D7V8, binary
                               cls
clus                              0   1
  AMP PEAK  8(2Q37.2) MUTATED     2   1
  AMP PEAK  8(2Q37.2) WILD-TYPE 183 289
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(2Q37.2) MUTATED      2    1
  AMP PEAK  8(2Q37.2) WILD-TYPE  183  289
     clus
vv    AMP PEAK  8(2Q37.2) MUTATED AMP PEAK  8(2Q37.2) WILD-TYPE
  NO                            2                           183
  YES                           1                           289
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK  8(2Q37.2) MUTATED                0
  AMP PEAK  8(2Q37.2) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK  8(2Q37.2) MUTATED                                               1
  AMP PEAK  8(2Q37.2) WILD-TYPE                                           354
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK  8(2Q37.2) MUTATED                                                                        1
  AMP PEAK  8(2Q37.2) WILD-TYPE                                                                     99
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK  8(2Q37.2) MUTATED                                                                     1
  AMP PEAK  8(2Q37.2) WILD-TYPE                                                                  35
D7V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK  8(2Q37.2) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    1
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              1
                                                                        clus
vv                                                                       AMP PEAK  8(2Q37.2) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    354
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            99
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, binary
                               cls
clus                              0   1
  AMP PEAK  8(2Q37.2) MUTATED     2   0
  AMP PEAK  8(2Q37.2) WILD-TYPE 418  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(2Q37.2) MUTATED      2    0
  AMP PEAK  8(2Q37.2) WILD-TYPE  418   17
     clus
vv    AMP PEAK  8(2Q37.2) MUTATED AMP PEAK  8(2Q37.2) WILD-TYPE
  NO                            2                           418
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK  8(2Q37.2) MUTATED              1                       0    1
  AMP PEAK  8(2Q37.2) WILD-TYPE          131                      18  329
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK  8(2Q37.2) MUTATED                     0
  AMP PEAK  8(2Q37.2) WILD-TYPE                   1
D7V11, multiclass
[1] "Remove cluster labels:"      "AMP PEAK  8(2Q37.2) MUTATED"
clus
  AMP PEAK  8(2Q37.2) MUTATED AMP PEAK  8(2Q37.2) WILD-TYPE 
                            2                           479 
                   TCGA-4C-A93U                    TCGA-BJ-A0YZ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0Z0                    TCGA-BJ-A0Z2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0Z3                    TCGA-BJ-A0Z9 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0ZA                    TCGA-BJ-A0ZB 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0ZC                    TCGA-BJ-A0ZE 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0ZG                    TCGA-BJ-A0ZH 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0ZJ                    TCGA-BJ-A18Y 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A18Z                    TCGA-BJ-A190 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A191                    TCGA-BJ-A192 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A28X                    TCGA-BJ-A28Z 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A2N7                    TCGA-BJ-A2N9 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A2NA                    TCGA-BJ-A3EZ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A3F0                    TCGA-BJ-A3PR 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A3PU                    TCGA-BJ-A45C 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A45D                    TCGA-BJ-A45G 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A45H                    TCGA-BJ-A45I 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A45K                    TCGA-BJ-A4O8 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A4O9                    TCGA-CE-A13K 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A27D                    TCGA-CE-A3MD 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A3ME                    TCGA-CE-A481 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A482                    TCGA-CE-A483 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A484                    TCGA-CE-A485 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A0XZ                    TCGA-DE-A0Y2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A2OL                    TCGA-DE-A3KN 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A4M8                    TCGA-DE-A4M9 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A4MA                    TCGA-DE-A4MB 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A4MC                    TCGA-DE-A4MD 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A69J                    TCGA-DE-A69K 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13L                    TCGA-DJ-A13O 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13P                    TCGA-DJ-A13R 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13S                    TCGA-DJ-A13T 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13U                    TCGA-DJ-A13V 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13W                    TCGA-DJ-A13X 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QD                    TCGA-DJ-A1QE 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QF                    TCGA-DJ-A1QG 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QH                    TCGA-DJ-A1QI 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QL                    TCGA-DJ-A1QM 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QN                    TCGA-DJ-A1QO 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QQ                    TCGA-DJ-A2PN 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PO                    TCGA-DJ-A2PP 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PQ                    TCGA-DJ-A2PR 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PS                    TCGA-DJ-A2PT 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PU                    TCGA-DJ-A2PV 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PW                    TCGA-DJ-A2PX 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PY                    TCGA-DJ-A2PZ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q0                    TCGA-DJ-A2Q1 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q2                    TCGA-DJ-A2Q3 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q4                    TCGA-DJ-A2Q5 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q6                    TCGA-DJ-A2Q7 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q8                    TCGA-DJ-A2Q9 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2QA                    TCGA-DJ-A2QB 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2QC                    TCGA-DJ-A3UK 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UM                    TCGA-DJ-A3UN 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UO                    TCGA-DJ-A3UP 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UQ                    TCGA-DJ-A3UR 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3US                    TCGA-DJ-A3UT 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UU                    TCGA-DJ-A3UW 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UX                    TCGA-DJ-A3UY 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UZ                    TCGA-DJ-A3V0 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V2                    TCGA-DJ-A3V3 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V4                    TCGA-DJ-A3V5 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V7                    TCGA-DJ-A3V8 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V9                    TCGA-DJ-A3VA 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VB                    TCGA-DJ-A3VD 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VE                    TCGA-DJ-A3VF 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VG                    TCGA-DJ-A3VI 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VJ                    TCGA-DJ-A3VK 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VL                    TCGA-DJ-A3VM 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4UL                    TCGA-DJ-A4UP 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4UQ                    TCGA-DJ-A4UR 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4UT                    TCGA-DJ-A4UW 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4V0                    TCGA-DJ-A4V2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4V4                    TCGA-DJ-A4V5 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DO-A1JZ                    TCGA-DO-A1K0 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DO-A2HM                    TCGA-E3-A3DY 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E3-A3DZ                    TCGA-E3-A3E0 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E3-A3E1                    TCGA-E3-A3E2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E3-A3E3                    TCGA-E3-A3E5 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A242                    TCGA-E8-A2EA 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A3X7                    TCGA-E8-A413 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A414                    TCGA-E8-A415 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A416                    TCGA-E8-A417 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A418                    TCGA-E8-A419 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A432                    TCGA-E8-A433 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A434                    TCGA-E8-A436 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A437                    TCGA-E8-A438 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A44K                    TCGA-E8-A44M 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CL                    TCGA-EL-A3CM 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CN                    TCGA-EL-A3CO 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CP                    TCGA-EL-A3CR 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CS                    TCGA-EL-A3CT 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CU                    TCGA-EL-A3CV 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CW                    TCGA-EL-A3CX 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CY                    TCGA-EL-A3CZ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3D0                    TCGA-EL-A3D1 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3D4                    TCGA-EL-A3D5 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3D6                    TCGA-EL-A3GO 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GP                    TCGA-EL-A3GQ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GR                    TCGA-EL-A3GS 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GU                    TCGA-EL-A3GV 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GW                    TCGA-EL-A3GX 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GY                    TCGA-EL-A3GZ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3H1                    TCGA-EL-A3H2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3H3                    TCGA-EL-A3H4 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3H5                    TCGA-EL-A3H7 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3H8                    TCGA-EL-A3MW 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3MX                    TCGA-EL-A3MY 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3MZ                    TCGA-EL-A3N2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3N3                    TCGA-EL-A3T0 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3T1                    TCGA-EL-A3T2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3T3                    TCGA-EL-A3T6 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3T7                    TCGA-EL-A3T8 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3T9                    TCGA-EL-A3TA 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3TB                    TCGA-EL-A3ZG 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZH                    TCGA-EL-A3ZK 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZL                    TCGA-EL-A3ZM 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZN                    TCGA-EL-A3ZO 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZP                    TCGA-EL-A3ZQ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZR                    TCGA-EL-A3ZS 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZT                    TCGA-EL-A4JV 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4JW                    TCGA-EL-A4JX 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4JZ                    TCGA-EL-A4K0 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4K1                    TCGA-EL-A4K2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4K4                    TCGA-EL-A4K6 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4K7                    TCGA-EL-A4K9 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4KD                    TCGA-EL-A4KG 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4KH                    TCGA-EL-A4KI 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1CS                    TCGA-EM-A1CT 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1CU                    TCGA-EM-A1CV 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1CW                    TCGA-EM-A1YA 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1YB                    TCGA-EM-A1YC 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1YD                    TCGA-EM-A1YE 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22I                    TCGA-EM-A22J 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22K                    TCGA-EM-A22L 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22M                    TCGA-EM-A22N 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22O                    TCGA-EM-A22P 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22Q                    TCGA-EM-A2CJ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CK                    TCGA-EM-A2CL 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CN                    TCGA-EM-A2CO 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CP                    TCGA-EM-A2CQ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CT                    TCGA-EM-A2CU 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2OV                    TCGA-EM-A2OW 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2OX                    TCGA-EM-A2OY 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2OZ                    TCGA-EM-A2P0 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2P1                    TCGA-EM-A2P2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2P3                    TCGA-EM-A3AI 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AJ                    TCGA-EM-A3AK 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AL                    TCGA-EM-A3AN 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AO                    TCGA-EM-A3AP 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AQ                    TCGA-EM-A3AR 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FJ                    TCGA-EM-A3FK 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FL                    TCGA-EM-A3FM 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FN                    TCGA-EM-A3FO 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FP                    TCGA-EM-A3FQ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FR                    TCGA-EM-A3O3 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3O6                    TCGA-EM-A3O7 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3O8                    TCGA-EM-A3O9 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3OA                    TCGA-EM-A3OB 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3ST                    TCGA-EM-A3SU 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3SX                    TCGA-EM-A3SY 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3SZ                    TCGA-EM-A4FF 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FH                    TCGA-EM-A4FK 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FM                    TCGA-EM-A4FN 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FO                    TCGA-EM-A4FQ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FR                    TCGA-EM-A4FU 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FV                    TCGA-EM-A4G1 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25G                    TCGA-ET-A25I 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25J                    TCGA-ET-A25K 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25L                    TCGA-ET-A25M 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25N                    TCGA-ET-A25O 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25P                    TCGA-ET-A25R 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A2MX                    TCGA-ET-A2MY 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A2MZ                    TCGA-ET-A2N0 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A2N1                    TCGA-ET-A2N3 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A2N4                    TCGA-ET-A2N5 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39I                    TCGA-ET-A39J 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39K                    TCGA-ET-A39L 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39M                    TCGA-ET-A39N 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39O                    TCGA-ET-A39P 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39R                    TCGA-ET-A39S 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39T                    TCGA-ET-A3BN 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BO                    TCGA-ET-A3BP 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BQ                    TCGA-ET-A3BS 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BT                    TCGA-ET-A3BU 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BV                    TCGA-ET-A3BW 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BX                    TCGA-ET-A3DO 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3DP                    TCGA-ET-A3DQ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3DR                    TCGA-ET-A3DS 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3DT                    TCGA-ET-A3DU 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3DV                    TCGA-ET-A3DW 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A40P                    TCGA-ET-A40Q 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A40R                    TCGA-ET-A40S 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A40T                    TCGA-ET-A4KN 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A4KQ                    TCGA-FE-A22Z 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A230                    TCGA-FE-A231 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A232                    TCGA-FE-A233 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A234                    TCGA-FE-A235 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A236                    TCGA-FE-A237 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A238                    TCGA-FE-A239 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A23A                    TCGA-FE-A3PA 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A3PB                    TCGA-FE-A3PC 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A3PD                    TCGA-FK-A3S3 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FK-A3SB                    TCGA-FK-A3SE 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FK-A3SG                    TCGA-FK-A3SH 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FK-A4UB                    TCGA-FY-A2QD 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3BL                    TCGA-FY-A3I4 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3I5                    TCGA-FY-A3NM 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3NN                    TCGA-FY-A3ON 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3R6                    TCGA-FY-A3R7 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3R8                    TCGA-FY-A3R9 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3RA                    TCGA-FY-A3TY 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3W9                    TCGA-FY-A3WA 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3YR                    TCGA-FY-A40K 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A40L                    TCGA-FY-A40M 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A40N                    TCGA-FY-A4B0 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A4B3                    TCGA-FY-A4B4 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A76V                    TCGA-GE-A2C6 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-H2-A26U                    TCGA-H2-A2K9 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-H2-A3RH                    TCGA-H2-A3RI 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-H2-A421                    TCGA-H2-A422 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A3EB                    TCGA-IM-A3ED 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A3U2                    TCGA-IM-A3U3 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A41Y                    TCGA-IM-A41Z 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A420                    TCGA-IM-A4EB 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3NZ                    TCGA-J8-A3O0 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3O1                    TCGA-J8-A3O2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3YD                    TCGA-J8-A3YE 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3YF                    TCGA-J8-A3YG 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3YH                    TCGA-J8-A42S 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A4HW                    TCGA-J8-A4HY 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A41F                    TCGA-KS-A41I 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A41J                    TCGA-KS-A41L 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4I1                    TCGA-KS-A4I3 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4I5                    TCGA-KS-A4I7 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4I9                    TCGA-KS-A4IB 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4IC                    TCGA-KS-A4ID 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-L6-A4EP                    TCGA-L6-A4EQ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-L6-A4ET                    TCGA-L6-A4EU 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-MK-A4N7                    TCGA-MK-A4N9 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-QD-A8IV 
"AMP PEAK  8(2Q37.2) WILD-TYPE" 
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  8(2Q37.2) MUTATED     2   0   0   0
  AMP PEAK  8(2Q37.2) WILD-TYPE 381  51   4  30
D7V12, multiclass
[1] "Remove cluster labels:"      "AMP PEAK  8(2Q37.2) MUTATED"
clus
  AMP PEAK  8(2Q37.2) MUTATED AMP PEAK  8(2Q37.2) WILD-TYPE 
                            2                           466 
                   TCGA-4C-A93U                    TCGA-BJ-A0YZ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0Z0                    TCGA-BJ-A0Z2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0Z3                    TCGA-BJ-A0Z9 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0ZA                    TCGA-BJ-A0ZB 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0ZC                    TCGA-BJ-A0ZE 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0ZG                    TCGA-BJ-A0ZH 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0ZJ                    TCGA-BJ-A18Y 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A18Z                    TCGA-BJ-A190 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A191                    TCGA-BJ-A192 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A28X                    TCGA-BJ-A2N7 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A2N9                    TCGA-BJ-A2NA 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A2P4                    TCGA-BJ-A3EZ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A3F0                    TCGA-BJ-A3PR 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A3PU                    TCGA-BJ-A45I 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A4O8                    TCGA-CE-A13K 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A27D                    TCGA-CE-A3MD 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A3ME                    TCGA-CE-A481 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A482                    TCGA-CE-A483 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A484                    TCGA-CE-A485 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A0XZ                    TCGA-DE-A0Y2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A0Y3                    TCGA-DE-A2OL 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A3KN                    TCGA-DE-A4M8 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A4M9                    TCGA-DE-A4MA 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A4MB                    TCGA-DE-A4MC 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A4MD                    TCGA-DE-A69J 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A69K                    TCGA-DE-A7U5 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13L                    TCGA-DJ-A13O 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13P                    TCGA-DJ-A13R 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13S                    TCGA-DJ-A13T 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13U                    TCGA-DJ-A13V 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13W                    TCGA-DJ-A13X 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QD                    TCGA-DJ-A1QE 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QF                    TCGA-DJ-A1QG 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QH                    TCGA-DJ-A1QI 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QL                    TCGA-DJ-A1QM 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QN                    TCGA-DJ-A1QO 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QQ                    TCGA-DJ-A2PN 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PO                    TCGA-DJ-A2PP 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PQ                    TCGA-DJ-A2PR 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PS                    TCGA-DJ-A2PT 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PU                    TCGA-DJ-A2PV 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PW                    TCGA-DJ-A2PX 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PY                    TCGA-DJ-A2PZ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q0                    TCGA-DJ-A2Q1 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q2                    TCGA-DJ-A2Q3 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q4                    TCGA-DJ-A2Q5 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q6                    TCGA-DJ-A2Q7 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q8                    TCGA-DJ-A2Q9 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2QA                    TCGA-DJ-A2QB 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2QC                    TCGA-DJ-A3UK 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UM                    TCGA-DJ-A3UN 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UO                    TCGA-DJ-A3UP 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UQ                    TCGA-DJ-A3UR 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3US                    TCGA-DJ-A3UT 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UU                    TCGA-DJ-A3UW 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UX                    TCGA-DJ-A3UY 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UZ                    TCGA-DJ-A3V0 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V2                    TCGA-DJ-A3V3 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V4                    TCGA-DJ-A3V5 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V7                    TCGA-DJ-A3V8 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V9                    TCGA-DJ-A3VA 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VB                    TCGA-DJ-A3VD 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VE                    TCGA-DJ-A3VF 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VG                    TCGA-DJ-A3VI 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VJ                    TCGA-DJ-A3VK 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VL                    TCGA-DJ-A3VM 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4UL                    TCGA-DJ-A4UP 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4UQ                    TCGA-DJ-A4UR 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4UT                    TCGA-DJ-A4UW 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4V0                    TCGA-DJ-A4V2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4V4                    TCGA-DJ-A4V5 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DO-A1JZ                    TCGA-DO-A1K0 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DO-A2HM                    TCGA-E3-A3DY 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E3-A3DZ                    TCGA-E3-A3E0 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E3-A3E1                    TCGA-E3-A3E2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E3-A3E3                    TCGA-E3-A3E5 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A242                    TCGA-E8-A2EA 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A3X7                    TCGA-E8-A413 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A414                    TCGA-E8-A415 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A416                    TCGA-E8-A417 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A418                    TCGA-E8-A419 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A432                    TCGA-E8-A433 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A434                    TCGA-E8-A436 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A437                    TCGA-E8-A438 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A44K                    TCGA-E8-A44M 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CL                    TCGA-EL-A3CM 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CN                    TCGA-EL-A3CO 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CP                    TCGA-EL-A3CR 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CS                    TCGA-EL-A3CT 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CU                    TCGA-EL-A3CV 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CW                    TCGA-EL-A3CX 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CY                    TCGA-EL-A3CZ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3D0                    TCGA-EL-A3D1 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3D4                    TCGA-EL-A3D5 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3D6                    TCGA-EL-A3GO 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GP                    TCGA-EL-A3GQ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GR                    TCGA-EL-A3GS 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GU                    TCGA-EL-A3GV 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GW                    TCGA-EL-A3GX 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GY                    TCGA-EL-A3GZ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3H1                    TCGA-EL-A3H2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3H3                    TCGA-EL-A3H4 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3H5                    TCGA-EL-A3H7 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3H8                    TCGA-EL-A3MW 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3MX                    TCGA-EL-A3MY 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3MZ                    TCGA-EL-A3N2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3N3                    TCGA-EL-A3T0 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3T1                    TCGA-EL-A3T2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3T3                    TCGA-EL-A3T6 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3T7                    TCGA-EL-A3T8 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3T9                    TCGA-EL-A3TA 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3TB                    TCGA-EL-A3ZG 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZH                    TCGA-EL-A3ZK 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZL                    TCGA-EL-A3ZM 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZN                    TCGA-EL-A3ZO 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZP                    TCGA-EL-A3ZQ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZR                    TCGA-EL-A3ZS 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZT                    TCGA-EL-A4JV 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4JW                    TCGA-EL-A4JX 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4JZ                    TCGA-EL-A4K0 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4K1                    TCGA-EL-A4K2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4K4                    TCGA-EL-A4K6 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4K7                    TCGA-EL-A4K9 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4KD                    TCGA-EL-A4KG 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4KH                    TCGA-EL-A4KI 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1CS                    TCGA-EM-A1CW 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1YA                    TCGA-EM-A1YB 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1YC                    TCGA-EM-A1YD 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1YE                    TCGA-EM-A22I 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22J                    TCGA-EM-A22K 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22L                    TCGA-EM-A22M 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22N                    TCGA-EM-A22O 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22P                    TCGA-EM-A22Q 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CJ                    TCGA-EM-A2CK 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CL                    TCGA-EM-A2CN 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CO                    TCGA-EM-A2CP 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CQ                    TCGA-EM-A2CT 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CU                    TCGA-EM-A2OV 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2OW                    TCGA-EM-A2OX 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2OY                    TCGA-EM-A2OZ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2P0                    TCGA-EM-A2P1 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2P2                    TCGA-EM-A2P3 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AI                    TCGA-EM-A3AJ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AK                    TCGA-EM-A3AL 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AN                    TCGA-EM-A3AO 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AP                    TCGA-EM-A3AQ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AR                    TCGA-EM-A3FJ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FK                    TCGA-EM-A3FL 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FM                    TCGA-EM-A3FN 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FO                    TCGA-EM-A3FP 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FQ                    TCGA-EM-A3FR 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3O3                    TCGA-EM-A3O6 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3O7                    TCGA-EM-A3O8 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3O9                    TCGA-EM-A3OA 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3OB                    TCGA-EM-A3ST 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3SU                    TCGA-EM-A3SX 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3SY                    TCGA-EM-A3SZ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FF                    TCGA-EM-A4FH 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FK                    TCGA-EM-A4FM 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FN                    TCGA-EM-A4FO 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FQ                    TCGA-EM-A4FR 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FU                    TCGA-EM-A4FV 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4G1                    TCGA-ET-A25G 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25I                    TCGA-ET-A25J 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25K                    TCGA-ET-A25L 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25M                    TCGA-ET-A25N 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25O                    TCGA-ET-A25P 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25R                    TCGA-ET-A2MX 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A2MY                    TCGA-ET-A2MZ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A2N0                    TCGA-ET-A2N1 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A2N3                    TCGA-ET-A2N4 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A2N5                    TCGA-ET-A39I 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39J                    TCGA-ET-A39K 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39L                    TCGA-ET-A39M 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39N                    TCGA-ET-A39O 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39P                    TCGA-ET-A39R 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39S                    TCGA-ET-A39T 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BN                    TCGA-ET-A3BO 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BP                    TCGA-ET-A3BQ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BS                    TCGA-ET-A3BT 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BU                    TCGA-ET-A3BV 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BW                    TCGA-ET-A3BX 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3DO                    TCGA-ET-A3DP 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3DQ                    TCGA-ET-A3DR 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3DS                    TCGA-ET-A3DT 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3DU                    TCGA-ET-A3DV 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3DW                    TCGA-ET-A40P 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A40Q                    TCGA-ET-A40R 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A40S                    TCGA-ET-A40T 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A4KN                    TCGA-ET-A4KQ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A22Z                    TCGA-FE-A230 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A231                    TCGA-FE-A232 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A233                    TCGA-FE-A234 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A235                    TCGA-FE-A236 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A237                    TCGA-FE-A238 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A239                    TCGA-FE-A23A 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A3PA                    TCGA-FE-A3PB 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A3PC                    TCGA-FE-A3PD 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FK-A3S3                    TCGA-FK-A3SB 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FK-A3SE                    TCGA-FK-A3SG 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FK-A3SH                    TCGA-FK-A4UB 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3BL                    TCGA-FY-A3I4 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3I5                    TCGA-FY-A3NM 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3NN                    TCGA-FY-A3ON 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3R6                    TCGA-FY-A3R8 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3R9                    TCGA-FY-A3RA 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3TY                    TCGA-FY-A3W9 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3WA                    TCGA-FY-A3YR 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A40K                    TCGA-FY-A40L 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A40M                    TCGA-FY-A40N 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A4B0                    TCGA-FY-A4B3 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A4B4                    TCGA-FY-A76V 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-GE-A2C6                    TCGA-H2-A422 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A3EB                    TCGA-IM-A3ED 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A3U2                    TCGA-IM-A3U3 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A41Y                    TCGA-IM-A41Z 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A420                    TCGA-IM-A4EB 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3NZ                    TCGA-J8-A3O0 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3O1                    TCGA-J8-A3O2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3YD                    TCGA-J8-A3YE 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3YF                    TCGA-J8-A3YG 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3YH                    TCGA-J8-A42S 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A4HW                    TCGA-J8-A4HY 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A41F                    TCGA-KS-A41I 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A41J                    TCGA-KS-A41L 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4I1                    TCGA-KS-A4I3 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4I5                    TCGA-KS-A4I7 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4I9                    TCGA-KS-A4IB 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4IC                    TCGA-KS-A4ID 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-L6-A4EP                    TCGA-L6-A4EQ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-L6-A4ET                    TCGA-L6-A4EU 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-MK-A4N6                    TCGA-MK-A4N7 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-MK-A4N9                    TCGA-QD-A8IV 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
D7V13, continuous
[1] "Remove cluster labels:"      "AMP PEAK  8(2Q37.2) MUTATED"
clus
  AMP PEAK  8(2Q37.2) MUTATED AMP PEAK  8(2Q37.2) WILD-TYPE 
                            2                           383 
                   TCGA-4C-A93U                    TCGA-BJ-A0Z0 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0Z3                    TCGA-BJ-A0Z9 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0ZA                    TCGA-BJ-A0ZB 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0ZH                    TCGA-BJ-A0ZJ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A18Y                    TCGA-BJ-A18Z 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A190                    TCGA-BJ-A191 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A28R                    TCGA-BJ-A28T 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A28W                    TCGA-BJ-A28X 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A28Z                    TCGA-BJ-A291 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A2N8                    TCGA-BJ-A2N9 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A2NA                    TCGA-BJ-A3EZ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A3PR                    TCGA-BJ-A3PU 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A45C                    TCGA-BJ-A45D 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A45E                    TCGA-BJ-A45G 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A45I                    TCGA-BJ-A45J 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A45K                    TCGA-BJ-A4O8 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A4O9                    TCGA-CE-A13K 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A3MD                    TCGA-CE-A483 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A484                    TCGA-CE-A485 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A0XZ                    TCGA-DE-A0Y2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A0Y3                    TCGA-DE-A3KN 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A4M8                    TCGA-DE-A4MA 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A4MB                    TCGA-DE-A4MC 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A4MD                    TCGA-DE-A69K 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A7U5                    TCGA-DJ-A13O 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13R                    TCGA-DJ-A13T 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13V                    TCGA-DJ-A13W 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13X                    TCGA-DJ-A1QG 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QH                    TCGA-DJ-A1QM 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PO                    TCGA-DJ-A2PP 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PQ                    TCGA-DJ-A2PR 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PS                    TCGA-DJ-A2PT 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PU                    TCGA-DJ-A2PV 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PW                    TCGA-DJ-A2PX 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PY                    TCGA-DJ-A2PZ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q0                    TCGA-DJ-A2Q1 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q2                    TCGA-DJ-A2Q3 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q4                    TCGA-DJ-A2Q5 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q6                    TCGA-DJ-A2Q7 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q8                    TCGA-DJ-A2Q9 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2QA                    TCGA-DJ-A2QB 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UK                    TCGA-DJ-A3UM 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UN                    TCGA-DJ-A3UO 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UP                    TCGA-DJ-A3UQ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UR                    TCGA-DJ-A3UU 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UW                    TCGA-DJ-A3UX 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UZ                    TCGA-DJ-A3V0 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V2                    TCGA-DJ-A3V3 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V4                    TCGA-DJ-A3V5 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V7                    TCGA-DJ-A3V8 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V9                    TCGA-DJ-A3VA 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VB                    TCGA-DJ-A3VD 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VF                    TCGA-DJ-A3VG 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VI                    TCGA-DJ-A3VJ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VK                    TCGA-DJ-A3VL 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4UL                    TCGA-DJ-A4UP 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4UQ                    TCGA-DJ-A4UR 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4UW                    TCGA-DJ-A4V2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4V5                    TCGA-DO-A1K0 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DO-A2HM                    TCGA-E3-A3DY 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E3-A3DZ                    TCGA-E3-A3E0 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E3-A3E1                    TCGA-E3-A3E2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E3-A3E3                    TCGA-E3-A3E5 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A242                    TCGA-E8-A2EA 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A414                    TCGA-E8-A415 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A417                    TCGA-E8-A419 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A433                    TCGA-E8-A436 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A438                    TCGA-E8-A44K 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CM                    TCGA-EL-A3CN 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CO                    TCGA-EL-A3CR 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CS                    TCGA-EL-A3CT 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CU                    TCGA-EL-A3CV 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CW                    TCGA-EL-A3CX 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CY                    TCGA-EL-A3CZ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3D0                    TCGA-EL-A3D1 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3D4                    TCGA-EL-A3D5 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3D6                    TCGA-EL-A3GO 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GP                    TCGA-EL-A3GQ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GS                    TCGA-EL-A3GU 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GV                    TCGA-EL-A3GX 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3H3                    TCGA-EL-A3H4 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3H5                    TCGA-EL-A3H7 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3H8                    TCGA-EL-A3MW 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3MX                    TCGA-EL-A3MZ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3N2                    TCGA-EL-A3T0 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3T1                    TCGA-EL-A3T2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3TB                    TCGA-EL-A3ZH 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZK                    TCGA-EL-A3ZL 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZM                    TCGA-EL-A3ZN 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZO                    TCGA-EL-A3ZP 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZS                    TCGA-EL-A4JV 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4JW                    TCGA-EL-A4JX 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4JZ                    TCGA-EL-A4K0 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4K1                    TCGA-EL-A4K2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4K4                    TCGA-EL-A4K6 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4K7                    TCGA-EL-A4KD 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4KG                    TCGA-EL-A4KI 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1CS                    TCGA-EM-A1CT 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1CU                    TCGA-EM-A1CV 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1CW                    TCGA-EM-A1YC 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1YD                    TCGA-EM-A1YE 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22I                    TCGA-EM-A22J 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22K                    TCGA-EM-A22L 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22M                    TCGA-EM-A22N 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22O                    TCGA-EM-A22P 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22Q                    TCGA-EM-A2CK 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CN                    TCGA-EM-A2CP 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CQ                    TCGA-EM-A2CT 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CU                    TCGA-EM-A2OV 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2OX                    TCGA-EM-A2OY 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2OZ                    TCGA-EM-A2P0 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2P1                    TCGA-EM-A2P2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AJ                    TCGA-EM-A3AK 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AL                    TCGA-EM-A3AN 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AO                    TCGA-EM-A3AQ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AR                    TCGA-EM-A3FJ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FK                    TCGA-EM-A3FM 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FN                    TCGA-EM-A3FO 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FP                    TCGA-EM-A3FQ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FR                    TCGA-EM-A3O3 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3O8                    TCGA-EM-A3O9 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3OA                    TCGA-EM-A3OB 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3ST                    TCGA-EM-A3SU 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3SX                    TCGA-EM-A3SZ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FF                    TCGA-EM-A4FM 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FN                    TCGA-EM-A4FO 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FQ                    TCGA-EM-A4FR 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FV                    TCGA-EM-A4G1 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25G                    TCGA-ET-A25I 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25J                    TCGA-ET-A25K 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25L                    TCGA-ET-A25M 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25N                    TCGA-ET-A25O 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25P                    TCGA-ET-A2MX 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A2MZ                    TCGA-ET-A2N0 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A2N1                    TCGA-ET-A2N4 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39K                    TCGA-ET-A39L 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39O                    TCGA-ET-A39P 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39R                    TCGA-ET-A39S 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39T                    TCGA-ET-A3BO 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BP                    TCGA-ET-A3BQ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BS                    TCGA-ET-A3BT 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BU                    TCGA-ET-A3BV 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BX                    TCGA-ET-A3DQ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3DR                    TCGA-ET-A3DS 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3DT                    TCGA-ET-A3DU 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3DV                    TCGA-ET-A3DW 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A40P                    TCGA-ET-A40Q 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A40R                    TCGA-ET-A40S 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A40T                    TCGA-ET-A4KN 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A22Z                    TCGA-FE-A230 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A231                    TCGA-FE-A232 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A233                    TCGA-FE-A234 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A235                    TCGA-FE-A236 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A237                    TCGA-FE-A238 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A239                    TCGA-FE-A23A 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A3PB                    TCGA-FE-A3PC 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A3PD                    TCGA-FK-A3S3 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FK-A3SB                    TCGA-FK-A3SE 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FK-A3SG                    TCGA-FK-A3SH 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FK-A4UB                    TCGA-FY-A2QD 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3I4                    TCGA-FY-A3I5 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3NM                    TCGA-FY-A3NN 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3ON                    TCGA-FY-A3R6 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3R7                    TCGA-FY-A3R9 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3TY                    TCGA-FY-A3W9 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3YR                    TCGA-FY-A40K 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A40L                    TCGA-FY-A40M 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A40N                    TCGA-FY-A4B3 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A4B4                    TCGA-GE-A2C6 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-H2-A26U                    TCGA-H2-A2K9 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-H2-A3RH                    TCGA-H2-A3RI 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-H2-A421                    TCGA-H2-A422 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A3EB                    TCGA-IM-A3ED 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A3U2                    TCGA-IM-A3U3 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A41Y                    TCGA-IM-A41Z 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A420                    TCGA-IM-A4EB 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3NZ                    TCGA-J8-A3O0 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3O1                    TCGA-J8-A3O2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3YD                    TCGA-J8-A3YE 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3YF                    TCGA-J8-A3YG 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3YH                    TCGA-J8-A42S 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A4HW                    TCGA-J8-A4HY 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A41F                    TCGA-KS-A41I 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A41J                    TCGA-KS-A41L 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4I1                    TCGA-KS-A4I3 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4I5                    TCGA-KS-A4I7 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4I9                    TCGA-KS-A4IB 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4IC                    TCGA-KS-A4ID 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-L6-A4EP                    TCGA-L6-A4EQ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-L6-A4EU                    TCGA-MK-A4N6 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-MK-A4N7                    TCGA-MK-A4N9 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-QD-A8IV 
"AMP PEAK  8(2Q37.2) WILD-TYPE" 
D7V14, binary
                               cls
clus                              0   1
  AMP PEAK  8(2Q37.2) MUTATED     1   2
  AMP PEAK  8(2Q37.2) WILD-TYPE 224 262
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(2Q37.2) MUTATED      1    2
  AMP PEAK  8(2Q37.2) WILD-TYPE  224  262
            clus
vv           AMP PEAK  8(2Q37.2) MUTATED AMP PEAK  8(2Q37.2) WILD-TYPE
  MULTIFOCAL                           1                           224
  UNIFOCAL                             2                           262
[1] 2 2
[1] FALSE
D7V15, continuous
[1] "Remove cluster labels:"      "AMP PEAK  8(2Q37.2) MUTATED"
clus
  AMP PEAK  8(2Q37.2) MUTATED AMP PEAK  8(2Q37.2) WILD-TYPE 
                            2                           399 
                   TCGA-4C-A93U                    TCGA-BJ-A0Z2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0Z3                    TCGA-BJ-A0Z9 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0ZA                    TCGA-BJ-A0ZB 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0ZC                    TCGA-BJ-A0ZE 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0ZG                    TCGA-BJ-A0ZH 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0ZJ                    TCGA-BJ-A18Y 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A18Z                    TCGA-BJ-A190 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A191                    TCGA-BJ-A192 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A28R                    TCGA-BJ-A28S 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A28T                    TCGA-BJ-A28V 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A28W                    TCGA-BJ-A28Z 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A291                    TCGA-BJ-A2N8 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A2N9                    TCGA-BJ-A2P4 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A3PU                    TCGA-BJ-A45C 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A45D                    TCGA-BJ-A45E 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A45F                    TCGA-BJ-A45G 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A45H                    TCGA-BJ-A45I 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A45J                    TCGA-BJ-A45K 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A4O8                    TCGA-BJ-A4O9 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A13K                    TCGA-CE-A27D 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A3MD                    TCGA-CE-A3ME 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A481                    TCGA-CE-A482 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A483                    TCGA-CE-A484 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A485                    TCGA-DE-A0XZ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A0Y2                    TCGA-DE-A0Y3 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A2OL                    TCGA-DE-A3KN 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A4M8                    TCGA-DE-A4M9 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A4MA                    TCGA-DE-A4MB 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A4MC                    TCGA-DE-A4MD 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A69J                    TCGA-DE-A69K 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A7U5                    TCGA-DJ-A13L 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13O                    TCGA-DJ-A13R 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13S                    TCGA-DJ-A13U 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13V                    TCGA-DJ-A13W 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13X                    TCGA-DJ-A1QD 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QE                    TCGA-DJ-A1QF 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QG                    TCGA-DJ-A1QH 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QI                    TCGA-DJ-A1QL 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QM                    TCGA-DJ-A1QN 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QO                    TCGA-DJ-A1QQ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PN                    TCGA-DJ-A2PO 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PP                    TCGA-DJ-A2PQ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PR                    TCGA-DJ-A2PS 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PT                    TCGA-DJ-A2PU 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PV                    TCGA-DJ-A2PW 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PY                    TCGA-DJ-A2PZ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q0                    TCGA-DJ-A2Q1 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q2                    TCGA-DJ-A2Q3 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q4                    TCGA-DJ-A2Q5 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q6                    TCGA-DJ-A2Q7 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q8                    TCGA-DJ-A2Q9 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2QA                    TCGA-DJ-A2QC 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UK                    TCGA-DJ-A3UM 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UN                    TCGA-DJ-A3UO 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UP                    TCGA-DJ-A3UQ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UR                    TCGA-DJ-A3US 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UT                    TCGA-DJ-A3UU 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UW                    TCGA-DJ-A3UX 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UY                    TCGA-DJ-A3V0 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V2                    TCGA-DJ-A3V3 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V4                    TCGA-DJ-A3V5 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V7                    TCGA-DJ-A3V8 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VA                    TCGA-DJ-A3VB 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VD                    TCGA-DJ-A3VE 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VF                    TCGA-DJ-A3VG 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VJ                    TCGA-DJ-A3VK 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VL                    TCGA-DJ-A3VM 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4UL                    TCGA-DJ-A4UP 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4UQ                    TCGA-DJ-A4UT 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4V0                    TCGA-DJ-A4V2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4V4                    TCGA-DJ-A4V5 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DO-A1JZ                    TCGA-DO-A1K0 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-DO-A2HM                    TCGA-E3-A3DY 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E3-A3DZ                    TCGA-E3-A3E0 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E3-A3E1                    TCGA-E3-A3E2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-E3-A3E3                    TCGA-E8-A419 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CN                    TCGA-EL-A3CO 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CR                    TCGA-EL-A3CS 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CT                    TCGA-EL-A3CU 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CV                    TCGA-EL-A3CW 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CX                    TCGA-EL-A3CY 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CZ                    TCGA-EL-A3D0 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3D1                    TCGA-EL-A3D4 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3D5                    TCGA-EL-A3D6 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GO                    TCGA-EL-A3GP 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GQ                    TCGA-EL-A3GR 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GS                    TCGA-EL-A3GU 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GV                    TCGA-EL-A3GW 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GX                    TCGA-EL-A3GY 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GZ                    TCGA-EL-A3H2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3H3                    TCGA-EL-A3H4 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3H5                    TCGA-EL-A3H7 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3H8                    TCGA-EL-A3MW 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3MX                    TCGA-EL-A3MY 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3MZ                    TCGA-EL-A3N2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3N3                    TCGA-EL-A3T1 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3T2                    TCGA-EL-A3T3 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3T6                    TCGA-EL-A3T7 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3T8                    TCGA-EL-A3T9 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3TA                    TCGA-EL-A3TB 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZG                    TCGA-EL-A3ZH 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZK                    TCGA-EL-A3ZL 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZM                    TCGA-EL-A3ZN 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZO                    TCGA-EL-A3ZP 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZQ                    TCGA-EL-A3ZR 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZS                    TCGA-EL-A3ZT 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4JV                    TCGA-EL-A4JW 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4JX                    TCGA-EL-A4JZ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4K0                    TCGA-EL-A4K1 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4K2                    TCGA-EL-A4K4 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4K6                    TCGA-EL-A4K7 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4K9                    TCGA-EL-A4KD 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4KG                    TCGA-EL-A4KH 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4KI                    TCGA-EM-A1CS 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1CT                    TCGA-EM-A1CU 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1CV                    TCGA-EM-A1CW 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1YA                    TCGA-EM-A1YB 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1YC                    TCGA-EM-A1YD 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1YE                    TCGA-EM-A22I 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22J                    TCGA-EM-A22K 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22L                    TCGA-EM-A22N 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22O                    TCGA-EM-A22P 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22Q                    TCGA-EM-A2CJ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CK                    TCGA-EM-A2CL 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CN                    TCGA-EM-A2CO 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CP                    TCGA-EM-A2CQ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CT                    TCGA-EM-A2CU 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2OW                    TCGA-EM-A2OX 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2OY                    TCGA-EM-A2P0 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2P1                    TCGA-EM-A2P2 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2P3                    TCGA-EM-A3AI 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AJ                    TCGA-EM-A3AK 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AL                    TCGA-EM-A3AN 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AO                    TCGA-EM-A3AP 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AQ                    TCGA-EM-A3AR 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FJ                    TCGA-EM-A3FM 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FN                    TCGA-EM-A3FO 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FP                    TCGA-EM-A3FR 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3O3                    TCGA-EM-A3O6 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3O7                    TCGA-EM-A3O8 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3O9                    TCGA-EM-A3OA 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3OB                    TCGA-EM-A3ST 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3SU                    TCGA-EM-A3SX 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3SY                    TCGA-EM-A3SZ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FF                    TCGA-EM-A4FH 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FK                    TCGA-EM-A4FM 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FN                    TCGA-EM-A4FQ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FR                    TCGA-EM-A4FU 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FV                    TCGA-EM-A4G1 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25G                    TCGA-ET-A25I 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25J                    TCGA-ET-A25K 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25L                    TCGA-ET-A25M 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25N                    TCGA-ET-A25O 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25P                    TCGA-ET-A25R 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A2MY                    TCGA-ET-A2MZ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A2N0                    TCGA-ET-A2N5 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39J                    TCGA-ET-A39M 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39N                    TCGA-ET-A39O 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39P                    TCGA-ET-A39T 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BN                    TCGA-ET-A3BO 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BP                    TCGA-ET-A3BQ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BS                    TCGA-ET-A3BT 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BU                    TCGA-ET-A3BV 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BW                    TCGA-ET-A3BX 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3DO                    TCGA-ET-A3DS 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3DT                    TCGA-ET-A40P 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A40Q                    TCGA-ET-A40R 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A40S                    TCGA-ET-A4KN 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A4KQ                    TCGA-FE-A22Z 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A230                    TCGA-FE-A232 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A233                    TCGA-FE-A234 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A235                    TCGA-FE-A236 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A237                    TCGA-FE-A238 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A239                    TCGA-FE-A23A 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A3PA                    TCGA-FE-A3PB 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A3PC                    TCGA-FE-A3PD 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A2QD                    TCGA-FY-A3I4 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3I5                    TCGA-FY-A3ON 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3R8                    TCGA-FY-A3TY 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3W9                    TCGA-FY-A3YR 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A40K                    TCGA-FY-A40L 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A40M                    TCGA-FY-A40N 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A4B3                    TCGA-FY-A76V 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-GE-A2C6                    TCGA-H2-A421 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A3EB                    TCGA-IM-A3ED 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A3U2                    TCGA-IM-A3U3 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A41Y                    TCGA-IM-A41Z 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A420                    TCGA-IM-A4EB 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3O0                    TCGA-J8-A3YD 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3YG                    TCGA-KS-A41F 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A41I                    TCGA-KS-A41J 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A41L                    TCGA-KS-A4I3 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4I5                    TCGA-KS-A4I7 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4I9                    TCGA-KS-A4IB 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4IC                    TCGA-KS-A4ID 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-L6-A4EP                    TCGA-L6-A4EQ 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-L6-A4ET                    TCGA-L6-A4EU 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-MK-A4N6                    TCGA-MK-A4N7 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-MK-A4N9                    TCGA-MK-A84Z 
"AMP PEAK  8(2Q37.2) WILD-TYPE" "AMP PEAK  8(2Q37.2) WILD-TYPE" 
                   TCGA-QD-A8IV 
"AMP PEAK  8(2Q37.2) WILD-TYPE" 
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  8(2Q37.2) MUTATED                                  0     0
  AMP PEAK  8(2Q37.2) WILD-TYPE                                1    52
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(2Q37.2) MUTATED                           0     3
  AMP PEAK  8(2Q37.2) WILD-TYPE                        27   325
D7V16, multiclass
                                  clus
vv                                 AMP PEAK  8(2Q37.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      3
                                  clus
vv                                 AMP PEAK  8(2Q37.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       52
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V17, binary
                               cls
clus                              0   1
  AMP PEAK  8(2Q37.2) MUTATED     0   3
  AMP PEAK  8(2Q37.2) WILD-TYPE  38 356
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(2Q37.2) MUTATED      0    3
  AMP PEAK  8(2Q37.2) WILD-TYPE   38  356
                        clus
vv                       AMP PEAK  8(2Q37.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           3
                        clus
vv                       AMP PEAK  8(2Q37.2) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           356
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  9(3P22.3) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  9(3P22.3) MUTATED     3   1
  AMP PEAK  9(3P22.3) WILD-TYPE 478  15
  AMP PEAK  9(3P22.3) MUTATED AMP PEAK  9(3P22.3) WILD-TYPE 
                            4                           493 
  AMP PEAK  9(3P22.3) MUTATED AMP PEAK  9(3P22.3) WILD-TYPE 
                            1                            15 
$`AMP PEAK  9(3P22.3) MUTATED`
TCGA-BJ-A0Z0 TCGA-EL-A3MX TCGA-EM-A22N TCGA-EM-A2CO 
       13.78        57.63        10.65         6.05 

$`AMP PEAK  9(3P22.3) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
        4.24        24.79        49.78        16.34        14.73        41.33 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73        25.48        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       42.08        51.39        41.52        20.58         4.83        44.35 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
       42.15        21.04        35.54        32.45        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.08        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        30.61         0.16         0.23        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        33.50         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        69.57        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       49.51        50.24       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       150.48       108.66 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       47.84        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       78.61        57.01        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       10.45        14.53        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       17.88        13.18        23.51         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        40.34        19.73        32.32        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ 
       17.59        17.46        17.29        14.60        22.52        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        33.07        13.38         8.35        29.72 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        47.38        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 
       17.49        17.39        16.18        15.02        14.50        15.06 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33         0.49         9.24        13.91        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       29.95        29.85        13.51        12.79        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
       21.34         5.33        26.37        26.37        22.45        21.53 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       60.49        24.46        13.68        81.93        81.70        77.56 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       70.42        56.58        60.20        63.39        65.29        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       63.45        88.41        58.75        37.25        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       83.34         2.66        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      108.46        84.89       123.32       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        98.20        28.24        50.40        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.79        87.62        77.82        75.42        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       62.83       166.62        24.72        43.99        46.26        44.38 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       40.21        37.48        33.17        31.40        73.74        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
      112.80        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        13.28 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10       116.09         1.25        20.42        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        7.82         0.99        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08         0.30         0.76        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       15.16         6.58        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83        31.10         8.22        25.64        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        23.93 
TCGA-QD-A8IV 
       12.89 

  AMP PEAK  9(3P22.3) MUTATED AMP PEAK  9(3P22.3) WILD-TYPE 
                         6.05                          0.16 
  AMP PEAK  9(3P22.3) MUTATED AMP PEAK  9(3P22.3) WILD-TYPE 
                        57.63                        169.32 
  AMP PEAK  9(3P22.3) MUTATED AMP PEAK  9(3P22.3) WILD-TYPE 
                       12.215                        30.610 
[1] "6.0 - 57.6 (12.2)"  "0.2 - 169.3 (30.6)"
[1] "hr=" "12" 
D8V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK  9(3P22.3) MUTATED         1        2         0        0         0
  AMP PEAK  9(3P22.3) WILD-TYPE     281       48       111        2        46
                               vv
clus                            STAGE IVC
  AMP PEAK  9(3P22.3) MUTATED           1
  AMP PEAK  9(3P22.3) WILD-TYPE         5
D8V3, multiclass
           clus
vv          AMP PEAK  9(3P22.3) MUTATED AMP PEAK  9(3P22.3) WILD-TYPE
  STAGE I                             1                           281
  STAGE II                            2                            48
  STAGE III                           0                           111
  STAGE IV                            0                             2
  STAGE IVA                           0                            46
  STAGE IVC                           1                             5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  9(3P22.3) MUTATED     1   2   0   1
  AMP PEAK  9(3P22.3) WILD-TYPE 141 163 167  22
D8V4, multiclass
    clus
vv   AMP PEAK  9(3P22.3) MUTATED AMP PEAK  9(3P22.3) WILD-TYPE
  T1                           1                           141
  T2                           2                           163
  T3                           0                           167
  T4                           1                            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"
D8V5, binary
                               cls
clus                              0   1
  AMP PEAK  9(3P22.3) MUTATED     2   1
  AMP PEAK  9(3P22.3) WILD-TYPE 223 223
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(3P22.3) MUTATED      2    1
  AMP PEAK  9(3P22.3) WILD-TYPE  223  223
   clus
vv  AMP PEAK  9(3P22.3) MUTATED AMP PEAK  9(3P22.3) WILD-TYPE
  0                           2                           223
  1                           1                           223
[1] 2 2
[1] FALSE
D8V6, binary
                               cls
clus                              0   1
  AMP PEAK  9(3P22.3) MUTATED     0   1
  AMP PEAK  9(3P22.3) WILD-TYPE 278   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(3P22.3) MUTATED      0    1
  AMP PEAK  9(3P22.3) WILD-TYPE  278    8
   clus
vv  AMP PEAK  9(3P22.3) MUTATED AMP PEAK  9(3P22.3) WILD-TYPE
  0                           0                           278
  1                           1                             8
[1] 2 2
[1] FALSE
D8V7, binary
                               cls
clus                              0   1
  AMP PEAK  9(3P22.3) MUTATED     3   1
  AMP PEAK  9(3P22.3) WILD-TYPE 362 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(3P22.3) MUTATED      3    1
  AMP PEAK  9(3P22.3) WILD-TYPE  362  133
        clus
vv       AMP PEAK  9(3P22.3) MUTATED AMP PEAK  9(3P22.3) WILD-TYPE
  FEMALE                           3                           362
  MALE                             1                           133
[1] 2 2
[1] FALSE
D8V8, binary
                               cls
clus                              0   1
  AMP PEAK  9(3P22.3) MUTATED     0   4
  AMP PEAK  9(3P22.3) WILD-TYPE 185 286
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(3P22.3) MUTATED      0    4
  AMP PEAK  9(3P22.3) WILD-TYPE  185  286
     clus
vv    AMP PEAK  9(3P22.3) MUTATED AMP PEAK  9(3P22.3) WILD-TYPE
  NO                            0                           185
  YES                           4                           286
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK  9(3P22.3) MUTATED                0
  AMP PEAK  9(3P22.3) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK  9(3P22.3) MUTATED                                               2
  AMP PEAK  9(3P22.3) WILD-TYPE                                           353
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK  9(3P22.3) MUTATED                                                                        2
  AMP PEAK  9(3P22.3) WILD-TYPE                                                                     98
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK  9(3P22.3) MUTATED                                                                     0
  AMP PEAK  9(3P22.3) WILD-TYPE                                                                  36
D8V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK  9(3P22.3) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       AMP PEAK  9(3P22.3) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, binary
                               cls
clus                              0   1
  AMP PEAK  9(3P22.3) MUTATED     3   0
  AMP PEAK  9(3P22.3) WILD-TYPE 417  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(3P22.3) MUTATED      3    0
  AMP PEAK  9(3P22.3) WILD-TYPE  417   17
     clus
vv    AMP PEAK  9(3P22.3) MUTATED AMP PEAK  9(3P22.3) WILD-TYPE
  NO                            3                           417
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK  9(3P22.3) MUTATED              0                       0    4
  AMP PEAK  9(3P22.3) WILD-TYPE          132                      18  326
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK  9(3P22.3) MUTATED                     0
  AMP PEAK  9(3P22.3) WILD-TYPE                   1
D8V11, multiclass
                         clus
vv                        AMP PEAK  9(3P22.3) MUTATED
  MINIMAL (T3)                                      0
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              4
  VERY ADVANCED (T4B)                               0
                         clus
vv                        AMP PEAK  9(3P22.3) WILD-TYPE
  MINIMAL (T3)                                      132
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              326
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  9(3P22.3) MUTATED     2   0   0   2
  AMP PEAK  9(3P22.3) WILD-TYPE 381  51   4  28
D8V12, multiclass
    clus
vv   AMP PEAK  9(3P22.3) MUTATED AMP PEAK  9(3P22.3) WILD-TYPE
  R0                           2                           381
  R1                           0                            51
  R2                           0                             4
  RX                           2                            28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V13, continuous
D8V14, binary
                               cls
clus                              0   1
  AMP PEAK  9(3P22.3) MUTATED     1   3
  AMP PEAK  9(3P22.3) WILD-TYPE 224 261
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(3P22.3) MUTATED      1    3
  AMP PEAK  9(3P22.3) WILD-TYPE  224  261
            clus
vv           AMP PEAK  9(3P22.3) MUTATED AMP PEAK  9(3P22.3) WILD-TYPE
  MULTIFOCAL                           1                           224
  UNIFOCAL                             3                           261
[1] 2 2
[1] FALSE
D8V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  9(3P22.3) MUTATED                                  0     0
  AMP PEAK  9(3P22.3) WILD-TYPE                                1    52
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(3P22.3) MUTATED                           0     1
  AMP PEAK  9(3P22.3) WILD-TYPE                        27   327
D8V16, multiclass
[1] "Remove cluster labels:"      "AMP PEAK  9(3P22.3) MUTATED"
clus
  AMP PEAK  9(3P22.3) MUTATED AMP PEAK  9(3P22.3) WILD-TYPE 
                            1                           407 
                   TCGA-4C-A93U                    TCGA-BJ-A0YZ 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A0Z2                    TCGA-BJ-A0Z3 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A0Z5                    TCGA-BJ-A0Z9 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A0ZA                    TCGA-BJ-A0ZB 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A0ZC                    TCGA-BJ-A0ZE 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A0ZG                    TCGA-BJ-A0ZH 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A0ZJ                    TCGA-BJ-A18Y 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A18Z                    TCGA-BJ-A190 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A191                    TCGA-BJ-A192 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A28R                    TCGA-BJ-A28S 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A28T                    TCGA-BJ-A28V 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A28W                    TCGA-BJ-A28X 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A28Z                    TCGA-BJ-A290 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A291                    TCGA-BJ-A2N7 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A2N8                    TCGA-BJ-A2N9 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A2NA                    TCGA-BJ-A2P4 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A3EZ                    TCGA-BJ-A3F0 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A3PR                    TCGA-BJ-A3PT 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A3PU                    TCGA-BJ-A45C 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A45D                    TCGA-BJ-A45E 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A45F                    TCGA-BJ-A45G 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A45H                    TCGA-BJ-A45I 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A45J                    TCGA-BJ-A45K 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A4O8                    TCGA-BJ-A4O9 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-CE-A13K                    TCGA-CE-A27D 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-CE-A3MD                    TCGA-CE-A3ME 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-CE-A481                    TCGA-CE-A482 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-CE-A483                    TCGA-CE-A484 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-CE-A485                    TCGA-DE-A0XZ 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DE-A0Y2                    TCGA-DE-A0Y3 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DE-A2OL                    TCGA-DE-A3KN 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DE-A4M8                    TCGA-DE-A4M9 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DE-A4MA                    TCGA-DE-A4MB 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DE-A4MC                    TCGA-DE-A4MD 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DE-A69J                    TCGA-DE-A69K 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DE-A7U5                    TCGA-DJ-A13L 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A13M                    TCGA-DJ-A13O 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A13P                    TCGA-DJ-A13R 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A13S                    TCGA-DJ-A13T 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A13U                    TCGA-DJ-A13W 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A1QD                    TCGA-DJ-A1QE 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A1QF                    TCGA-DJ-A1QG 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A1QH                    TCGA-DJ-A1QI 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A1QM                    TCGA-DJ-A1QO 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A1QQ                    TCGA-DJ-A2PN 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PO                    TCGA-DJ-A2PQ 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PR                    TCGA-DJ-A2PS 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PT                    TCGA-DJ-A2PU 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PV                    TCGA-DJ-A2PW 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PX                    TCGA-DJ-A2PY 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PZ                    TCGA-DJ-A2Q0 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q1                    TCGA-DJ-A2Q2 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q3                    TCGA-DJ-A2Q4 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q5                    TCGA-DJ-A2Q6 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q7                    TCGA-DJ-A2Q9 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A2QA                    TCGA-DJ-A2QB 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UK                    TCGA-DJ-A3UM 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UN                    TCGA-DJ-A3UO 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UQ                    TCGA-DJ-A3UR 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A3US                    TCGA-DJ-A3UT 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UU                    TCGA-DJ-A3UW 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UX                    TCGA-DJ-A3UY 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UZ                    TCGA-DJ-A3V2 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A3V3                    TCGA-DJ-A3V4 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A3V5                    TCGA-DJ-A3V7 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A3V8                    TCGA-DJ-A3V9 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A3VD                    TCGA-DJ-A3VE 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A3VF                    TCGA-DJ-A3VG 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A3VI                    TCGA-DJ-A3VJ 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A3VK                    TCGA-DJ-A3VL 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A3VM                    TCGA-DJ-A4UL 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A4UP                    TCGA-DJ-A4UQ 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A4UR                    TCGA-DJ-A4UT 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A4UW                    TCGA-DJ-A4V0 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A4V4                    TCGA-DJ-A4V5 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DO-A1JZ                    TCGA-DO-A1K0 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-DO-A2HM                    TCGA-E3-A3DY 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-E3-A3DZ                    TCGA-E3-A3E0 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-E3-A3E1                    TCGA-E3-A3E2 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-E3-A3E3                    TCGA-E3-A3E5 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-E8-A242                    TCGA-E8-A2EA 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-E8-A3X7                    TCGA-E8-A413 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-E8-A414                    TCGA-E8-A415 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-E8-A416                    TCGA-E8-A417 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-E8-A418                    TCGA-E8-A419 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-E8-A432                    TCGA-E8-A433 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-E8-A434                    TCGA-E8-A436 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-E8-A437                    TCGA-E8-A438 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-E8-A44K                    TCGA-E8-A44M 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3CL                    TCGA-EL-A3CM 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3CN                    TCGA-EL-A3CO 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3CP                    TCGA-EL-A3CR 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3CS                    TCGA-EL-A3CT 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3CU                    TCGA-EL-A3CV 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3CW                    TCGA-EL-A3CX 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3CY                    TCGA-EL-A3CZ 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3D0                    TCGA-EL-A3D1 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3D4                    TCGA-EL-A3D5 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3D6                    TCGA-EL-A3GO 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3GP                    TCGA-EL-A3GQ 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3GR                    TCGA-EL-A3GS 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3GU                    TCGA-EL-A3GV 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3GW                    TCGA-EL-A3GX 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3GY                    TCGA-EL-A3GZ 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3H1                    TCGA-EL-A3H2 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3H3                    TCGA-EL-A3H4 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3H5                    TCGA-EL-A3H7 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3H8                    TCGA-EL-A3MW 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3MY                    TCGA-EL-A3MZ 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3N2                    TCGA-EL-A3N3 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3T0                    TCGA-EL-A3T1 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3T2                    TCGA-EL-A3T3 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3T6                    TCGA-EL-A3T7 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3T8                    TCGA-EL-A3T9 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3TA                    TCGA-EL-A3TB 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZG                    TCGA-EL-A3ZH 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZK                    TCGA-EL-A3ZL 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZN                    TCGA-EL-A3ZO 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZP                    TCGA-EL-A3ZQ 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZR                    TCGA-EL-A3ZS 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZT                    TCGA-EL-A4JV 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A4JW                    TCGA-EL-A4JX 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A4JZ                    TCGA-EL-A4K0 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A4K1                    TCGA-EL-A4K2 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A4K4                    TCGA-EL-A4K6 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A4K7                    TCGA-EL-A4K9 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A4KD                    TCGA-EL-A4KG 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EL-A4KH                    TCGA-EL-A4KI 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EM-A22M                    TCGA-EM-A22O 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-EM-A2OV                    TCGA-EM-A3AI 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-ET-A25G                    TCGA-ET-A25I 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-ET-A25J                    TCGA-ET-A25K 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-ET-A25L                    TCGA-ET-A25M 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-ET-A25N                    TCGA-ET-A25O 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-ET-A25P                    TCGA-ET-A25R 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-ET-A2MX                    TCGA-ET-A2MY 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-ET-A2MZ                    TCGA-ET-A2N0 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-ET-A2N1                    TCGA-ET-A2N3 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-ET-A2N4                    TCGA-ET-A2N5 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-ET-A39I                    TCGA-ET-A39J 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-ET-A39K                    TCGA-ET-A39M 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-ET-A39N                    TCGA-ET-A39O 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-ET-A39P                    TCGA-ET-A39R 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-ET-A39S                    TCGA-ET-A39T 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-ET-A3BN                    TCGA-ET-A3BO 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-ET-A3BP                    TCGA-ET-A3BQ 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-ET-A3BS                    TCGA-ET-A3BT 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-ET-A3BU                    TCGA-ET-A3BV 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-ET-A3BW                    TCGA-ET-A3BX 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-ET-A3DO                    TCGA-ET-A3DP 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-ET-A3DQ                    TCGA-ET-A3DR 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-ET-A3DS                    TCGA-ET-A3DT 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-ET-A3DU                    TCGA-ET-A3DV 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-ET-A3DW                    TCGA-ET-A40P 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-ET-A40Q                    TCGA-ET-A40R 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-ET-A40S                    TCGA-ET-A40T 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-ET-A4KN                    TCGA-ET-A4KQ 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-FE-A22Z                    TCGA-FE-A230 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-FE-A231                    TCGA-FE-A232 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-FE-A233                    TCGA-FE-A234 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-FE-A235                    TCGA-FE-A236 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-FE-A237                    TCGA-FE-A238 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-FE-A239                    TCGA-FE-A23A 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-FE-A3PA                    TCGA-FE-A3PB 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-FE-A3PC                    TCGA-FE-A3PD 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-FK-A3S3                    TCGA-FK-A3SB 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-FK-A3SD                    TCGA-FK-A3SE 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-FK-A3SG                    TCGA-FK-A3SH 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-FK-A4UB                    TCGA-FY-A2QD 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-FY-A3BL                    TCGA-FY-A3I4 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-FY-A3I5                    TCGA-FY-A3NM 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-FY-A3ON                    TCGA-FY-A3R6 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-FY-A3R7                    TCGA-FY-A3R8 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-FY-A3R9                    TCGA-FY-A3RA 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-FY-A3W9                    TCGA-FY-A3WA 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-FY-A3YR                    TCGA-FY-A40K 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-FY-A40L                    TCGA-FY-A40M 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-FY-A40N                    TCGA-FY-A4B0 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-FY-A4B3                    TCGA-FY-A4B4 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-FY-A76V                    TCGA-GE-A2C6 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-H2-A26U                    TCGA-H2-A2K9 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-H2-A3RH                    TCGA-H2-A3RI 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-H2-A421                    TCGA-H2-A422 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-IM-A3EB                    TCGA-IM-A3ED 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-IM-A3U2                    TCGA-IM-A3U3 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-IM-A41Y                    TCGA-IM-A41Z 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-IM-A420                    TCGA-IM-A4EB 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-J8-A3NZ                    TCGA-J8-A3O0 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-J8-A3O1                    TCGA-J8-A3O2 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-J8-A3YD                    TCGA-J8-A3YE 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-J8-A3YF                    TCGA-J8-A3YG 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-J8-A3YH                    TCGA-J8-A42S 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-J8-A4HW                    TCGA-J8-A4HY 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-KS-A41F                    TCGA-KS-A41I 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-KS-A41J                    TCGA-KS-A41L 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-KS-A4I1                    TCGA-KS-A4I3 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-KS-A4I5                    TCGA-KS-A4I7 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-KS-A4I9                    TCGA-KS-A4IB 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-KS-A4IC                    TCGA-KS-A4ID 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-L6-A4EP                    TCGA-L6-A4EQ 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-L6-A4ET                    TCGA-L6-A4EU 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-MK-A4N6                    TCGA-MK-A4N7 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-MK-A4N9                    TCGA-MK-A84Z 
"AMP PEAK  9(3P22.3) WILD-TYPE" "AMP PEAK  9(3P22.3) WILD-TYPE" 
                   TCGA-QD-A8IV 
"AMP PEAK  9(3P22.3) WILD-TYPE" 
D8V17, binary
                               cls
clus                              0   1
  AMP PEAK  9(3P22.3) MUTATED     0   2
  AMP PEAK  9(3P22.3) WILD-TYPE  38 357
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(3P22.3) MUTATED      0    2
  AMP PEAK  9(3P22.3) WILD-TYPE   38  357
                        clus
vv                       AMP PEAK  9(3P22.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           2
                        clus
vv                       AMP PEAK  9(3P22.3) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           357
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK 10(3P14.1) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(3P14.1) MUTATED     4   1
  AMP PEAK 10(3P14.1) WILD-TYPE 477  15
  AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE 
                            5                           492 
  AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE 
                            1                            15 
$`AMP PEAK 10(3P14.1) MUTATED`
TCGA-DJ-A2PR TCGA-DJ-A3UY TCGA-EL-A3MX TCGA-EM-A22N TCGA-EM-A2CO 
       27.45        35.87        57.63        10.65         6.05 

$`AMP PEAK 10(3P14.1) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       30.58        35.41        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UZ 
       32.81        36.33        17.69        59.57        11.34        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        42.54        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL 
        7.76        35.67         3.12        36.43        24.76        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        21.34        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        52.44        39.95        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MY 
       49.71        83.57       139.00       150.48       108.66        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       52.50        29.65       147.42       142.52       129.57        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      132.07        98.24        41.29       107.47         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM 
       82.82        89.56        78.97        51.78        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        65.49        61.22        60.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       34.39        30.51        53.36        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       43.59        24.30        27.06        23.90        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        48.49        18.05        19.79        19.46        78.61 
TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       57.01        54.08        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       14.53        44.19        41.29        14.24        47.57        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU 
       13.18        23.51         2.99        12.30        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        40.34        19.73        32.32        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.46        17.29        14.60        22.52        30.94        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR 
       14.14        33.07        13.38         8.35        29.72        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        47.38        21.01        12.07        17.49 
TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 
       17.39        16.18        15.02        14.50        15.06         7.33 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
        0.49         9.24        13.91        38.66        38.86        29.95 
TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       29.85        13.51        12.79        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        5.33        26.37        26.37        22.45        21.53        60.49 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       24.46        13.68        81.93        81.70        77.56        70.42 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       56.58        60.20        63.39        65.29        18.38        63.45 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       88.41        58.75        37.25        52.60        54.35        83.34 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       84.89       123.32       100.57        95.34        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       98.20        28.24        50.40        79.10        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       87.62        77.82        75.42        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       94.59        84.85        80.58        66.84        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      166.62        24.72        43.99        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        13.28         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 
       48.10       116.09         1.25        20.42        17.82         7.82 
TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
        0.99        19.56        13.91        16.27        15.68        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08         0.30         0.76        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58        22.49        19.04         1.35        21.60         1.68 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46         2.99        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        18.51        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
       31.10         8.22        25.64        17.23        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
      113.85        26.70        43.69        18.64        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       84.72        35.28        33.24        33.40        40.37        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        9.50        36.10        32.45        30.21        23.93        12.89 

  AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE 
                         6.05                          0.16 
  AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE 
                        57.63                        169.32 
  AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE 
                        27.45                         30.61 
[1] "6.0 - 57.6 (27.4)"  "0.2 - 169.3 (30.6)"
[1] "hr=" "8.4"
D9V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 10(3P14.1) MUTATED         3        1         0        0         0
  AMP PEAK 10(3P14.1) WILD-TYPE     279       49       111        2        46
                               vv
clus                            STAGE IVC
  AMP PEAK 10(3P14.1) MUTATED           1
  AMP PEAK 10(3P14.1) WILD-TYPE         5
D9V3, multiclass
           clus
vv          AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE
  STAGE I                             3                           279
  STAGE II                            1                            49
  STAGE III                           0                           111
  STAGE IV                            0                             2
  STAGE IVA                           0                            46
  STAGE IVC                           1                             5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 10(3P14.1) MUTATED     2   1   1   1
  AMP PEAK 10(3P14.1) WILD-TYPE 140 164 166  22
D9V4, multiclass
    clus
vv   AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE
  T1                           2                           140
  T2                           1                           164
  T3                           1                           166
  T4                           1                            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"
D9V5, binary
                               cls
clus                              0   1
  AMP PEAK 10(3P14.1) MUTATED     2   2
  AMP PEAK 10(3P14.1) WILD-TYPE 223 222
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(3P14.1) MUTATED      2    2
  AMP PEAK 10(3P14.1) WILD-TYPE  223  222
   clus
vv  AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE
  0                           2                           223
  1                           2                           222
[1] 2 2
[1] FALSE
D9V6, binary
                               cls
clus                              0   1
  AMP PEAK 10(3P14.1) MUTATED     2   1
  AMP PEAK 10(3P14.1) WILD-TYPE 276   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(3P14.1) MUTATED      2    1
  AMP PEAK 10(3P14.1) WILD-TYPE  276    8
   clus
vv  AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE
  0                           2                           276
  1                           1                             8
[1] 2 2
[1] FALSE
D9V7, binary
                               cls
clus                              0   1
  AMP PEAK 10(3P14.1) MUTATED     4   1
  AMP PEAK 10(3P14.1) WILD-TYPE 361 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(3P14.1) MUTATED      4    1
  AMP PEAK 10(3P14.1) WILD-TYPE  361  133
        clus
vv       AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE
  FEMALE                           4                           361
  MALE                             1                           133
[1] 2 2
[1] FALSE
D9V8, binary
                               cls
clus                              0   1
  AMP PEAK 10(3P14.1) MUTATED     2   3
  AMP PEAK 10(3P14.1) WILD-TYPE 183 287
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(3P14.1) MUTATED      2    3
  AMP PEAK 10(3P14.1) WILD-TYPE  183  287
     clus
vv    AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE
  NO                            2                           183
  YES                           3                           287
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 10(3P14.1) MUTATED                0
  AMP PEAK 10(3P14.1) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 10(3P14.1) MUTATED                                               3
  AMP PEAK 10(3P14.1) WILD-TYPE                                           352
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 10(3P14.1) MUTATED                                                                        2
  AMP PEAK 10(3P14.1) WILD-TYPE                                                                     98
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 10(3P14.1) MUTATED                                                                     0
  AMP PEAK 10(3P14.1) WILD-TYPE                                                                  36
D9V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 10(3P14.1) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       AMP PEAK 10(3P14.1) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, binary
                               cls
clus                              0   1
  AMP PEAK 10(3P14.1) MUTATED     4   1
  AMP PEAK 10(3P14.1) WILD-TYPE 416  16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(3P14.1) MUTATED      4    1
  AMP PEAK 10(3P14.1) WILD-TYPE  416   16
     clus
vv    AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE
  NO                            4                           416
  YES                           1                            16
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 10(3P14.1) MUTATED              1                       0    4
  AMP PEAK 10(3P14.1) WILD-TYPE          131                      18  326
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 10(3P14.1) MUTATED                     0
  AMP PEAK 10(3P14.1) WILD-TYPE                   1
D9V11, multiclass
                         clus
vv                        AMP PEAK 10(3P14.1) MUTATED
  MINIMAL (T3)                                      1
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              4
  VERY ADVANCED (T4B)                               0
                         clus
vv                        AMP PEAK 10(3P14.1) WILD-TYPE
  MINIMAL (T3)                                      131
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              326
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 10(3P14.1) MUTATED     3   0   0   2
  AMP PEAK 10(3P14.1) WILD-TYPE 380  51   4  28
D9V12, multiclass
    clus
vv   AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE
  R0                           3                           380
  R1                           0                            51
  R2                           0                             4
  RX                           2                            28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V13, continuous
D9V14, binary
                               cls
clus                              0   1
  AMP PEAK 10(3P14.1) MUTATED     2   3
  AMP PEAK 10(3P14.1) WILD-TYPE 223 261
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(3P14.1) MUTATED      2    3
  AMP PEAK 10(3P14.1) WILD-TYPE  223  261
            clus
vv           AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE
  MULTIFOCAL                           2                           223
  UNIFOCAL                             3                           261
[1] 2 2
[1] FALSE
D9V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 10(3P14.1) MUTATED                                  0     1
  AMP PEAK 10(3P14.1) WILD-TYPE                                1    51
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(3P14.1) MUTATED                           0     2
  AMP PEAK 10(3P14.1) WILD-TYPE                        27   326
D9V16, multiclass
                                  clus
vv                                 AMP PEAK 10(3P14.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      2
                                  clus
vv                                 AMP PEAK 10(3P14.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       51
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V17, binary
                               cls
clus                              0   1
  AMP PEAK 10(3P14.1) MUTATED     0   3
  AMP PEAK 10(3P14.1) WILD-TYPE  38 356
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(3P14.1) MUTATED      0    3
  AMP PEAK 10(3P14.1) WILD-TYPE   38  356
                        clus
vv                       AMP PEAK 10(3P14.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           3
                        clus
vv                       AMP PEAK 10(3P14.1) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           356
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 11(4P16.1) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 11(4P16.1) MUTATED     6   1
  AMP PEAK 11(4P16.1) WILD-TYPE 475  15
  AMP PEAK 11(4P16.1) MUTATED AMP PEAK 11(4P16.1) WILD-TYPE 
                            7                           490 
  AMP PEAK 11(4P16.1) MUTATED AMP PEAK 11(4P16.1) WILD-TYPE 
                            1                            15 
$`AMP PEAK 11(4P16.1) MUTATED`
TCGA-BJ-A0Z0 TCGA-DJ-A1QQ TCGA-EM-A1YD TCGA-EM-A22N TCGA-FE-A239 TCGA-FY-A3I5 
       13.78        17.56        57.01        10.65        33.63         7.82 
TCGA-FY-A3NM 
        0.99 

$`AMP PEAK 11(4P16.1) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
        4.24        24.79        49.78        16.34        14.73        41.33 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73        25.48        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       42.08        51.39        41.52        20.58         4.83        44.35 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
       42.15        21.04        35.54        32.45        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.08        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
       42.58        47.41        10.09         7.82        30.58        35.41 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       27.45        26.20        38.83        33.96        31.99        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       28.96         8.78         8.42        34.36        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24        33.93        37.48        36.46        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        33.53        35.18        15.88        36.92        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       32.42        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        17.69        59.57        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        42.54        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL 
        7.76        35.67         3.12        36.43        24.76        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        21.34        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        52.44        39.95        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       47.84        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       78.61        54.08        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       14.53        44.19        41.29        14.24        47.57        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       13.18        23.51         6.05         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        40.34        19.73        32.32        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ 
       17.59        17.46        17.29        14.60        22.52        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        33.07        13.38         8.35        29.72 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        47.38        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 
       17.49        17.39        16.18        15.02        14.50        15.06 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33         0.49         9.24        13.91        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       29.95        29.85        13.51        12.79        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
       21.34         5.33        26.37        26.37        22.45        21.53 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       60.49        24.46        13.68        81.93        81.70        77.56 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       70.42        56.58        60.20        63.39        65.29        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       63.45        88.41        58.75        37.25        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       83.34         2.66        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      108.46        84.89       123.32       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        98.20        28.24        50.40        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.79        87.62        77.82        75.42        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       62.83       166.62        24.72        43.99        46.26        44.38 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       40.21        37.48        33.17        31.40        73.74        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
      112.80        39.95        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        13.28         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON 
       48.10       116.09         1.25        20.42        17.82        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
       13.91        16.27        15.68        16.57        18.08         0.30 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
        0.76        17.06        17.36        15.16         6.58        22.49 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04         1.35        21.60         1.68        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46         2.99        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        18.51        16.90        21.83        31.10         8.22 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
       25.64        17.23        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW 
       27.85        24.69        22.29         5.75         2.47         2.60 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       43.69        18.64        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       33.24        33.40        40.37        21.83         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45        30.21        23.93        12.89 

  AMP PEAK 11(4P16.1) MUTATED AMP PEAK 11(4P16.1) WILD-TYPE 
                         0.99                          0.16 
  AMP PEAK 11(4P16.1) MUTATED AMP PEAK 11(4P16.1) WILD-TYPE 
                        57.01                        169.32 
  AMP PEAK 11(4P16.1) MUTATED AMP PEAK 11(4P16.1) WILD-TYPE 
                        13.78                         30.74 
[1] "1.0 - 57.0 (13.8)"  "0.2 - 169.3 (30.7)"
[1] "hr=" "8.8"
D10V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 11(4P16.1) MUTATED         2        2         3        0         0
  AMP PEAK 11(4P16.1) WILD-TYPE     280       48       108        2        46
                               vv
clus                            STAGE IVC
  AMP PEAK 11(4P16.1) MUTATED           0
  AMP PEAK 11(4P16.1) WILD-TYPE         6
D10V3, multiclass
           clus
vv          AMP PEAK 11(4P16.1) MUTATED AMP PEAK 11(4P16.1) WILD-TYPE
  STAGE I                             2                           280
  STAGE II                            2                            48
  STAGE III                           3                           108
  STAGE IV                            0                             2
  STAGE IVA                           0                            46
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 11(4P16.1) MUTATED     1   2   4   0
  AMP PEAK 11(4P16.1) WILD-TYPE 141 163 163  23
D10V4, multiclass
    clus
vv   AMP PEAK 11(4P16.1) MUTATED AMP PEAK 11(4P16.1) WILD-TYPE
  T1                           1                           141
  T2                           2                           163
  T3                           4                           163
  T4                           0                            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"
D10V5, binary
                               cls
clus                              0   1
  AMP PEAK 11(4P16.1) MUTATED     7   0
  AMP PEAK 11(4P16.1) WILD-TYPE 218 224
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(4P16.1) MUTATED      7    0
  AMP PEAK 11(4P16.1) WILD-TYPE  218  224
   clus
vv  AMP PEAK 11(4P16.1) MUTATED AMP PEAK 11(4P16.1) WILD-TYPE
  0                           7                           218
  1                           0                           224
[1] 2 2
[1] FALSE
D10V6, binary
                               cls
clus                              0   1
  AMP PEAK 11(4P16.1) MUTATED     1   0
  AMP PEAK 11(4P16.1) WILD-TYPE 277   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(4P16.1) MUTATED      1    0
  AMP PEAK 11(4P16.1) WILD-TYPE  277    9
   clus
vv  AMP PEAK 11(4P16.1) MUTATED AMP PEAK 11(4P16.1) WILD-TYPE
  0                           1                           277
  1                           0                             9
[1] 2 2
[1] FALSE
D10V7, binary
                               cls
clus                              0   1
  AMP PEAK 11(4P16.1) MUTATED     4   3
  AMP PEAK 11(4P16.1) WILD-TYPE 361 131
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(4P16.1) MUTATED      4    3
  AMP PEAK 11(4P16.1) WILD-TYPE  361  131
        clus
vv       AMP PEAK 11(4P16.1) MUTATED AMP PEAK 11(4P16.1) WILD-TYPE
  FEMALE                           4                           361
  MALE                             3                           131
[1] 2 2
[1] FALSE
D10V8, binary
                               cls
clus                              0   1
  AMP PEAK 11(4P16.1) MUTATED     2   3
  AMP PEAK 11(4P16.1) WILD-TYPE 183 287
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(4P16.1) MUTATED      2    3
  AMP PEAK 11(4P16.1) WILD-TYPE  183  287
     clus
vv    AMP PEAK 11(4P16.1) MUTATED AMP PEAK 11(4P16.1) WILD-TYPE
  NO                            2                           183
  YES                           3                           287
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 11(4P16.1) MUTATED                0
  AMP PEAK 11(4P16.1) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 11(4P16.1) MUTATED                                               4
  AMP PEAK 11(4P16.1) WILD-TYPE                                           351
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 11(4P16.1) MUTATED                                                                        3
  AMP PEAK 11(4P16.1) WILD-TYPE                                                                     97
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 11(4P16.1) MUTATED                                                                     0
  AMP PEAK 11(4P16.1) WILD-TYPE                                                                  36
D10V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 11(4P16.1) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       AMP PEAK 11(4P16.1) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            97
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, binary
                               cls
clus                              0   1
  AMP PEAK 11(4P16.1) MUTATED     5   0
  AMP PEAK 11(4P16.1) WILD-TYPE 415  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(4P16.1) MUTATED      5    0
  AMP PEAK 11(4P16.1) WILD-TYPE  415   17
     clus
vv    AMP PEAK 11(4P16.1) MUTATED AMP PEAK 11(4P16.1) WILD-TYPE
  NO                            5                           415
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 11(4P16.1) MUTATED              2                       0    5
  AMP PEAK 11(4P16.1) WILD-TYPE          130                      18  325
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 11(4P16.1) MUTATED                     0
  AMP PEAK 11(4P16.1) WILD-TYPE                   1
D10V11, multiclass
                         clus
vv                        AMP PEAK 11(4P16.1) MUTATED
  MINIMAL (T3)                                      2
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              5
  VERY ADVANCED (T4B)                               0
                         clus
vv                        AMP PEAK 11(4P16.1) WILD-TYPE
  MINIMAL (T3)                                      130
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              325
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 11(4P16.1) MUTATED     6   0   0   1
  AMP PEAK 11(4P16.1) WILD-TYPE 377  51   4  29
D10V12, multiclass
    clus
vv   AMP PEAK 11(4P16.1) MUTATED AMP PEAK 11(4P16.1) WILD-TYPE
  R0                           6                           377
  R1                           0                            51
  R2                           0                             4
  RX                           1                            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"
D10V13, continuous
D10V14, binary
                               cls
clus                              0   1
  AMP PEAK 11(4P16.1) MUTATED     5   2
  AMP PEAK 11(4P16.1) WILD-TYPE 220 262
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(4P16.1) MUTATED      5    2
  AMP PEAK 11(4P16.1) WILD-TYPE  220  262
            clus
vv           AMP PEAK 11(4P16.1) MUTATED AMP PEAK 11(4P16.1) WILD-TYPE
  MULTIFOCAL                           5                           220
  UNIFOCAL                             2                           262
[1] 2 2
[1] FALSE
D10V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 11(4P16.1) MUTATED                                  0     1
  AMP PEAK 11(4P16.1) WILD-TYPE                                1    51
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(4P16.1) MUTATED                           0     3
  AMP PEAK 11(4P16.1) WILD-TYPE                        27   325
D10V16, multiclass
                                  clus
vv                                 AMP PEAK 11(4P16.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      3
                                  clus
vv                                 AMP PEAK 11(4P16.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       51
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V17, binary
                               cls
clus                              0   1
  AMP PEAK 11(4P16.1) MUTATED     0   5
  AMP PEAK 11(4P16.1) WILD-TYPE  38 354
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(4P16.1) MUTATED      0    5
  AMP PEAK 11(4P16.1) WILD-TYPE   38  354
                        clus
vv                       AMP PEAK 11(4P16.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           5
                        clus
vv                       AMP PEAK 11(4P16.1) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           354
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 12(4Q28.2) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 12(4Q28.2) MUTATED     5   1
  AMP PEAK 12(4Q28.2) WILD-TYPE 476  15
  AMP PEAK 12(4Q28.2) MUTATED AMP PEAK 12(4Q28.2) WILD-TYPE 
                            6                           491 
  AMP PEAK 12(4Q28.2) MUTATED AMP PEAK 12(4Q28.2) WILD-TYPE 
                            1                            15 
$`AMP PEAK 12(4Q28.2) MUTATED`
TCGA-DJ-A1QQ TCGA-EM-A1YD TCGA-EM-A22N TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3NM 
       17.56        57.01        10.65        33.63         7.82         0.99 

$`AMP PEAK 12(4Q28.2) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
        6.02        42.58        47.41        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        30.61         0.16         0.23        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        33.50         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        69.57        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       49.51        50.24       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       150.48       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        89.56        78.97        51.78 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        47.38        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       60.16         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        47.84        43.59        24.30        27.06        23.90 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.46        78.61        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       10.45        14.53        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
       17.88        13.18        23.51         6.05         2.99        12.30 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       48.46        13.15        22.16        40.34        19.73        32.32 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       33.96        17.59        17.46        17.29        14.60        22.52 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.06         7.33         0.49         9.24        13.91        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.86        29.95        29.85        13.51        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
      107.41       108.46        84.89       123.32       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       94.13        55.10        98.20        28.24        50.40        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
       76.64         5.79        87.62        77.82        75.42        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
       52.47       116.78        94.59        84.85        80.58        66.84 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       43.73        62.83       166.62        24.72        43.99        46.26 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
       44.38        40.21        37.48        33.17        31.40        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       71.44        31.59        79.69        24.69        68.22       117.40 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       66.77       112.80        39.95        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        13.28 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10       116.09         1.25        20.42        17.82 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
        0.30         0.76        17.06        17.36        15.16         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
       22.49        19.04         1.35        21.60         1.68        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46         2.99        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        8.22        25.64        17.23        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
       26.70        43.69        18.64        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       36.10        32.45        30.21        23.93        12.89 

  AMP PEAK 12(4Q28.2) MUTATED AMP PEAK 12(4Q28.2) WILD-TYPE 
                         0.99                          0.16 
  AMP PEAK 12(4Q28.2) MUTATED AMP PEAK 12(4Q28.2) WILD-TYPE 
                        57.01                        169.32 
  AMP PEAK 12(4Q28.2) MUTATED AMP PEAK 12(4Q28.2) WILD-TYPE 
                       14.105                        30.610 
[1] "1.0 - 57.0 (14.1)"  "0.2 - 169.3 (30.6)"
[1] "hr=" "9.3"
D11V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 12(4Q28.2) MUTATED         2        1         3        0         0
  AMP PEAK 12(4Q28.2) WILD-TYPE     280       49       108        2        46
                               vv
clus                            STAGE IVC
  AMP PEAK 12(4Q28.2) MUTATED           0
  AMP PEAK 12(4Q28.2) WILD-TYPE         6
D11V3, multiclass
           clus
vv          AMP PEAK 12(4Q28.2) MUTATED AMP PEAK 12(4Q28.2) WILD-TYPE
  STAGE I                             2                           280
  STAGE II                            1                            49
  STAGE III                           3                           108
  STAGE IV                            0                             2
  STAGE IVA                           0                            46
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 12(4Q28.2) MUTATED     1   1   4   0
  AMP PEAK 12(4Q28.2) WILD-TYPE 141 164 163  23
D11V4, multiclass
    clus
vv   AMP PEAK 12(4Q28.2) MUTATED AMP PEAK 12(4Q28.2) WILD-TYPE
  T1                           1                           141
  T2                           1                           164
  T3                           4                           163
  T4                           0                            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"
D11V5, binary
                               cls
clus                              0   1
  AMP PEAK 12(4Q28.2) MUTATED     6   0
  AMP PEAK 12(4Q28.2) WILD-TYPE 219 224
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(4Q28.2) MUTATED      6    0
  AMP PEAK 12(4Q28.2) WILD-TYPE  219  224
   clus
vv  AMP PEAK 12(4Q28.2) MUTATED AMP PEAK 12(4Q28.2) WILD-TYPE
  0                           6                           219
  1                           0                           224
[1] 2 2
[1] FALSE
D11V6, binary
                               cls
clus                              0   1
  AMP PEAK 12(4Q28.2) MUTATED     1   0
  AMP PEAK 12(4Q28.2) WILD-TYPE 277   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(4Q28.2) MUTATED      1    0
  AMP PEAK 12(4Q28.2) WILD-TYPE  277    9
   clus
vv  AMP PEAK 12(4Q28.2) MUTATED AMP PEAK 12(4Q28.2) WILD-TYPE
  0                           1                           277
  1                           0                             9
[1] 2 2
[1] FALSE
D11V7, binary
                               cls
clus                              0   1
  AMP PEAK 12(4Q28.2) MUTATED     4   2
  AMP PEAK 12(4Q28.2) WILD-TYPE 361 132
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(4Q28.2) MUTATED      4    2
  AMP PEAK 12(4Q28.2) WILD-TYPE  361  132
        clus
vv       AMP PEAK 12(4Q28.2) MUTATED AMP PEAK 12(4Q28.2) WILD-TYPE
  FEMALE                           4                           361
  MALE                             2                           132
[1] 2 2
[1] FALSE
D11V8, binary
                               cls
clus                              0   1
  AMP PEAK 12(4Q28.2) MUTATED     2   2
  AMP PEAK 12(4Q28.2) WILD-TYPE 183 288
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(4Q28.2) MUTATED      2    2
  AMP PEAK 12(4Q28.2) WILD-TYPE  183  288
     clus
vv    AMP PEAK 12(4Q28.2) MUTATED AMP PEAK 12(4Q28.2) WILD-TYPE
  NO                            2                           183
  YES                           2                           288
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 12(4Q28.2) MUTATED                0
  AMP PEAK 12(4Q28.2) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 12(4Q28.2) MUTATED                                               3
  AMP PEAK 12(4Q28.2) WILD-TYPE                                           352
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 12(4Q28.2) MUTATED                                                                        3
  AMP PEAK 12(4Q28.2) WILD-TYPE                                                                     97
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 12(4Q28.2) MUTATED                                                                     0
  AMP PEAK 12(4Q28.2) WILD-TYPE                                                                  36
D11V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 12(4Q28.2) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       AMP PEAK 12(4Q28.2) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            97
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, binary
                               cls
clus                              0   1
  AMP PEAK 12(4Q28.2) MUTATED     5   0
  AMP PEAK 12(4Q28.2) WILD-TYPE 415  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(4Q28.2) MUTATED      5    0
  AMP PEAK 12(4Q28.2) WILD-TYPE  415   17
     clus
vv    AMP PEAK 12(4Q28.2) MUTATED AMP PEAK 12(4Q28.2) WILD-TYPE
  NO                            5                           415
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 12(4Q28.2) MUTATED              2                       0    4
  AMP PEAK 12(4Q28.2) WILD-TYPE          130                      18  326
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 12(4Q28.2) MUTATED                     0
  AMP PEAK 12(4Q28.2) WILD-TYPE                   1
D11V11, multiclass
                         clus
vv                        AMP PEAK 12(4Q28.2) MUTATED
  MINIMAL (T3)                                      2
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              4
  VERY ADVANCED (T4B)                               0
                         clus
vv                        AMP PEAK 12(4Q28.2) WILD-TYPE
  MINIMAL (T3)                                      130
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              326
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 12(4Q28.2) MUTATED     5   0   0   1
  AMP PEAK 12(4Q28.2) WILD-TYPE 378  51   4  29
D11V12, multiclass
    clus
vv   AMP PEAK 12(4Q28.2) MUTATED AMP PEAK 12(4Q28.2) WILD-TYPE
  R0                           5                           378
  R1                           0                            51
  R2                           0                             4
  RX                           1                            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"
D11V13, continuous
D11V14, binary
                               cls
clus                              0   1
  AMP PEAK 12(4Q28.2) MUTATED     5   1
  AMP PEAK 12(4Q28.2) WILD-TYPE 220 263
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(4Q28.2) MUTATED      5    1
  AMP PEAK 12(4Q28.2) WILD-TYPE  220  263
            clus
vv           AMP PEAK 12(4Q28.2) MUTATED AMP PEAK 12(4Q28.2) WILD-TYPE
  MULTIFOCAL                           5                           220
  UNIFOCAL                             1                           263
[1] 2 2
[1] FALSE
D11V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 12(4Q28.2) MUTATED                                  0     1
  AMP PEAK 12(4Q28.2) WILD-TYPE                                1    51
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(4Q28.2) MUTATED                           0     3
  AMP PEAK 12(4Q28.2) WILD-TYPE                        27   325
D11V16, multiclass
                                  clus
vv                                 AMP PEAK 12(4Q28.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      3
                                  clus
vv                                 AMP PEAK 12(4Q28.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       51
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V17, binary
                               cls
clus                              0   1
  AMP PEAK 12(4Q28.2) MUTATED     0   4
  AMP PEAK 12(4Q28.2) WILD-TYPE  38 355
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(4Q28.2) MUTATED      0    4
  AMP PEAK 12(4Q28.2) WILD-TYPE   38  355
                        clus
vv                       AMP PEAK 12(4Q28.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           4
                        clus
vv                       AMP PEAK 12(4Q28.2) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           355
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 13(4Q31.21) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 13(4Q31.21) MUTATED     9   1
  AMP PEAK 13(4Q31.21) WILD-TYPE 472  15
  AMP PEAK 13(4Q31.21) MUTATED AMP PEAK 13(4Q31.21) WILD-TYPE 
                            10                            487 
  AMP PEAK 13(4Q31.21) MUTATED AMP PEAK 13(4Q31.21) WILD-TYPE 
                             1                             15 
$`AMP PEAK 13(4Q31.21) MUTATED`
TCGA-DJ-A3V2 TCGA-DJ-A3V7 TCGA-EL-A3T1 TCGA-EM-A1YD TCGA-EM-A22N TCGA-ET-A39P 
       20.22        23.21       129.57        57.01        10.65        95.34 
TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A76V 
       33.63         7.82         0.99         1.68 

$`AMP PEAK 13(4Q31.21) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
       30.58        35.41        27.45        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74         6.77        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        36.33        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       35.87        40.96        36.99        30.61        42.54        19.20 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL 
        7.76        35.67         3.12        36.43        24.76        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        21.34        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        52.44        39.95        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T2 
       17.52        52.50        29.65       147.42       142.52        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      132.07        98.24        41.29       107.47         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM 
       82.82        89.56        78.97        51.78        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        65.49        61.22        60.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       34.39        30.51        53.36        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       43.59        24.30        27.06        23.90        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        48.49        18.05        19.79        19.46        78.61 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       54.08        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       44.19        41.29        14.24        47.57        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         6.05         2.99        12.30        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        40.34        19.73        32.32        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.46        17.29        14.60        22.52        30.94        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR 
       14.14        33.07        13.38         8.35        29.72        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        47.38        21.01        12.07        17.49 
TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 
       17.39        16.18        15.02        14.50        15.06         7.33 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
        0.49         9.24        13.91        38.66        38.86        29.95 
TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       29.85        13.51        12.79        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        5.33        26.37        26.37        22.45        21.53        60.49 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       24.46        13.68        81.93        81.70        77.56        70.42 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       56.58        60.20        63.39        65.29        18.38        63.45 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       88.41        58.75        37.25        52.60        54.35        83.34 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89       123.32       100.57        94.13        55.10        98.20 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24        50.40        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       77.82        75.42        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.11         1.05        13.28         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        1.25        20.42        17.82        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
       21.60        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83        31.10         8.22        25.64        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        23.93 
TCGA-QD-A8IV 
       12.89 

  AMP PEAK 13(4Q31.21) MUTATED AMP PEAK 13(4Q31.21) WILD-TYPE 
                          0.99                           0.16 
  AMP PEAK 13(4Q31.21) MUTATED AMP PEAK 13(4Q31.21) WILD-TYPE 
                        129.57                         169.32 
  AMP PEAK 13(4Q31.21) MUTATED AMP PEAK 13(4Q31.21) WILD-TYPE 
                        21.715                         30.610 
[1] "1.0 - 129.6 (21.7)" "0.2 - 169.3 (30.6)"
[1] "hr=" "3.2"
D12V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 13(4Q31.21) MUTATED         3        2         5        0         0
  AMP PEAK 13(4Q31.21) WILD-TYPE     279       48       106        2        46
                                vv
clus                             STAGE IVC
  AMP PEAK 13(4Q31.21) MUTATED           0
  AMP PEAK 13(4Q31.21) WILD-TYPE         6
D12V3, multiclass
           clus
vv          AMP PEAK 13(4Q31.21) MUTATED AMP PEAK 13(4Q31.21) WILD-TYPE
  STAGE I                              3                            279
  STAGE II                             2                             48
  STAGE III                            5                            106
  STAGE IV                             0                              2
  STAGE IVA                            0                             46
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 13(4Q31.21) MUTATED     1   4   5   0
  AMP PEAK 13(4Q31.21) WILD-TYPE 141 161 162  23
D12V4, multiclass
    clus
vv   AMP PEAK 13(4Q31.21) MUTATED AMP PEAK 13(4Q31.21) WILD-TYPE
  T1                            1                            141
  T2                            4                            161
  T3                            5                            162
  T4                            0                             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"
D12V5, binary
                                cls
clus                               0   1
  AMP PEAK 13(4Q31.21) MUTATED     8   1
  AMP PEAK 13(4Q31.21) WILD-TYPE 217 223
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(4Q31.21) MUTATED      8    1
  AMP PEAK 13(4Q31.21) WILD-TYPE  217  223
   clus
vv  AMP PEAK 13(4Q31.21) MUTATED AMP PEAK 13(4Q31.21) WILD-TYPE
  0                            8                            217
  1                            1                            223
[1] 2 2
[1] FALSE
D12V6, binary
                                cls
clus                               0   1
  AMP PEAK 13(4Q31.21) MUTATED     3   0
  AMP PEAK 13(4Q31.21) WILD-TYPE 275   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(4Q31.21) MUTATED      3    0
  AMP PEAK 13(4Q31.21) WILD-TYPE  275    9
   clus
vv  AMP PEAK 13(4Q31.21) MUTATED AMP PEAK 13(4Q31.21) WILD-TYPE
  0                            3                            275
  1                            0                              9
[1] 2 2
[1] FALSE
D12V7, binary
                                cls
clus                               0   1
  AMP PEAK 13(4Q31.21) MUTATED     8   2
  AMP PEAK 13(4Q31.21) WILD-TYPE 357 132
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(4Q31.21) MUTATED      8    2
  AMP PEAK 13(4Q31.21) WILD-TYPE  357  132
        clus
vv       AMP PEAK 13(4Q31.21) MUTATED AMP PEAK 13(4Q31.21) WILD-TYPE
  FEMALE                            8                            357
  MALE                              2                            132
[1] 2 2
[1] FALSE
D12V8, binary
                                cls
clus                               0   1
  AMP PEAK 13(4Q31.21) MUTATED     3   4
  AMP PEAK 13(4Q31.21) WILD-TYPE 182 286
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(4Q31.21) MUTATED      3    4
  AMP PEAK 13(4Q31.21) WILD-TYPE  182  286
     clus
vv    AMP PEAK 13(4Q31.21) MUTATED AMP PEAK 13(4Q31.21) WILD-TYPE
  NO                             3                            182
  YES                            4                            286
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 13(4Q31.21) MUTATED                0
  AMP PEAK 13(4Q31.21) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 13(4Q31.21) MUTATED                                               6
  AMP PEAK 13(4Q31.21) WILD-TYPE                                           349
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 13(4Q31.21) MUTATED                                                                        3
  AMP PEAK 13(4Q31.21) WILD-TYPE                                                                     97
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 13(4Q31.21) MUTATED                                                                     1
  AMP PEAK 13(4Q31.21) WILD-TYPE                                                                  35
D12V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 13(4Q31.21) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     6
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               1
                                                                        clus
vv                                                                       AMP PEAK 13(4Q31.21) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     349
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             97
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V10, binary
                                cls
clus                               0   1
  AMP PEAK 13(4Q31.21) MUTATED     9   0
  AMP PEAK 13(4Q31.21) WILD-TYPE 411  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(4Q31.21) MUTATED      9    0
  AMP PEAK 13(4Q31.21) WILD-TYPE  411   17
     clus
vv    AMP PEAK 13(4Q31.21) MUTATED AMP PEAK 13(4Q31.21) WILD-TYPE
  NO                             9                            411
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 13(4Q31.21) MUTATED              4                       0    6
  AMP PEAK 13(4Q31.21) WILD-TYPE          128                      18  324
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 13(4Q31.21) MUTATED                     0
  AMP PEAK 13(4Q31.21) WILD-TYPE                   1
D12V11, multiclass
                         clus
vv                        AMP PEAK 13(4Q31.21) MUTATED
  MINIMAL (T3)                                       4
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               6
  VERY ADVANCED (T4B)                                0
                         clus
vv                        AMP PEAK 13(4Q31.21) WILD-TYPE
  MINIMAL (T3)                                       128
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               324
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 13(4Q31.21) MUTATED     8   1   0   1
  AMP PEAK 13(4Q31.21) WILD-TYPE 375  50   4  29
D12V12, multiclass
    clus
vv   AMP PEAK 13(4Q31.21) MUTATED AMP PEAK 13(4Q31.21) WILD-TYPE
  R0                            8                            375
  R1                            1                             50
  R2                            0                              4
  RX                            1                             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"
D12V13, continuous
D12V14, binary
                                cls
clus                               0   1
  AMP PEAK 13(4Q31.21) MUTATED     7   3
  AMP PEAK 13(4Q31.21) WILD-TYPE 218 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(4Q31.21) MUTATED      7    3
  AMP PEAK 13(4Q31.21) WILD-TYPE  218  261
            clus
vv           AMP PEAK 13(4Q31.21) MUTATED AMP PEAK 13(4Q31.21) WILD-TYPE
  MULTIFOCAL                            7                            218
  UNIFOCAL                              3                            261
[1] 2 2
[1] FALSE
D12V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 13(4Q31.21) MUTATED                                  0     0
  AMP PEAK 13(4Q31.21) WILD-TYPE                                1    52
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(4Q31.21) MUTATED                           3     5
  AMP PEAK 13(4Q31.21) WILD-TYPE                        24   323
D12V16, multiclass
                                  clus
vv                                 AMP PEAK 13(4Q31.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                       5
                                  clus
vv                                 AMP PEAK 13(4Q31.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        52
  BLACK OR AFRICAN AMERICAN                                    24
  WHITE                                                       323
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V17, binary
                                cls
clus                               0   1
  AMP PEAK 13(4Q31.21) MUTATED     0   8
  AMP PEAK 13(4Q31.21) WILD-TYPE  38 351
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(4Q31.21) MUTATED      0    8
  AMP PEAK 13(4Q31.21) WILD-TYPE   38  351
                        clus
vv                       AMP PEAK 13(4Q31.21) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            8
                        clus
vv                       AMP PEAK 13(4Q31.21) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            351
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 14(4Q32.3) MUTATION ANALYSIS
D13V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 14(4Q32.3) MUTATED     6   1
  AMP PEAK 14(4Q32.3) WILD-TYPE 475  15
  AMP PEAK 14(4Q32.3) MUTATED AMP PEAK 14(4Q32.3) WILD-TYPE 
                            7                           490 
  AMP PEAK 14(4Q32.3) MUTATED AMP PEAK 14(4Q32.3) WILD-TYPE 
                            1                            15 
$`AMP PEAK 14(4Q32.3) MUTATED`
TCGA-EL-A3CN TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A22Q TCGA-FE-A239 TCGA-FY-A3I5 
      155.54        57.01        10.65        14.24        33.63         7.82 
TCGA-FY-A3NM 
        0.99 

$`AMP PEAK 14(4Q32.3) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
       30.58        35.41        27.45        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74         6.77        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        36.33        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       35.87        40.96        36.99        20.22        30.61        42.54 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20        23.21        21.27        20.48        24.82        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ 
       21.01        18.97         7.76        35.67         3.12        36.43 
TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       24.76        17.23        27.62        30.87        21.34        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        80.52        63.19        52.44        39.95        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04         0.72 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
        0.26         3.02        25.45        30.61         0.16         0.23 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        33.50         0.39         0.39        31.66 
TCGA-EL-A3CM TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
       26.73        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        69.57        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       49.51        50.24       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       150.48       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        89.56        78.97        51.78 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        47.38        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       60.16         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        47.84        43.59        24.30        27.06        23.90 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.46        78.61        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.45        14.53        44.19        41.29        47.57        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       13.18        23.51         6.05         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        40.34        19.73        32.32        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ 
       17.59        17.46        17.29        14.60        22.52        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        33.07        13.38         8.35        29.72 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        47.38        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 
       17.49        17.39        16.18        15.02        14.50        15.06 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33         0.49         9.24        13.91        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       29.95        29.85        13.51        12.79        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
       21.34         5.33        26.37        26.37        22.45        21.53 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       60.49        24.46        13.68        81.93        81.70        77.56 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       70.42        56.58        60.20        63.39        65.29        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       63.45        88.41        58.75        37.25        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       83.34         2.66        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      108.46        84.89       123.32       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        98.20        28.24        50.40        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.79        87.62        77.82        75.42        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       62.83       166.62        24.72        43.99        46.26        44.38 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       40.21        37.48        33.17        31.40        73.74        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
      112.80        39.95        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        13.28         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON 
       48.10       116.09         1.25        20.42        17.82        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
       13.91        16.27        15.68        16.57        18.08         0.30 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
        0.76        17.06        17.36        15.16         6.58        22.49 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04         1.35        21.60         1.68        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46         2.99        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        18.51        16.90        21.83        31.10         8.22 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
       25.64        17.23        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW 
       27.85        24.69        22.29         5.75         2.47         2.60 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       43.69        18.64        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       33.24        33.40        40.37        21.83         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45        30.21        23.93        12.89 

  AMP PEAK 14(4Q32.3) MUTATED AMP PEAK 14(4Q32.3) WILD-TYPE 
                         0.99                          0.16 
  AMP PEAK 14(4Q32.3) MUTATED AMP PEAK 14(4Q32.3) WILD-TYPE 
                       155.54                        169.32 
  AMP PEAK 14(4Q32.3) MUTATED AMP PEAK 14(4Q32.3) WILD-TYPE 
                        14.24                         30.61 
[1] "1.0 - 155.5 (14.2)" "0.2 - 169.3 (30.6)"
[1] "hr=" "4.7"
D13V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 14(4Q32.3) MUTATED         2        2         3        0         0
  AMP PEAK 14(4Q32.3) WILD-TYPE     280       48       108        2        46
                               vv
clus                            STAGE IVC
  AMP PEAK 14(4Q32.3) MUTATED           0
  AMP PEAK 14(4Q32.3) WILD-TYPE         6
D13V3, multiclass
           clus
vv          AMP PEAK 14(4Q32.3) MUTATED AMP PEAK 14(4Q32.3) WILD-TYPE
  STAGE I                             2                           280
  STAGE II                            2                            48
  STAGE III                           3                           108
  STAGE IV                            0                             2
  STAGE IVA                           0                            46
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 14(4Q32.3) MUTATED     1   1   5   0
  AMP PEAK 14(4Q32.3) WILD-TYPE 141 164 162  23
D13V4, multiclass
    clus
vv   AMP PEAK 14(4Q32.3) MUTATED AMP PEAK 14(4Q32.3) WILD-TYPE
  T1                           1                           141
  T2                           1                           164
  T3                           5                           162
  T4                           0                            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"
D13V5, binary
                               cls
clus                              0   1
  AMP PEAK 14(4Q32.3) MUTATED     7   0
  AMP PEAK 14(4Q32.3) WILD-TYPE 218 224
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(4Q32.3) MUTATED      7    0
  AMP PEAK 14(4Q32.3) WILD-TYPE  218  224
   clus
vv  AMP PEAK 14(4Q32.3) MUTATED AMP PEAK 14(4Q32.3) WILD-TYPE
  0                           7                           218
  1                           0                           224
[1] 2 2
[1] FALSE
D13V6, binary
                               cls
clus                              0   1
  AMP PEAK 14(4Q32.3) MUTATED     1   0
  AMP PEAK 14(4Q32.3) WILD-TYPE 277   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(4Q32.3) MUTATED      1    0
  AMP PEAK 14(4Q32.3) WILD-TYPE  277    9
   clus
vv  AMP PEAK 14(4Q32.3) MUTATED AMP PEAK 14(4Q32.3) WILD-TYPE
  0                           1                           277
  1                           0                             9
[1] 2 2
[1] FALSE
D13V7, binary
                               cls
clus                              0   1
  AMP PEAK 14(4Q32.3) MUTATED     5   2
  AMP PEAK 14(4Q32.3) WILD-TYPE 360 132
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(4Q32.3) MUTATED      5    2
  AMP PEAK 14(4Q32.3) WILD-TYPE  360  132
        clus
vv       AMP PEAK 14(4Q32.3) MUTATED AMP PEAK 14(4Q32.3) WILD-TYPE
  FEMALE                           5                           360
  MALE                             2                           132
[1] 2 2
[1] FALSE
D13V8, binary
                               cls
clus                              0   1
  AMP PEAK 14(4Q32.3) MUTATED     2   3
  AMP PEAK 14(4Q32.3) WILD-TYPE 183 287
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(4Q32.3) MUTATED      2    3
  AMP PEAK 14(4Q32.3) WILD-TYPE  183  287
     clus
vv    AMP PEAK 14(4Q32.3) MUTATED AMP PEAK 14(4Q32.3) WILD-TYPE
  NO                            2                           183
  YES                           3                           287
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 14(4Q32.3) MUTATED                0
  AMP PEAK 14(4Q32.3) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 14(4Q32.3) MUTATED                                               3
  AMP PEAK 14(4Q32.3) WILD-TYPE                                           352
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 14(4Q32.3) MUTATED                                                                        4
  AMP PEAK 14(4Q32.3) WILD-TYPE                                                                     96
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 14(4Q32.3) MUTATED                                                                     0
  AMP PEAK 14(4Q32.3) WILD-TYPE                                                                  36
D13V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 14(4Q32.3) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           4
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       AMP PEAK 14(4Q32.3) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V10, binary
                               cls
clus                              0   1
  AMP PEAK 14(4Q32.3) MUTATED     6   0
  AMP PEAK 14(4Q32.3) WILD-TYPE 414  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(4Q32.3) MUTATED      6    0
  AMP PEAK 14(4Q32.3) WILD-TYPE  414   17
     clus
vv    AMP PEAK 14(4Q32.3) MUTATED AMP PEAK 14(4Q32.3) WILD-TYPE
  NO                            6                           414
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 14(4Q32.3) MUTATED              2                       0    5
  AMP PEAK 14(4Q32.3) WILD-TYPE          130                      18  325
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 14(4Q32.3) MUTATED                     0
  AMP PEAK 14(4Q32.3) WILD-TYPE                   1
D13V11, multiclass
                         clus
vv                        AMP PEAK 14(4Q32.3) MUTATED
  MINIMAL (T3)                                      2
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              5
  VERY ADVANCED (T4B)                               0
                         clus
vv                        AMP PEAK 14(4Q32.3) WILD-TYPE
  MINIMAL (T3)                                      130
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              325
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 14(4Q32.3) MUTATED     5   0   1   1
  AMP PEAK 14(4Q32.3) WILD-TYPE 378  51   3  29
D13V12, multiclass
    clus
vv   AMP PEAK 14(4Q32.3) MUTATED AMP PEAK 14(4Q32.3) WILD-TYPE
  R0                           5                           378
  R1                           0                            51
  R2                           1                             3
  RX                           1                            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"
D13V13, continuous
D13V14, binary
                               cls
clus                              0   1
  AMP PEAK 14(4Q32.3) MUTATED     4   3
  AMP PEAK 14(4Q32.3) WILD-TYPE 221 261
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(4Q32.3) MUTATED      4    3
  AMP PEAK 14(4Q32.3) WILD-TYPE  221  261
            clus
vv           AMP PEAK 14(4Q32.3) MUTATED AMP PEAK 14(4Q32.3) WILD-TYPE
  MULTIFOCAL                           4                           221
  UNIFOCAL                             3                           261
[1] 2 2
[1] FALSE
D13V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 14(4Q32.3) MUTATED                                  0     0
  AMP PEAK 14(4Q32.3) WILD-TYPE                                1    52
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(4Q32.3) MUTATED                           0     4
  AMP PEAK 14(4Q32.3) WILD-TYPE                        27   324
D13V16, multiclass
                                  clus
vv                                 AMP PEAK 14(4Q32.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      4
                                  clus
vv                                 AMP PEAK 14(4Q32.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       52
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V17, binary
                               cls
clus                              0   1
  AMP PEAK 14(4Q32.3) MUTATED     0   4
  AMP PEAK 14(4Q32.3) WILD-TYPE  38 355
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(4Q32.3) MUTATED      0    4
  AMP PEAK 14(4Q32.3) WILD-TYPE   38  355
                        clus
vv                       AMP PEAK 14(4Q32.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           4
                        clus
vv                       AMP PEAK 14(4Q32.3) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           355
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 15(5P14.3) MUTATION ANALYSIS
D14V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 15(5P14.3) MUTATED    21   2
  AMP PEAK 15(5P14.3) WILD-TYPE 460  14
  AMP PEAK 15(5P14.3) MUTATED AMP PEAK 15(5P14.3) WILD-TYPE 
                           23                           474 
  AMP PEAK 15(5P14.3) MUTATED AMP PEAK 15(5P14.3) WILD-TYPE 
                            2                            14 
$`AMP PEAK 15(5P14.3) MUTATED`
TCGA-BJ-A0ZB TCGA-BJ-A190 TCGA-BJ-A2N9 TCGA-DE-A4MB TCGA-EL-A3GU TCGA-EL-A3T9 
        4.01        20.58        20.48        11.57       136.01         5.72 
TCGA-EL-A3ZM TCGA-EL-A3ZO TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N 
       36.03        47.38        23.90        78.61        57.01        10.65 
TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3O3 TCGA-EM-A3SY TCGA-ET-A25L 
        6.05        32.32        22.52        14.50        13.51        56.58 
TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3NM 
       37.25       123.32        33.63         7.82         0.99 

$`AMP PEAK 15(5P14.3) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       41.33        18.87        11.57        16.73        25.48        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       42.08        51.39        41.52         4.83        44.35        42.15 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04        35.54        32.45        11.31        30.97        11.08 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA TCGA-BJ-A2P4 
       30.21        22.88        18.38        16.57        18.97         7.04 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.01        13.94        36.39        23.31        18.64         7.99 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
       10.88        21.01         3.45        23.84        28.44        15.45 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
       21.63        23.18        19.43        23.47        12.66        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.66        35.84        21.63        50.17        37.64        15.85 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.54        18.84        30.12        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.27         2.76         9.96        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        23.38        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        11.01       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS 
       10.09         7.82        30.58        35.41        27.45        26.20 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY 
       38.83        33.96        31.99        34.85        28.96         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.42        34.36        37.74         6.77        40.24        33.93 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
       37.48        36.46        35.11        39.09        35.90        33.53 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       35.18        15.88        36.92        31.04        32.42        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU 
       16.41        19.56        36.33        32.81        36.33        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       59.57        11.34        35.87        40.96        36.99        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        42.54        19.20        23.21        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       24.82        22.92        21.01        18.97         7.76        35.67 
TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        3.12        36.43        24.76        17.23        27.62        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       21.34        33.04        34.78        27.06        26.93        35.54 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        35.38        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       92.55        47.21        66.38        80.52        63.19        52.44 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       39.95        31.23        35.67        31.27        29.98        31.50 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 
       31.04         0.72         0.26         3.02        25.45        30.61 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
        0.16         0.23        14.96         7.69        33.50         0.39 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
        0.39        31.66        26.73       155.54        97.74       158.83 
TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
        7.66        45.53        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 
      106.62         4.18        79.50       139.86        98.53        69.57 
TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR 
       57.11       108.36        64.87        49.51        50.24       115.10 
TCGA-EL-A3GS TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
       65.39        50.37        50.20       147.75       101.13       139.99 
TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
       49.32        33.50        43.36        49.71        83.57       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 
      150.48       108.66        57.63        17.52        52.50        29.65 
TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
      147.42       142.52       129.57        32.48       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
       41.29       107.47        66.90        82.82        89.56        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       51.78        62.30        53.06        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT 
       47.84        43.59        24.30        27.06        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE 
       20.91        48.49        18.05        19.79        19.46        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O 
       14.73        14.50        15.75        10.45        14.53        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       19.73        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O6 
       12.07        17.49        17.39        16.18        15.02        15.06 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33         0.49         9.24        13.91        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       29.95        29.85        12.79        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        5.33        26.37        26.37        22.45        21.53        60.49 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       24.46        13.68        81.93        81.70        77.56        70.42 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       60.20        63.39        65.29        18.38        63.45        88.41 
TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       58.75        52.60        54.35        83.34         2.66        80.88 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O 
       33.24       106.09       107.41       108.46        84.89       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       95.34        94.13        55.10        98.20        28.24        50.40 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
       79.10        76.64         5.79        87.62        77.82        75.42 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
       46.65        52.47       116.78        94.59        84.85        80.58 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
       66.84        43.73        62.83       166.62        24.72        43.99 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
       46.26        44.38        40.21        37.48        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA 
      117.40        66.77       112.80        39.95        81.83       106.36 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD 
       85.15        85.68        78.77        71.08         4.11         1.05 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       13.28         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
       17.82        19.56        13.91        16.27        15.68        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08         0.30         0.76        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58        22.49        19.04         1.35        21.60         1.68 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46         2.99        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        18.51        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
       31.10         8.22        25.64        17.23        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
      113.85        26.70        43.69        18.64        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       84.72        35.28        33.24        33.40        40.37        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        9.50        36.10        32.45        30.21        23.93        12.89 

  AMP PEAK 15(5P14.3) MUTATED AMP PEAK 15(5P14.3) WILD-TYPE 
                         0.99                          0.16 
  AMP PEAK 15(5P14.3) MUTATED AMP PEAK 15(5P14.3) WILD-TYPE 
                       136.01                        169.32 
  AMP PEAK 15(5P14.3) MUTATED AMP PEAK 15(5P14.3) WILD-TYPE 
                        22.52                         30.74 
[1] "1.0 - 136.0 (22.5)" "0.2 - 169.3 (30.7)"
[1] "hr=" "3.4"
D14V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 15(5P14.3) MUTATED         5        5         8        1         4
  AMP PEAK 15(5P14.3) WILD-TYPE     277       45       103        1        42
                               vv
clus                            STAGE IVC
  AMP PEAK 15(5P14.3) MUTATED           0
  AMP PEAK 15(5P14.3) WILD-TYPE         6
D14V3, multiclass
           clus
vv          AMP PEAK 15(5P14.3) MUTATED AMP PEAK 15(5P14.3) WILD-TYPE
  STAGE I                             5                           277
  STAGE II                            5                            45
  STAGE III                           8                           103
  STAGE IV                            1                             1
  STAGE IVA                           4                            42
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 15(5P14.3) MUTATED     3   7  11   2
  AMP PEAK 15(5P14.3) WILD-TYPE 139 158 156  21
D14V4, multiclass
    clus
vv   AMP PEAK 15(5P14.3) MUTATED AMP PEAK 15(5P14.3) WILD-TYPE
  T1                           3                           139
  T2                           7                           158
  T3                          11                           156
  T4                           2                            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"
D14V5, binary
                               cls
clus                              0   1
  AMP PEAK 15(5P14.3) MUTATED    11   8
  AMP PEAK 15(5P14.3) WILD-TYPE 214 216
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(5P14.3) MUTATED     11    8
  AMP PEAK 15(5P14.3) WILD-TYPE  214  216
   clus
vv  AMP PEAK 15(5P14.3) MUTATED AMP PEAK 15(5P14.3) WILD-TYPE
  0                          11                           214
  1                           8                           216
[1] 2 2
[1] FALSE
D14V6, binary
                               cls
clus                              0   1
  AMP PEAK 15(5P14.3) MUTATED     6   0
  AMP PEAK 15(5P14.3) WILD-TYPE 272   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(5P14.3) MUTATED      6    0
  AMP PEAK 15(5P14.3) WILD-TYPE  272    9
   clus
vv  AMP PEAK 15(5P14.3) MUTATED AMP PEAK 15(5P14.3) WILD-TYPE
  0                           6                           272
  1                           0                             9
[1] 2 2
[1] FALSE
D14V7, binary
                               cls
clus                              0   1
  AMP PEAK 15(5P14.3) MUTATED    16   7
  AMP PEAK 15(5P14.3) WILD-TYPE 349 127
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(5P14.3) MUTATED     16    7
  AMP PEAK 15(5P14.3) WILD-TYPE  349  127
        clus
vv       AMP PEAK 15(5P14.3) MUTATED AMP PEAK 15(5P14.3) WILD-TYPE
  FEMALE                          16                           349
  MALE                             7                           127
[1] 2 2
[1] FALSE
D14V8, binary
                               cls
clus                              0   1
  AMP PEAK 15(5P14.3) MUTATED     5  15
  AMP PEAK 15(5P14.3) WILD-TYPE 180 275
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(5P14.3) MUTATED      5   15
  AMP PEAK 15(5P14.3) WILD-TYPE  180  275
     clus
vv    AMP PEAK 15(5P14.3) MUTATED AMP PEAK 15(5P14.3) WILD-TYPE
  NO                            5                           180
  YES                          15                           275
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 15(5P14.3) MUTATED                0
  AMP PEAK 15(5P14.3) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 15(5P14.3) MUTATED                                              14
  AMP PEAK 15(5P14.3) WILD-TYPE                                           341
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 15(5P14.3) MUTATED                                                                        8
  AMP PEAK 15(5P14.3) WILD-TYPE                                                                     92
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 15(5P14.3) MUTATED                                                                     1
  AMP PEAK 15(5P14.3) WILD-TYPE                                                                  35
D14V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 15(5P14.3) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   14
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           8
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              1
                                                                        clus
vv                                                                       AMP PEAK 15(5P14.3) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    341
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            92
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V10, binary
                               cls
clus                              0   1
  AMP PEAK 15(5P14.3) MUTATED    22   0
  AMP PEAK 15(5P14.3) WILD-TYPE 398  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(5P14.3) MUTATED     22    0
  AMP PEAK 15(5P14.3) WILD-TYPE  398   17
     clus
vv    AMP PEAK 15(5P14.3) MUTATED AMP PEAK 15(5P14.3) WILD-TYPE
  NO                           22                           398
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 15(5P14.3) MUTATED              6                       2   14
  AMP PEAK 15(5P14.3) WILD-TYPE          126                      16  316
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 15(5P14.3) MUTATED                     1
  AMP PEAK 15(5P14.3) WILD-TYPE                   0
D14V11, multiclass
                         clus
vv                        AMP PEAK 15(5P14.3) MUTATED
  MINIMAL (T3)                                      6
  MODERATE/ADVANCED (T4A)                           2
  NONE                                             14
  VERY ADVANCED (T4B)                               1
                         clus
vv                        AMP PEAK 15(5P14.3) WILD-TYPE
  MINIMAL (T3)                                      126
  MODERATE/ADVANCED (T4A)                            16
  NONE                                              316
  VERY ADVANCED (T4B)                                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 15(5P14.3) MUTATED    15   6   0   2
  AMP PEAK 15(5P14.3) WILD-TYPE 368  45   4  28
D14V12, multiclass
    clus
vv   AMP PEAK 15(5P14.3) MUTATED AMP PEAK 15(5P14.3) WILD-TYPE
  R0                          15                           368
  R1                           6                            45
  R2                           0                             4
  RX                           2                            28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V13, continuous
D14V14, binary
                               cls
clus                              0   1
  AMP PEAK 15(5P14.3) MUTATED     9  14
  AMP PEAK 15(5P14.3) WILD-TYPE 216 250
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(5P14.3) MUTATED      9   14
  AMP PEAK 15(5P14.3) WILD-TYPE  216  250
            clus
vv           AMP PEAK 15(5P14.3) MUTATED AMP PEAK 15(5P14.3) WILD-TYPE
  MULTIFOCAL                           9                           216
  UNIFOCAL                            14                           250
[1] 2 2
[1] FALSE
D14V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 15(5P14.3) MUTATED                                  0     0
  AMP PEAK 15(5P14.3) WILD-TYPE                                1    52
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(5P14.3) MUTATED                           0    15
  AMP PEAK 15(5P14.3) WILD-TYPE                        27   313
D14V16, multiclass
                                  clus
vv                                 AMP PEAK 15(5P14.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                     15
                                  clus
vv                                 AMP PEAK 15(5P14.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       52
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      313
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V17, binary
                               cls
clus                              0   1
  AMP PEAK 15(5P14.3) MUTATED     2  13
  AMP PEAK 15(5P14.3) WILD-TYPE  36 346
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(5P14.3) MUTATED      2   13
  AMP PEAK 15(5P14.3) WILD-TYPE   36  346
                        clus
vv                       AMP PEAK 15(5P14.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          13
                        clus
vv                       AMP PEAK 15(5P14.3) WILD-TYPE
  HISPANIC OR LATINO                                36
  NOT HISPANIC OR LATINO                           346
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 16(5Q21.1) MUTATION ANALYSIS
D15V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 16(5Q21.1) MUTATED    21   2
  AMP PEAK 16(5Q21.1) WILD-TYPE 460  14
  AMP PEAK 16(5Q21.1) MUTATED AMP PEAK 16(5Q21.1) WILD-TYPE 
                           23                           474 
  AMP PEAK 16(5Q21.1) MUTATED AMP PEAK 16(5Q21.1) WILD-TYPE 
                            2                            14 
$`AMP PEAK 16(5Q21.1) MUTATED`
TCGA-BJ-A190 TCGA-BJ-A28X TCGA-BJ-A2N9 TCGA-DJ-A3UK TCGA-DJ-A3US TCGA-DO-A2HM 
       20.58        30.97        20.48        36.92        32.81         2.33 
TCGA-EL-A3T3 TCGA-EL-A3T9 TCGA-EL-A3ZM TCGA-EL-A4K9 TCGA-EL-A4KI TCGA-EM-A1YC 
      132.07         5.72        36.03        47.84        23.90        78.61 
TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3SY 
       57.01        10.65         6.05        32.32        22.52        13.51 
TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3NM 
       37.25       123.32        33.63         7.82         0.99 

$`AMP PEAK 16(5Q21.1) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        42.08        51.39        41.52         4.83        44.35 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28Z 
       42.15        21.04        35.54        32.45        11.31        11.08 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA TCGA-BJ-A2P4 
       30.21        22.88        18.38        16.57        18.97         7.04 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.01        13.94        36.39        23.31        18.64         7.99 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
       10.88        21.01         3.45        23.84        28.44        15.45 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
       21.63        23.18        19.43        23.47        12.66        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.66        35.84        21.63        50.17        37.64        15.85 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O 
       14.70        14.27         2.76         9.96        48.79        38.17 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      169.32        18.58         8.71        56.19        23.38        43.17 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       52.37         8.32        11.01       135.91        30.61        44.98 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
       42.51        14.96        17.59         6.02        42.58        47.41 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
       17.56        10.09         7.82        30.58        35.41        27.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
       26.20        38.83        33.96        31.99        34.85        28.96 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42        34.36        37.74         6.77        40.24 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
       33.93        37.48        36.46        35.11        39.09        35.90 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       33.53        35.18        15.88        31.04        32.42        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW 
       16.41        19.56        36.33        36.33        17.69        59.57 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       11.34        35.87        40.96        36.99        20.22        30.61 
TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       42.54        19.20        23.21        21.27        20.48        24.82 
TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI 
       22.92        21.01        18.97         7.76        35.67         3.12 
TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       36.43        24.76        17.23        27.62        30.87        21.34 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3DZ 
       15.81        35.38        54.90        21.53        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        80.52        63.19        52.44        39.95        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04         0.72 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
        0.26         3.02        25.45        30.61         0.16         0.23 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        33.50         0.39         0.39        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS 
       26.73       155.54        97.74       158.83         7.66        45.53 
TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY 
       60.95       157.15        37.94        57.01       106.62         4.18 
TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 
       79.50       139.86        98.53        69.57        57.11       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
       64.87        49.51        50.24       115.10        65.39       136.01 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        50.20       147.75       101.13       139.99        49.32 
TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 
       33.50        43.36        49.71        83.57       139.00       150.48 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 
      108.66        57.63        17.52        52.50        29.65       147.42 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      142.52       129.57        32.48        98.24        41.29       107.47 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        65.49        61.22        60.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4KD 
       34.39        30.51        53.36        44.15        41.13        43.59 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       24.30        27.06        26.86        18.18        20.91        48.49 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J 
       18.05        19.79        19.46        54.08        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       15.75        10.45        14.53        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ 
       47.57        17.88        13.18        23.51         2.99        12.30 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ 
       48.46        13.15        22.16        40.34        19.73        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.59        17.46        17.29        14.60        30.94        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR 
       14.14        33.07        13.38         8.35        29.72        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        47.38        21.01        12.07        17.49 
TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 
       17.39        16.18        15.02        14.50        15.06         7.33 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
        0.49         9.24        13.91        38.66        38.86        29.95 
TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       29.85        12.79        84.59        29.33        21.34         5.33 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
       26.37        26.37        22.45        21.53        60.49        24.46 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
       13.68        81.93        81.70        77.56        70.42        56.58 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       60.20        63.39        65.29        18.38        63.45        88.41 
TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       58.75        52.60        54.35        83.34         2.66        80.88 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O 
       33.24       106.09       107.41       108.46        84.89       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       95.34        94.13        55.10        98.20        28.24        50.40 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
       79.10        76.64         5.79        87.62        77.82        75.42 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
       46.65        52.47       116.78        94.59        84.85        80.58 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
       66.84        43.73        62.83       166.62        24.72        43.99 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
       46.26        44.38        40.21        37.48        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA 
      117.40        66.77       112.80        39.95        81.83       106.36 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD 
       85.15        85.68        78.77        71.08         4.11         1.05 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       13.28         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
       17.82        19.56        13.91        16.27        15.68        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08         0.30         0.76        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58        22.49        19.04         1.35        21.60         1.68 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46         2.99        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        18.51        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
       31.10         8.22        25.64        17.23        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
      113.85        26.70        43.69        18.64        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       84.72        35.28        33.24        33.40        40.37        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        9.50        36.10        32.45        30.21        23.93        12.89 

  AMP PEAK 16(5Q21.1) MUTATED AMP PEAK 16(5Q21.1) WILD-TYPE 
                         0.99                          0.16 
  AMP PEAK 16(5Q21.1) MUTATED AMP PEAK 16(5Q21.1) WILD-TYPE 
                       132.07                        169.32 
  AMP PEAK 16(5Q21.1) MUTATED AMP PEAK 16(5Q21.1) WILD-TYPE 
                        30.97                         30.61 
[1] "1.0 - 132.1 (31.0)" "0.2 - 169.3 (30.6)"
[1] "hr=" "3.4"
D15V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 16(5Q21.1) MUTATED         8        7         5        1         2
  AMP PEAK 16(5Q21.1) WILD-TYPE     274       43       106        1        44
                               vv
clus                            STAGE IVC
  AMP PEAK 16(5Q21.1) MUTATED           0
  AMP PEAK 16(5Q21.1) WILD-TYPE         6
D15V3, multiclass
           clus
vv          AMP PEAK 16(5Q21.1) MUTATED AMP PEAK 16(5Q21.1) WILD-TYPE
  STAGE I                             8                           274
  STAGE II                            7                            43
  STAGE III                           5                           106
  STAGE IV                            1                             1
  STAGE IVA                           2                            44
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 16(5Q21.1) MUTATED     6   8   7   2
  AMP PEAK 16(5Q21.1) WILD-TYPE 136 157 160  21
D15V4, multiclass
    clus
vv   AMP PEAK 16(5Q21.1) MUTATED AMP PEAK 16(5Q21.1) WILD-TYPE
  T1                           6                           136
  T2                           8                           157
  T3                           7                           160
  T4                           2                            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"
D15V5, binary
                               cls
clus                              0   1
  AMP PEAK 16(5Q21.1) MUTATED    15   4
  AMP PEAK 16(5Q21.1) WILD-TYPE 210 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(5Q21.1) MUTATED     15    4
  AMP PEAK 16(5Q21.1) WILD-TYPE  210  220
   clus
vv  AMP PEAK 16(5Q21.1) MUTATED AMP PEAK 16(5Q21.1) WILD-TYPE
  0                          15                           210
  1                           4                           220
[1] 2 2
[1] FALSE
D15V6, binary
                               cls
clus                              0   1
  AMP PEAK 16(5Q21.1) MUTATED     7   0
  AMP PEAK 16(5Q21.1) WILD-TYPE 271   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(5Q21.1) MUTATED      7    0
  AMP PEAK 16(5Q21.1) WILD-TYPE  271    9
   clus
vv  AMP PEAK 16(5Q21.1) MUTATED AMP PEAK 16(5Q21.1) WILD-TYPE
  0                           7                           271
  1                           0                             9
[1] 2 2
[1] FALSE
D15V7, binary
                               cls
clus                              0   1
  AMP PEAK 16(5Q21.1) MUTATED    14   9
  AMP PEAK 16(5Q21.1) WILD-TYPE 351 125
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(5Q21.1) MUTATED     14    9
  AMP PEAK 16(5Q21.1) WILD-TYPE  351  125
        clus
vv       AMP PEAK 16(5Q21.1) MUTATED AMP PEAK 16(5Q21.1) WILD-TYPE
  FEMALE                          14                           351
  MALE                             9                           125
[1] 2 2
[1] FALSE
D15V8, binary
                               cls
clus                              0   1
  AMP PEAK 16(5Q21.1) MUTATED     6  13
  AMP PEAK 16(5Q21.1) WILD-TYPE 179 277
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(5Q21.1) MUTATED      6   13
  AMP PEAK 16(5Q21.1) WILD-TYPE  179  277
     clus
vv    AMP PEAK 16(5Q21.1) MUTATED AMP PEAK 16(5Q21.1) WILD-TYPE
  NO                            6                           179
  YES                          13                           277
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 16(5Q21.1) MUTATED                0
  AMP PEAK 16(5Q21.1) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 16(5Q21.1) MUTATED                                              14
  AMP PEAK 16(5Q21.1) WILD-TYPE                                           341
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 16(5Q21.1) MUTATED                                                                        8
  AMP PEAK 16(5Q21.1) WILD-TYPE                                                                     92
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 16(5Q21.1) MUTATED                                                                     1
  AMP PEAK 16(5Q21.1) WILD-TYPE                                                                  35
D15V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 16(5Q21.1) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   14
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           8
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              1
                                                                        clus
vv                                                                       AMP PEAK 16(5Q21.1) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    341
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            92
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V10, binary
                               cls
clus                              0   1
  AMP PEAK 16(5Q21.1) MUTATED    21   0
  AMP PEAK 16(5Q21.1) WILD-TYPE 399  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(5Q21.1) MUTATED     21    0
  AMP PEAK 16(5Q21.1) WILD-TYPE  399   17
     clus
vv    AMP PEAK 16(5Q21.1) MUTATED AMP PEAK 16(5Q21.1) WILD-TYPE
  NO                           21                           399
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 16(5Q21.1) MUTATED              4                       1   17
  AMP PEAK 16(5Q21.1) WILD-TYPE          128                      17  313
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 16(5Q21.1) MUTATED                     1
  AMP PEAK 16(5Q21.1) WILD-TYPE                   0
D15V11, multiclass
                         clus
vv                        AMP PEAK 16(5Q21.1) MUTATED
  MINIMAL (T3)                                      4
  MODERATE/ADVANCED (T4A)                           1
  NONE                                             17
  VERY ADVANCED (T4B)                               1
                         clus
vv                        AMP PEAK 16(5Q21.1) WILD-TYPE
  MINIMAL (T3)                                      128
  MODERATE/ADVANCED (T4A)                            17
  NONE                                              313
  VERY ADVANCED (T4B)                                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 16(5Q21.1) MUTATED    17   3   0   3
  AMP PEAK 16(5Q21.1) WILD-TYPE 366  48   4  27
D15V12, multiclass
    clus
vv   AMP PEAK 16(5Q21.1) MUTATED AMP PEAK 16(5Q21.1) WILD-TYPE
  R0                          17                           366
  R1                           3                            48
  R2                           0                             4
  RX                           3                            27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V13, continuous
D15V14, binary
                               cls
clus                              0   1
  AMP PEAK 16(5Q21.1) MUTATED    10  13
  AMP PEAK 16(5Q21.1) WILD-TYPE 215 251
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(5Q21.1) MUTATED     10   13
  AMP PEAK 16(5Q21.1) WILD-TYPE  215  251
            clus
vv           AMP PEAK 16(5Q21.1) MUTATED AMP PEAK 16(5Q21.1) WILD-TYPE
  MULTIFOCAL                          10                           215
  UNIFOCAL                            13                           251
[1] 2 2
[1] FALSE
D15V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 16(5Q21.1) MUTATED                                  0     0
  AMP PEAK 16(5Q21.1) WILD-TYPE                                1    52
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(5Q21.1) MUTATED                           0    16
  AMP PEAK 16(5Q21.1) WILD-TYPE                        27   312
D15V16, multiclass
                                  clus
vv                                 AMP PEAK 16(5Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                     16
                                  clus
vv                                 AMP PEAK 16(5Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       52
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      312
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V17, binary
                               cls
clus                              0   1
  AMP PEAK 16(5Q21.1) MUTATED     1  15
  AMP PEAK 16(5Q21.1) WILD-TYPE  37 344
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(5Q21.1) MUTATED      1   15
  AMP PEAK 16(5Q21.1) WILD-TYPE   37  344
                        clus
vv                       AMP PEAK 16(5Q21.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          15
                        clus
vv                       AMP PEAK 16(5Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                37
  NOT HISPANIC OR LATINO                           344
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 17(5Q21.1) MUTATION ANALYSIS
D16V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 17(5Q21.1) MUTATED    18   2
  AMP PEAK 17(5Q21.1) WILD-TYPE 463  14
  AMP PEAK 17(5Q21.1) MUTATED AMP PEAK 17(5Q21.1) WILD-TYPE 
                           20                           477 
  AMP PEAK 17(5Q21.1) MUTATED AMP PEAK 17(5Q21.1) WILD-TYPE 
                            2                            14 
$`AMP PEAK 17(5Q21.1) MUTATED`
TCGA-BJ-A190 TCGA-BJ-A2N9 TCGA-DJ-A13X TCGA-EL-A3T3 TCGA-EL-A3T9 TCGA-EL-A3ZM 
       20.58        20.48         8.32       132.07         5.72        36.03 
TCGA-EL-A4K9 TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO 
       47.84        23.90        78.61        57.01        10.65         6.05 
TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FE-A239 
       32.32        22.52        13.51        37.25       123.32        33.63 
TCGA-FY-A3I5 TCGA-FY-A3NM 
        7.82         0.99 

$`AMP PEAK 17(5Q21.1) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        42.08        51.39        41.52         4.83        44.35 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
       42.15        21.04        35.54        32.45        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
       11.08        30.21        22.88        18.38        16.57        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        7.99        10.88        21.01         3.45        23.84        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
       15.45        21.63        23.18        19.43        23.47        12.66 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
       12.43        12.66        35.84        21.63        50.17        37.64 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M 
       25.12        14.70        14.27         2.76         9.96        48.79 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       38.17       169.32        18.58         8.71        56.19        23.38 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       43.17        52.37        11.01       135.91        30.61        44.98 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
       42.51        14.96        17.59         6.02        42.58        47.41 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
       17.56        10.09         7.82        30.58        35.41        27.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
       26.20        38.83        33.96        31.99        34.85        28.96 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42        34.36        37.74         6.77        40.24 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
       33.93        37.48        36.46        35.11        39.09        35.90 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       33.53        35.18        15.88        36.92        31.04        32.42 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        36.33 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        59.57        11.34        35.87        40.96        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        42.54        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM 
       35.67         3.12        36.43        24.76        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       30.87        21.34        33.04        34.78        27.06        26.93 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       35.54         3.12        15.81        35.38        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        92.55        47.21        66.38        80.52        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 
       52.44        39.95        31.23        35.67        31.27        29.98 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 
       31.50        31.04         0.72         0.26         3.02        25.45 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       30.61         0.16         0.23        14.96         7.69        33.50 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
        0.39         0.39        31.66        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      158.83         7.66        45.53        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 
       57.01       106.62         4.18        79.50       139.86        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       69.57        57.11       108.36        64.87        49.51        50.24 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
      115.10        65.39       136.01        50.37        50.20       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       83.57       139.00       150.48       108.66        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       52.50        29.65       147.42       142.52       129.57        32.48 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       98.24        41.29       107.47        66.90        82.82        89.56 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       78.97        51.78        62.30        53.06        47.38        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        37.94        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS 
       44.15        41.13        43.59        24.30        27.06        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       54.08        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       44.19        41.29        14.24        47.57        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
       23.51         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       40.34        19.73        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       14.60        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33         0.49         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.66        38.86        29.95        29.85        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        63.45        88.41        58.75        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       83.34         2.66        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
      108.46        84.89       100.57        95.34        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       98.20        28.24        50.40        79.10        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       87.62        77.82        75.42        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       94.59        84.85        80.58        66.84        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      166.62        24.72        43.99        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       39.95        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       71.08         4.11         1.05        13.28         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 
      116.09         1.25        20.42        17.82        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08         0.30         0.76 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16         6.58        22.49        19.04 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35        21.60         1.68        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46         2.99        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       18.51        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       17.23        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY 
       24.69        22.29         5.75         2.47         2.60         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.40        40.37        21.83         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       30.21        23.93        12.89 

  AMP PEAK 17(5Q21.1) MUTATED AMP PEAK 17(5Q21.1) WILD-TYPE 
                         0.99                          0.16 
  AMP PEAK 17(5Q21.1) MUTATED AMP PEAK 17(5Q21.1) WILD-TYPE 
                       132.07                        169.32 
  AMP PEAK 17(5Q21.1) MUTATED AMP PEAK 17(5Q21.1) WILD-TYPE 
                        23.21                         30.61 
[1] "1.0 - 132.1 (23.2)" "0.2 - 169.3 (30.6)"
[1] "hr=" "3.8"
D16V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 17(5Q21.1) MUTATED         5        7         6        1         1
  AMP PEAK 17(5Q21.1) WILD-TYPE     277       43       105        1        45
                               vv
clus                            STAGE IVC
  AMP PEAK 17(5Q21.1) MUTATED           0
  AMP PEAK 17(5Q21.1) WILD-TYPE         6
D16V3, multiclass
           clus
vv          AMP PEAK 17(5Q21.1) MUTATED AMP PEAK 17(5Q21.1) WILD-TYPE
  STAGE I                             5                           277
  STAGE II                            7                            43
  STAGE III                           6                           105
  STAGE IV                            1                             1
  STAGE IVA                           1                            45
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 17(5Q21.1) MUTATED     3   8   7   2
  AMP PEAK 17(5Q21.1) WILD-TYPE 139 157 160  21
D16V4, multiclass
    clus
vv   AMP PEAK 17(5Q21.1) MUTATED AMP PEAK 17(5Q21.1) WILD-TYPE
  T1                           3                           139
  T2                           8                           157
  T3                           7                           160
  T4                           2                            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"
D16V5, binary
                               cls
clus                              0   1
  AMP PEAK 17(5Q21.1) MUTATED    14   2
  AMP PEAK 17(5Q21.1) WILD-TYPE 211 222
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(5Q21.1) MUTATED     14    2
  AMP PEAK 17(5Q21.1) WILD-TYPE  211  222
   clus
vv  AMP PEAK 17(5Q21.1) MUTATED AMP PEAK 17(5Q21.1) WILD-TYPE
  0                          14                           211
  1                           2                           222
[1] 2 2
[1] FALSE
D16V6, binary
                               cls
clus                              0   1
  AMP PEAK 17(5Q21.1) MUTATED     5   0
  AMP PEAK 17(5Q21.1) WILD-TYPE 273   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(5Q21.1) MUTATED      5    0
  AMP PEAK 17(5Q21.1) WILD-TYPE  273    9
   clus
vv  AMP PEAK 17(5Q21.1) MUTATED AMP PEAK 17(5Q21.1) WILD-TYPE
  0                           5                           273
  1                           0                             9
[1] 2 2
[1] FALSE
D16V7, binary
                               cls
clus                              0   1
  AMP PEAK 17(5Q21.1) MUTATED    12   8
  AMP PEAK 17(5Q21.1) WILD-TYPE 353 126
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(5Q21.1) MUTATED     12    8
  AMP PEAK 17(5Q21.1) WILD-TYPE  353  126
        clus
vv       AMP PEAK 17(5Q21.1) MUTATED AMP PEAK 17(5Q21.1) WILD-TYPE
  FEMALE                          12                           353
  MALE                             8                           126
[1] 2 2
[1] FALSE
D16V8, binary
                               cls
clus                              0   1
  AMP PEAK 17(5Q21.1) MUTATED     5  12
  AMP PEAK 17(5Q21.1) WILD-TYPE 180 278
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(5Q21.1) MUTATED      5   12
  AMP PEAK 17(5Q21.1) WILD-TYPE  180  278
     clus
vv    AMP PEAK 17(5Q21.1) MUTATED AMP PEAK 17(5Q21.1) WILD-TYPE
  NO                            5                           180
  YES                          12                           278
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 17(5Q21.1) MUTATED                0
  AMP PEAK 17(5Q21.1) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 17(5Q21.1) MUTATED                                              11
  AMP PEAK 17(5Q21.1) WILD-TYPE                                           344
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 17(5Q21.1) MUTATED                                                                        9
  AMP PEAK 17(5Q21.1) WILD-TYPE                                                                     91
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 17(5Q21.1) MUTATED                                                                     0
  AMP PEAK 17(5Q21.1) WILD-TYPE                                                                  36
D16V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 17(5Q21.1) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   11
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           9
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       AMP PEAK 17(5Q21.1) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    344
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            91
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V10, binary
                               cls
clus                              0   1
  AMP PEAK 17(5Q21.1) MUTATED    19   0
  AMP PEAK 17(5Q21.1) WILD-TYPE 401  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(5Q21.1) MUTATED     19    0
  AMP PEAK 17(5Q21.1) WILD-TYPE  401   17
     clus
vv    AMP PEAK 17(5Q21.1) MUTATED AMP PEAK 17(5Q21.1) WILD-TYPE
  NO                           19                           401
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 17(5Q21.1) MUTATED              3                       1   15
  AMP PEAK 17(5Q21.1) WILD-TYPE          129                      17  315
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 17(5Q21.1) MUTATED                     1
  AMP PEAK 17(5Q21.1) WILD-TYPE                   0
D16V11, multiclass
                         clus
vv                        AMP PEAK 17(5Q21.1) MUTATED
  MINIMAL (T3)                                      3
  MODERATE/ADVANCED (T4A)                           1
  NONE                                             15
  VERY ADVANCED (T4B)                               1
                         clus
vv                        AMP PEAK 17(5Q21.1) WILD-TYPE
  MINIMAL (T3)                                      129
  MODERATE/ADVANCED (T4A)                            17
  NONE                                              315
  VERY ADVANCED (T4B)                                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 17(5Q21.1) MUTATED    15   3   0   2
  AMP PEAK 17(5Q21.1) WILD-TYPE 368  48   4  28
D16V12, multiclass
    clus
vv   AMP PEAK 17(5Q21.1) MUTATED AMP PEAK 17(5Q21.1) WILD-TYPE
  R0                          15                           368
  R1                           3                            48
  R2                           0                             4
  RX                           2                            28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V13, continuous
D16V14, binary
                               cls
clus                              0   1
  AMP PEAK 17(5Q21.1) MUTATED     8  12
  AMP PEAK 17(5Q21.1) WILD-TYPE 217 252
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(5Q21.1) MUTATED      8   12
  AMP PEAK 17(5Q21.1) WILD-TYPE  217  252
            clus
vv           AMP PEAK 17(5Q21.1) MUTATED AMP PEAK 17(5Q21.1) WILD-TYPE
  MULTIFOCAL                           8                           217
  UNIFOCAL                            12                           252
[1] 2 2
[1] FALSE
D16V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 17(5Q21.1) MUTATED                                  0     0
  AMP PEAK 17(5Q21.1) WILD-TYPE                                1    52
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(5Q21.1) MUTATED                           0    12
  AMP PEAK 17(5Q21.1) WILD-TYPE                        27   316
D16V16, multiclass
                                  clus
vv                                 AMP PEAK 17(5Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                     12
                                  clus
vv                                 AMP PEAK 17(5Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       52
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      316
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V17, binary
                               cls
clus                              0   1
  AMP PEAK 17(5Q21.1) MUTATED     1  12
  AMP PEAK 17(5Q21.1) WILD-TYPE  37 347
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(5Q21.1) MUTATED      1   12
  AMP PEAK 17(5Q21.1) WILD-TYPE   37  347
                        clus
vv                       AMP PEAK 17(5Q21.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          12
                        clus
vv                       AMP PEAK 17(5Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                37
  NOT HISPANIC OR LATINO                           347
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 18(5Q33.1) MUTATION ANALYSIS
D17V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 18(5Q33.1) MUTATED    19   2
  AMP PEAK 18(5Q33.1) WILD-TYPE 462  14
  AMP PEAK 18(5Q33.1) MUTATED AMP PEAK 18(5Q33.1) WILD-TYPE 
                           21                           476 
  AMP PEAK 18(5Q33.1) MUTATED AMP PEAK 18(5Q33.1) WILD-TYPE 
                            2                            14 
$`AMP PEAK 18(5Q33.1) MUTATED`
TCGA-BJ-A0Z0 TCGA-BJ-A190 TCGA-BJ-A2N9 TCGA-DJ-A4UW TCGA-EL-A3T9 TCGA-EL-A3ZM 
       13.78        20.58        20.48        26.93         5.72        36.03 
TCGA-EL-A4K9 TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO 
       47.84        23.90        78.61        57.01        10.65         6.05 
TCGA-EM-A2OW TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N 
       40.34        32.32        22.52        13.51        37.25       123.32 
TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3NM 
       33.63         7.82         0.99 

$`AMP PEAK 18(5Q33.1) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
        4.24        24.79        49.78        16.34        14.73        41.33 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73        25.48        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       42.08        51.39        41.52         4.83        44.35        42.15 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04        35.54        32.45        11.31        30.97        11.08 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA TCGA-BJ-A2P4 
       30.21        22.88        18.38        16.57        18.97         7.04 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.01        13.94        36.39        23.31        18.64         7.99 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
       10.88        21.01         3.45        23.84        28.44        15.45 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
       21.63        23.18        19.43        23.47        12.66        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.66        35.84        21.63        50.17        37.64        15.85 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O 
       14.70        14.27         2.76         9.96        48.79        38.17 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      169.32        18.58         8.71        56.19        23.38        43.17 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       52.37         8.32        11.01       135.91        30.61        44.98 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
       42.51        14.96        17.59         6.02        42.58        47.41 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
       17.56        10.09         7.82        30.58        35.41        27.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
       26.20        38.83        33.96        31.99        34.85        28.96 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42        34.36        37.74         6.77        40.24 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
       33.93        37.48        36.46        35.11        39.09        35.90 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       33.53        35.18        15.88        36.92        31.04        32.42 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        36.33 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        59.57        11.34        35.87        40.96        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        42.54        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM 
       35.67         3.12        36.43        24.76        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4V0 
       30.87        21.34        33.04        34.78        27.06        35.54 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        35.38        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       92.55        47.21        66.38        80.52        63.19        52.44 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       39.95        31.23        35.67        31.27        29.98        31.50 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 
       31.04         0.72         0.26         3.02        25.45        30.61 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
        0.16         0.23        14.96         7.69        33.50         0.39 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
        0.39        31.66        26.73       155.54        97.74       158.83 
TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
        7.66        45.53        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 
      106.62         4.18        79.50       139.86        98.53        69.57 
TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR 
       57.11       108.36        64.87        49.51        50.24       115.10 
TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY 
       65.39       136.01        50.37        50.20       147.75       101.13 
TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 
      139.99        49.32        33.50        43.36        49.71        83.57 
TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ 
      139.00       150.48       108.66        57.63        17.52        52.50 
TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       29.65       147.42       142.52       129.57        32.48       132.07 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       98.24        41.29       107.47        66.90        82.82        89.56 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       78.97        51.78        62.30        53.06        47.38        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        37.94        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS 
       44.15        41.13        43.59        24.30        27.06        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       54.08        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       44.19        41.29        14.24        47.57        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
       23.51         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       19.73        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.06         7.33         0.49         9.24        13.91        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       38.86        29.95        29.85        12.79        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
       21.34         5.33        26.37        26.37        22.45        21.53 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       60.49        24.46        13.68        81.93        81.70        77.56 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       70.42        56.58        60.20        63.39        65.29        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       63.45        88.41        58.75        52.60        54.35        83.34 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89       100.57        95.34        94.13        55.10        98.20 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24        50.40        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       77.82        75.42        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.11         1.05        13.28         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        1.25        20.42        17.82        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83        31.10         8.22        25.64        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       23.93        12.89 

  AMP PEAK 18(5Q33.1) MUTATED AMP PEAK 18(5Q33.1) WILD-TYPE 
                         0.99                          0.16 
  AMP PEAK 18(5Q33.1) MUTATED AMP PEAK 18(5Q33.1) WILD-TYPE 
                       123.32                        169.32 
  AMP PEAK 18(5Q33.1) MUTATED AMP PEAK 18(5Q33.1) WILD-TYPE 
                        23.90                         30.74 
[1] "1.0 - 123.3 (23.9)" "0.2 - 169.3 (30.7)"
[1] "hr=" "4.3"
D17V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 18(5Q33.1) MUTATED         7        7         5        1         1
  AMP PEAK 18(5Q33.1) WILD-TYPE     275       43       106        1        45
                               vv
clus                            STAGE IVC
  AMP PEAK 18(5Q33.1) MUTATED           0
  AMP PEAK 18(5Q33.1) WILD-TYPE         6
D17V3, multiclass
           clus
vv          AMP PEAK 18(5Q33.1) MUTATED AMP PEAK 18(5Q33.1) WILD-TYPE
  STAGE I                             7                           275
  STAGE II                            7                            43
  STAGE III                           5                           106
  STAGE IV                            1                             1
  STAGE IVA                           1                            45
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 18(5Q33.1) MUTATED     5   8   6   2
  AMP PEAK 18(5Q33.1) WILD-TYPE 137 157 161  21
D17V4, multiclass
    clus
vv   AMP PEAK 18(5Q33.1) MUTATED AMP PEAK 18(5Q33.1) WILD-TYPE
  T1                           5                           137
  T2                           8                           157
  T3                           6                           161
  T4                           2                            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"
D17V5, binary
                               cls
clus                              0   1
  AMP PEAK 18(5Q33.1) MUTATED    13   3
  AMP PEAK 18(5Q33.1) WILD-TYPE 212 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(5Q33.1) MUTATED     13    3
  AMP PEAK 18(5Q33.1) WILD-TYPE  212  221
   clus
vv  AMP PEAK 18(5Q33.1) MUTATED AMP PEAK 18(5Q33.1) WILD-TYPE
  0                          13                           212
  1                           3                           221
[1] 2 2
[1] FALSE
D17V6, binary
                               cls
clus                              0   1
  AMP PEAK 18(5Q33.1) MUTATED     4   0
  AMP PEAK 18(5Q33.1) WILD-TYPE 274   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(5Q33.1) MUTATED      4    0
  AMP PEAK 18(5Q33.1) WILD-TYPE  274    9
   clus
vv  AMP PEAK 18(5Q33.1) MUTATED AMP PEAK 18(5Q33.1) WILD-TYPE
  0                           4                           274
  1                           0                             9
[1] 2 2
[1] FALSE
D17V7, binary
                               cls
clus                              0   1
  AMP PEAK 18(5Q33.1) MUTATED    13   8
  AMP PEAK 18(5Q33.1) WILD-TYPE 352 126
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(5Q33.1) MUTATED     13    8
  AMP PEAK 18(5Q33.1) WILD-TYPE  352  126
        clus
vv       AMP PEAK 18(5Q33.1) MUTATED AMP PEAK 18(5Q33.1) WILD-TYPE
  FEMALE                          13                           352
  MALE                             8                           126
[1] 2 2
[1] FALSE
D17V8, binary
                               cls
clus                              0   1
  AMP PEAK 18(5Q33.1) MUTATED     5  13
  AMP PEAK 18(5Q33.1) WILD-TYPE 180 277
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(5Q33.1) MUTATED      5   13
  AMP PEAK 18(5Q33.1) WILD-TYPE  180  277
     clus
vv    AMP PEAK 18(5Q33.1) MUTATED AMP PEAK 18(5Q33.1) WILD-TYPE
  NO                            5                           180
  YES                          13                           277
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 18(5Q33.1) MUTATED                0
  AMP PEAK 18(5Q33.1) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 18(5Q33.1) MUTATED                                              11
  AMP PEAK 18(5Q33.1) WILD-TYPE                                           344
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 18(5Q33.1) MUTATED                                                                        9
  AMP PEAK 18(5Q33.1) WILD-TYPE                                                                     91
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 18(5Q33.1) MUTATED                                                                     1
  AMP PEAK 18(5Q33.1) WILD-TYPE                                                                  35
D17V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 18(5Q33.1) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   11
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           9
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              1
                                                                        clus
vv                                                                       AMP PEAK 18(5Q33.1) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    344
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            91
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V10, binary
                               cls
clus                              0   1
  AMP PEAK 18(5Q33.1) MUTATED    19   0
  AMP PEAK 18(5Q33.1) WILD-TYPE 401  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(5Q33.1) MUTATED     19    0
  AMP PEAK 18(5Q33.1) WILD-TYPE  401   17
     clus
vv    AMP PEAK 18(5Q33.1) MUTATED AMP PEAK 18(5Q33.1) WILD-TYPE
  NO                           19                           401
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 18(5Q33.1) MUTATED              3                       1   16
  AMP PEAK 18(5Q33.1) WILD-TYPE          129                      17  314
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 18(5Q33.1) MUTATED                     1
  AMP PEAK 18(5Q33.1) WILD-TYPE                   0
D17V11, multiclass
                         clus
vv                        AMP PEAK 18(5Q33.1) MUTATED
  MINIMAL (T3)                                      3
  MODERATE/ADVANCED (T4A)                           1
  NONE                                             16
  VERY ADVANCED (T4B)                               1
                         clus
vv                        AMP PEAK 18(5Q33.1) WILD-TYPE
  MINIMAL (T3)                                      129
  MODERATE/ADVANCED (T4A)                            17
  NONE                                              314
  VERY ADVANCED (T4B)                                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 18(5Q33.1) MUTATED    15   4   0   2
  AMP PEAK 18(5Q33.1) WILD-TYPE 368  47   4  28
D17V12, multiclass
    clus
vv   AMP PEAK 18(5Q33.1) MUTATED AMP PEAK 18(5Q33.1) WILD-TYPE
  R0                          15                           368
  R1                           4                            47
  R2                           0                             4
  RX                           2                            28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V13, continuous
D17V14, binary
                               cls
clus                              0   1
  AMP PEAK 18(5Q33.1) MUTATED    10  11
  AMP PEAK 18(5Q33.1) WILD-TYPE 215 253
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(5Q33.1) MUTATED     10   11
  AMP PEAK 18(5Q33.1) WILD-TYPE  215  253
            clus
vv           AMP PEAK 18(5Q33.1) MUTATED AMP PEAK 18(5Q33.1) WILD-TYPE
  MULTIFOCAL                          10                           215
  UNIFOCAL                            11                           253
[1] 2 2
[1] FALSE
D17V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 18(5Q33.1) MUTATED                                  0     1
  AMP PEAK 18(5Q33.1) WILD-TYPE                                1    51
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(5Q33.1) MUTATED                           0    11
  AMP PEAK 18(5Q33.1) WILD-TYPE                        27   317
D17V16, multiclass
                                  clus
vv                                 AMP PEAK 18(5Q33.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                     11
                                  clus
vv                                 AMP PEAK 18(5Q33.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       51
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      317
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V17, binary
                               cls
clus                              0   1
  AMP PEAK 18(5Q33.1) MUTATED     0  13
  AMP PEAK 18(5Q33.1) WILD-TYPE  38 346
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(5Q33.1) MUTATED      0   13
  AMP PEAK 18(5Q33.1) WILD-TYPE   38  346
                        clus
vv                       AMP PEAK 18(5Q33.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          13
                        clus
vv                       AMP PEAK 18(5Q33.1) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           346
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 19(5Q35.2) MUTATION ANALYSIS
D18V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 19(5Q35.2) MUTATED    18   2
  AMP PEAK 19(5Q35.2) WILD-TYPE 463  14
  AMP PEAK 19(5Q35.2) MUTATED AMP PEAK 19(5Q35.2) WILD-TYPE 
                           20                           477 
  AMP PEAK 19(5Q35.2) MUTATED AMP PEAK 19(5Q35.2) WILD-TYPE 
                            2                            14 
$`AMP PEAK 19(5Q35.2) MUTATED`
TCGA-BJ-A190 TCGA-BJ-A2N9 TCGA-EL-A3T9 TCGA-EL-A3ZM TCGA-EL-A4K9 TCGA-EL-A4KI 
       20.58        20.48         5.72        36.03        47.84        23.90 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A2P2 
       78.61        57.01        10.65         6.05        32.32        17.29 
TCGA-EM-A3AI TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FE-A22Z TCGA-FE-A239 
       22.52        13.51        37.25       123.32        73.74        33.63 
TCGA-FY-A3I5 TCGA-FY-A3NM 
        7.82         0.99 

$`AMP PEAK 19(5Q35.2) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        42.08        51.39        41.52         4.83        44.35 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
       42.15        21.04        35.54        32.45        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
       11.08        30.21        22.88        18.38        16.57        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        7.99        10.88        21.01         3.45        23.84        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
       15.45        21.63        23.18        19.43        23.47        12.66 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
       12.43        12.66        35.84        21.63        50.17        37.64 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M 
       25.12        14.70        14.27         2.76         9.96        48.79 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       38.17       169.32        18.58         8.71        56.19        23.38 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       43.17        52.37         8.32        11.01       135.91        30.61 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       44.98        42.51        14.96        17.59         6.02        42.58 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
       47.41        17.56        10.09         7.82        30.58        35.41 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       27.45        26.20        38.83        33.96        31.99        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       28.96         8.78         8.42        34.36        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24        33.93        37.48        36.46        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        33.53        35.18        15.88        36.92        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       32.42        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        17.69        59.57        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        42.54        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL 
        7.76        35.67         3.12        36.43        24.76        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        21.34        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        52.44        39.95        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA 
       32.48       132.07        98.24        41.29       107.47        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN 
       82.82        89.56        78.97        51.78        62.30        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        65.49        61.22        60.16         7.07        59.44 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       57.47        34.72        45.96        37.94        31.04        34.39 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4KD TCGA-EL-A4KG 
       30.51        53.36        44.15        41.13        43.59        24.30 
TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       27.06        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.79        19.46        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       10.45        14.53        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       17.88        13.18        23.51         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 
       13.15        22.16        40.34        19.73        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       17.46        14.60        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        29.72        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 
       15.02        14.50        15.06         7.33         0.49         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ 
       13.91        38.66        38.86        29.95        29.85        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 
       65.29        18.38        63.45        88.41        58.75        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      107.41       108.46        84.89       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        98.20        28.24        50.40        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.79        87.62        77.82        75.42        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       62.83       166.62        24.72        43.99        46.26        44.38 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A230 TCGA-FE-A231 
       40.21        37.48        33.17        31.40        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       39.95        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       71.08         4.11         1.05        13.28         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 
      116.09         1.25        20.42        17.82        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08         0.30         0.76 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16         6.58        22.49        19.04 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35        21.60         1.68        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46         2.99        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       18.51        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       17.23        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY 
       24.69        22.29         5.75         2.47         2.60         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.40        40.37        21.83         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       30.21        23.93        12.89 

  AMP PEAK 19(5Q35.2) MUTATED AMP PEAK 19(5Q35.2) WILD-TYPE 
                         0.99                          0.16 
  AMP PEAK 19(5Q35.2) MUTATED AMP PEAK 19(5Q35.2) WILD-TYPE 
                       123.32                        169.32 
  AMP PEAK 19(5Q35.2) MUTATED AMP PEAK 19(5Q35.2) WILD-TYPE 
                        23.21                         30.61 
[1] "1.0 - 123.3 (23.2)" "0.2 - 169.3 (30.6)"
[1] "hr=" "3.9"
D18V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 19(5Q35.2) MUTATED         5        6         6        1         2
  AMP PEAK 19(5Q35.2) WILD-TYPE     277       44       105        1        44
                               vv
clus                            STAGE IVC
  AMP PEAK 19(5Q35.2) MUTATED           0
  AMP PEAK 19(5Q35.2) WILD-TYPE         6
D18V3, multiclass
           clus
vv          AMP PEAK 19(5Q35.2) MUTATED AMP PEAK 19(5Q35.2) WILD-TYPE
  STAGE I                             5                           277
  STAGE II                            6                            44
  STAGE III                           6                           105
  STAGE IV                            1                             1
  STAGE IVA                           2                            44
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 19(5Q35.2) MUTATED     3   7   7   3
  AMP PEAK 19(5Q35.2) WILD-TYPE 139 158 160  20
D18V4, multiclass
    clus
vv   AMP PEAK 19(5Q35.2) MUTATED AMP PEAK 19(5Q35.2) WILD-TYPE
  T1                           3                           139
  T2                           7                           158
  T3                           7                           160
  T4                           3                            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"
D18V5, binary
                               cls
clus                              0   1
  AMP PEAK 19(5Q35.2) MUTATED    13   3
  AMP PEAK 19(5Q35.2) WILD-TYPE 212 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 19(5Q35.2) MUTATED     13    3
  AMP PEAK 19(5Q35.2) WILD-TYPE  212  221
   clus
vv  AMP PEAK 19(5Q35.2) MUTATED AMP PEAK 19(5Q35.2) WILD-TYPE
  0                          13                           212
  1                           3                           221
[1] 2 2
[1] FALSE
D18V6, binary
                               cls
clus                              0   1
  AMP PEAK 19(5Q35.2) MUTATED     3   0
  AMP PEAK 19(5Q35.2) WILD-TYPE 275   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 19(5Q35.2) MUTATED      3    0
  AMP PEAK 19(5Q35.2) WILD-TYPE  275    9
   clus
vv  AMP PEAK 19(5Q35.2) MUTATED AMP PEAK 19(5Q35.2) WILD-TYPE
  0                           3                           275
  1                           0                             9
[1] 2 2
[1] FALSE
D18V7, binary
                               cls
clus                              0   1
  AMP PEAK 19(5Q35.2) MUTATED    12   8
  AMP PEAK 19(5Q35.2) WILD-TYPE 353 126
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 19(5Q35.2) MUTATED     12    8
  AMP PEAK 19(5Q35.2) WILD-TYPE  353  126
        clus
vv       AMP PEAK 19(5Q35.2) MUTATED AMP PEAK 19(5Q35.2) WILD-TYPE
  FEMALE                          12                           353
  MALE                             8                           126
[1] 2 2
[1] FALSE
D18V8, binary
                               cls
clus                              0   1
  AMP PEAK 19(5Q35.2) MUTATED     5  12
  AMP PEAK 19(5Q35.2) WILD-TYPE 180 278
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 19(5Q35.2) MUTATED      5   12
  AMP PEAK 19(5Q35.2) WILD-TYPE  180  278
     clus
vv    AMP PEAK 19(5Q35.2) MUTATED AMP PEAK 19(5Q35.2) WILD-TYPE
  NO                            5                           180
  YES                          12                           278
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 19(5Q35.2) MUTATED                0
  AMP PEAK 19(5Q35.2) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 19(5Q35.2) MUTATED                                              10
  AMP PEAK 19(5Q35.2) WILD-TYPE                                           345
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 19(5Q35.2) MUTATED                                                                       10
  AMP PEAK 19(5Q35.2) WILD-TYPE                                                                     90
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 19(5Q35.2) MUTATED                                                                     0
  AMP PEAK 19(5Q35.2) WILD-TYPE                                                                  36
D18V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 19(5Q35.2) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   10
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          10
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       AMP PEAK 19(5Q35.2) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    345
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            90
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V10, binary
                               cls
clus                              0   1
  AMP PEAK 19(5Q35.2) MUTATED    19   0
  AMP PEAK 19(5Q35.2) WILD-TYPE 401  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 19(5Q35.2) MUTATED     19    0
  AMP PEAK 19(5Q35.2) WILD-TYPE  401   17
     clus
vv    AMP PEAK 19(5Q35.2) MUTATED AMP PEAK 19(5Q35.2) WILD-TYPE
  NO                           19                           401
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 19(5Q35.2) MUTATED              3                       2   14
  AMP PEAK 19(5Q35.2) WILD-TYPE          129                      16  316
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 19(5Q35.2) MUTATED                     1
  AMP PEAK 19(5Q35.2) WILD-TYPE                   0
D18V11, multiclass
                         clus
vv                        AMP PEAK 19(5Q35.2) MUTATED
  MINIMAL (T3)                                      3
  MODERATE/ADVANCED (T4A)                           2
  NONE                                             14
  VERY ADVANCED (T4B)                               1
                         clus
vv                        AMP PEAK 19(5Q35.2) WILD-TYPE
  MINIMAL (T3)                                      129
  MODERATE/ADVANCED (T4A)                            16
  NONE                                              316
  VERY ADVANCED (T4B)                                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 19(5Q35.2) MUTATED    15   3   0   2
  AMP PEAK 19(5Q35.2) WILD-TYPE 368  48   4  28
D18V12, multiclass
    clus
vv   AMP PEAK 19(5Q35.2) MUTATED AMP PEAK 19(5Q35.2) WILD-TYPE
  R0                          15                           368
  R1                           3                            48
  R2                           0                             4
  RX                           2                            28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V13, continuous
D18V14, binary
                               cls
clus                              0   1
  AMP PEAK 19(5Q35.2) MUTATED     9  11
  AMP PEAK 19(5Q35.2) WILD-TYPE 216 253
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 19(5Q35.2) MUTATED      9   11
  AMP PEAK 19(5Q35.2) WILD-TYPE  216  253
            clus
vv           AMP PEAK 19(5Q35.2) MUTATED AMP PEAK 19(5Q35.2) WILD-TYPE
  MULTIFOCAL                           9                           216
  UNIFOCAL                            11                           253
[1] 2 2
[1] FALSE
D18V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 19(5Q35.2) MUTATED                                  0     0
  AMP PEAK 19(5Q35.2) WILD-TYPE                                1    52
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(5Q35.2) MUTATED                           0    12
  AMP PEAK 19(5Q35.2) WILD-TYPE                        27   316
D18V16, multiclass
                                  clus
vv                                 AMP PEAK 19(5Q35.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                     12
                                  clus
vv                                 AMP PEAK 19(5Q35.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       52
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      316
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V17, binary
                               cls
clus                              0   1
  AMP PEAK 19(5Q35.2) MUTATED     0  12
  AMP PEAK 19(5Q35.2) WILD-TYPE  38 347
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 19(5Q35.2) MUTATED      0   12
  AMP PEAK 19(5Q35.2) WILD-TYPE   38  347
                        clus
vv                       AMP PEAK 19(5Q35.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          12
                        clus
vv                       AMP PEAK 19(5Q35.2) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           347
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 20(6P22.3) MUTATION ANALYSIS
D19V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 20(6P22.3) MUTATED     2   1
  AMP PEAK 20(6P22.3) WILD-TYPE 479  15
  AMP PEAK 20(6P22.3) MUTATED AMP PEAK 20(6P22.3) WILD-TYPE 
                            3                           494 
  AMP PEAK 20(6P22.3) MUTATED AMP PEAK 20(6P22.3) WILD-TYPE 
                            1                            15 
$`AMP PEAK 20(6P22.3) MUTATED`
TCGA-DJ-A2Q0 TCGA-E8-A413 TCGA-FE-A239 
       34.36        29.98        33.63 

$`AMP PEAK 20(6P22.3) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
       30.58        35.41        27.45        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
       31.99        34.85        28.96         8.78         8.42        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       31.27        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       47.84        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       78.61        57.01        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       32.32        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       22.52        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33         0.49         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
      106.09       107.41       108.46        84.89       123.32       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       95.34        94.13        55.10        98.20        28.24        50.40 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
       79.10        76.64         5.79        87.62        77.82        75.42 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
       46.65        52.47       116.78        94.59        84.85        80.58 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
       66.84        43.73        62.83       166.62        24.72        43.99 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
       46.26        44.38        40.21        37.48        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA 
      117.40        66.77       112.80        39.95        81.83       106.36 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD 
       85.15        85.68        78.77        71.08         4.11         1.05 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       13.28         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       17.82         7.82         0.99        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83        31.10         8.22        25.64        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       23.93        12.89 

  AMP PEAK 20(6P22.3) MUTATED AMP PEAK 20(6P22.3) WILD-TYPE 
                        29.98                          0.16 
  AMP PEAK 20(6P22.3) MUTATED AMP PEAK 20(6P22.3) WILD-TYPE 
                        34.36                        169.32 
  AMP PEAK 20(6P22.3) MUTATED AMP PEAK 20(6P22.3) WILD-TYPE 
                        33.63                         30.61 
[1] "30.0 - 34.4 (33.6)" "0.2 - 169.3 (30.6)"
[1] "hr=" "15" 
D19V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 20(6P22.3) MUTATED         1        1         1        0         0
  AMP PEAK 20(6P22.3) WILD-TYPE     281       49       110        2        46
                               vv
clus                            STAGE IVC
  AMP PEAK 20(6P22.3) MUTATED           0
  AMP PEAK 20(6P22.3) WILD-TYPE         6
D19V3, multiclass
           clus
vv          AMP PEAK 20(6P22.3) MUTATED AMP PEAK 20(6P22.3) WILD-TYPE
  STAGE I                             1                           281
  STAGE II                            1                            49
  STAGE III                           1                           110
  STAGE IV                            0                             2
  STAGE IVA                           0                            46
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 20(6P22.3) MUTATED     1   1   1   0
  AMP PEAK 20(6P22.3) WILD-TYPE 141 164 166  23
D19V4, multiclass
    clus
vv   AMP PEAK 20(6P22.3) MUTATED AMP PEAK 20(6P22.3) WILD-TYPE
  T1                           1                           141
  T2                           1                           164
  T3                           1                           166
  T4                           0                            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"
D19V5, binary
                               cls
clus                              0   1
  AMP PEAK 20(6P22.3) MUTATED     3   0
  AMP PEAK 20(6P22.3) WILD-TYPE 222 224
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 20(6P22.3) MUTATED      3    0
  AMP PEAK 20(6P22.3) WILD-TYPE  222  224
   clus
vv  AMP PEAK 20(6P22.3) MUTATED AMP PEAK 20(6P22.3) WILD-TYPE
  0                           3                           222
  1                           0                           224
[1] 2 2
[1] FALSE
D19V6, binary
                               cls
clus                              0   1
  AMP PEAK 20(6P22.3) MUTATED     2   0
  AMP PEAK 20(6P22.3) WILD-TYPE 276   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 20(6P22.3) MUTATED      2    0
  AMP PEAK 20(6P22.3) WILD-TYPE  276    9
   clus
vv  AMP PEAK 20(6P22.3) MUTATED AMP PEAK 20(6P22.3) WILD-TYPE
  0                           2                           276
  1                           0                             9
[1] 2 2
[1] FALSE
D19V7, binary
                               cls
clus                              0   1
  AMP PEAK 20(6P22.3) MUTATED     2   1
  AMP PEAK 20(6P22.3) WILD-TYPE 363 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 20(6P22.3) MUTATED      2    1
  AMP PEAK 20(6P22.3) WILD-TYPE  363  133
        clus
vv       AMP PEAK 20(6P22.3) MUTATED AMP PEAK 20(6P22.3) WILD-TYPE
  FEMALE                           2                           363
  MALE                             1                           133
[1] 2 2
[1] FALSE
D19V8, binary
                               cls
clus                              0   1
  AMP PEAK 20(6P22.3) MUTATED     2   1
  AMP PEAK 20(6P22.3) WILD-TYPE 183 289
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 20(6P22.3) MUTATED      2    1
  AMP PEAK 20(6P22.3) WILD-TYPE  183  289
     clus
vv    AMP PEAK 20(6P22.3) MUTATED AMP PEAK 20(6P22.3) WILD-TYPE
  NO                            2                           183
  YES                           1                           289
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 20(6P22.3) MUTATED                0
  AMP PEAK 20(6P22.3) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 20(6P22.3) MUTATED                                               3
  AMP PEAK 20(6P22.3) WILD-TYPE                                           352
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 20(6P22.3) MUTATED                                                                        0
  AMP PEAK 20(6P22.3) WILD-TYPE                                                                    100
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 20(6P22.3) MUTATED                                                                     0
  AMP PEAK 20(6P22.3) WILD-TYPE                                                                  36
D19V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 20(6P22.3) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           0
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       AMP PEAK 20(6P22.3) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           100
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V10, binary
                               cls
clus                              0   1
  AMP PEAK 20(6P22.3) MUTATED     3   0
  AMP PEAK 20(6P22.3) WILD-TYPE 417  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 20(6P22.3) MUTATED      3    0
  AMP PEAK 20(6P22.3) WILD-TYPE  417   17
     clus
vv    AMP PEAK 20(6P22.3) MUTATED AMP PEAK 20(6P22.3) WILD-TYPE
  NO                            3                           417
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 20(6P22.3) MUTATED              0                       0    3
  AMP PEAK 20(6P22.3) WILD-TYPE          132                      18  327
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 20(6P22.3) MUTATED                     0
  AMP PEAK 20(6P22.3) WILD-TYPE                   1
D19V11, multiclass
                         clus
vv                        AMP PEAK 20(6P22.3) MUTATED
  MINIMAL (T3)                                      0
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              3
  VERY ADVANCED (T4B)                               0
                         clus
vv                        AMP PEAK 20(6P22.3) WILD-TYPE
  MINIMAL (T3)                                      132
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              327
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 20(6P22.3) MUTATED     3   0   0   0
  AMP PEAK 20(6P22.3) WILD-TYPE 380  51   4  30
D19V12, multiclass
    clus
vv   AMP PEAK 20(6P22.3) MUTATED AMP PEAK 20(6P22.3) WILD-TYPE
  R0                           3                           380
  R1                           0                            51
  R2                           0                             4
  RX                           0                            30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V13, continuous
[1] "Remove cluster labels:"      "AMP PEAK 20(6P22.3) MUTATED"
clus
  AMP PEAK 20(6P22.3) MUTATED AMP PEAK 20(6P22.3) WILD-TYPE 
                            2                           383 
                   TCGA-4C-A93U                    TCGA-BJ-A0Z0 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A0Z3                    TCGA-BJ-A0Z9 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A0ZA                    TCGA-BJ-A0ZB 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A0ZH                    TCGA-BJ-A0ZJ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A18Y                    TCGA-BJ-A18Z 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A190                    TCGA-BJ-A191 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A28R                    TCGA-BJ-A28T 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A28W                    TCGA-BJ-A28X 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A28Z                    TCGA-BJ-A290 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A291                    TCGA-BJ-A2N8 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A2N9                    TCGA-BJ-A2NA 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A3EZ                    TCGA-BJ-A3PR 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A3PU                    TCGA-BJ-A45C 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A45D                    TCGA-BJ-A45E 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A45G                    TCGA-BJ-A45I 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A45J                    TCGA-BJ-A45K 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A4O8                    TCGA-BJ-A4O9 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-CE-A13K                    TCGA-CE-A3MD 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-CE-A483                    TCGA-CE-A484 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-CE-A485                    TCGA-DE-A0XZ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DE-A0Y2                    TCGA-DE-A0Y3 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DE-A3KN                    TCGA-DE-A4M8 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DE-A4MA                    TCGA-DE-A4MB 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DE-A4MC                    TCGA-DE-A4MD 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DE-A69K                    TCGA-DE-A7U5 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A13M                    TCGA-DJ-A13O 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A13R                    TCGA-DJ-A13T 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A13V                    TCGA-DJ-A13W 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A13X                    TCGA-DJ-A1QG 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A1QH                    TCGA-DJ-A1QM 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PO                    TCGA-DJ-A2PP 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PQ                    TCGA-DJ-A2PR 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PS                    TCGA-DJ-A2PT 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PU                    TCGA-DJ-A2PV 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PW                    TCGA-DJ-A2PX 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PY                    TCGA-DJ-A2PZ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q1                    TCGA-DJ-A2Q2 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q3                    TCGA-DJ-A2Q4 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q5                    TCGA-DJ-A2Q6 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q7                    TCGA-DJ-A2Q8 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q9                    TCGA-DJ-A2QA 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2QB                    TCGA-DJ-A3UK 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UM                    TCGA-DJ-A3UN 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UO                    TCGA-DJ-A3UP 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UQ                    TCGA-DJ-A3UR 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UU                    TCGA-DJ-A3UW 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UX                    TCGA-DJ-A3UZ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3V0                    TCGA-DJ-A3V2 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3V3                    TCGA-DJ-A3V4 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3V5                    TCGA-DJ-A3V7 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3V8                    TCGA-DJ-A3V9 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3VA                    TCGA-DJ-A3VB 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3VD                    TCGA-DJ-A3VF 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3VG                    TCGA-DJ-A3VI 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3VJ                    TCGA-DJ-A3VK 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3VL                    TCGA-DJ-A4UL 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A4UP                    TCGA-DJ-A4UQ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A4UR                    TCGA-DJ-A4UW 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A4V2                    TCGA-DJ-A4V5 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DO-A1K0                    TCGA-DO-A2HM 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-E3-A3DY                    TCGA-E3-A3DZ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-E3-A3E0                    TCGA-E3-A3E1 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-E3-A3E2                    TCGA-E3-A3E3 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-E3-A3E5                    TCGA-E8-A242 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-E8-A2EA                    TCGA-E8-A414 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-E8-A415                    TCGA-E8-A417 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-E8-A419                    TCGA-E8-A433 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-E8-A436                    TCGA-E8-A438 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-E8-A44K                    TCGA-EL-A3CM 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3CN                    TCGA-EL-A3CO 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3CR                    TCGA-EL-A3CS 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3CT                    TCGA-EL-A3CU 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3CV                    TCGA-EL-A3CW 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3CX                    TCGA-EL-A3CY 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3CZ                    TCGA-EL-A3D0 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3D1                    TCGA-EL-A3D4 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3D5                    TCGA-EL-A3D6 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3GO                    TCGA-EL-A3GP 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3GQ                    TCGA-EL-A3GS 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3GU                    TCGA-EL-A3GV 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3GX                    TCGA-EL-A3H3 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3H4                    TCGA-EL-A3H5 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3H7                    TCGA-EL-A3H8 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3MW                    TCGA-EL-A3MX 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3MZ                    TCGA-EL-A3N2 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3T0                    TCGA-EL-A3T1 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3T2                    TCGA-EL-A3TB 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZH                    TCGA-EL-A3ZK 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZL                    TCGA-EL-A3ZM 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZN                    TCGA-EL-A3ZO 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZP                    TCGA-EL-A3ZS 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A4JV                    TCGA-EL-A4JW 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A4JX                    TCGA-EL-A4JZ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A4K0                    TCGA-EL-A4K1 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A4K2                    TCGA-EL-A4K4 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A4K6                    TCGA-EL-A4K7 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A4KD                    TCGA-EL-A4KG 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A4KI                    TCGA-EM-A1CS 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A1CT                    TCGA-EM-A1CU 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A1CV                    TCGA-EM-A1CW 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A1YC                    TCGA-EM-A1YD 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A1YE                    TCGA-EM-A22I 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A22J                    TCGA-EM-A22K 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A22L                    TCGA-EM-A22M 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A22N                    TCGA-EM-A22O 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A22P                    TCGA-EM-A22Q 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2CK                    TCGA-EM-A2CN 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2CP                    TCGA-EM-A2CQ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2CT                    TCGA-EM-A2CU 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2OV                    TCGA-EM-A2OX 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2OY                    TCGA-EM-A2OZ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2P0                    TCGA-EM-A2P1 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2P2                    TCGA-EM-A3AJ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3AK                    TCGA-EM-A3AL 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3AN                    TCGA-EM-A3AO 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3AQ                    TCGA-EM-A3AR 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3FJ                    TCGA-EM-A3FK 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3FM                    TCGA-EM-A3FN 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3FO                    TCGA-EM-A3FP 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3FQ                    TCGA-EM-A3FR 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3O3                    TCGA-EM-A3O8 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3O9                    TCGA-EM-A3OA 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3OB                    TCGA-EM-A3ST 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3SU                    TCGA-EM-A3SX 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3SZ                    TCGA-EM-A4FF 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A4FM                    TCGA-EM-A4FN 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A4FO                    TCGA-EM-A4FQ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A4FR                    TCGA-EM-A4FV 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A4G1                    TCGA-ET-A25G 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A25I                    TCGA-ET-A25J 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A25K                    TCGA-ET-A25L 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A25M                    TCGA-ET-A25N 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A25O                    TCGA-ET-A25P 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A2MX                    TCGA-ET-A2MZ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A2N0                    TCGA-ET-A2N1 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A2N4                    TCGA-ET-A39K 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A39L                    TCGA-ET-A39O 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A39P                    TCGA-ET-A39R 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A39S                    TCGA-ET-A39T 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A3BO                    TCGA-ET-A3BP 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A3BQ                    TCGA-ET-A3BS 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A3BT                    TCGA-ET-A3BU 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A3BV                    TCGA-ET-A3BX 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A3DQ                    TCGA-ET-A3DR 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A3DS                    TCGA-ET-A3DT 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A3DU                    TCGA-ET-A3DV 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A3DW                    TCGA-ET-A40P 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A40Q                    TCGA-ET-A40R 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A40S                    TCGA-ET-A40T 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A4KN                    TCGA-FE-A22Z 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FE-A230                    TCGA-FE-A231 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FE-A232                    TCGA-FE-A233 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FE-A234                    TCGA-FE-A235 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FE-A236                    TCGA-FE-A237 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FE-A238                    TCGA-FE-A23A 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FE-A3PB                    TCGA-FE-A3PC 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FE-A3PD                    TCGA-FK-A3S3 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FK-A3SB                    TCGA-FK-A3SE 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FK-A3SG                    TCGA-FK-A3SH 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FK-A4UB                    TCGA-FY-A2QD 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FY-A3I4                    TCGA-FY-A3I5 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FY-A3NM                    TCGA-FY-A3NN 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FY-A3ON                    TCGA-FY-A3R6 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FY-A3R7                    TCGA-FY-A3R9 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FY-A3TY                    TCGA-FY-A3W9 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FY-A3YR                    TCGA-FY-A40K 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FY-A40L                    TCGA-FY-A40M 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FY-A40N                    TCGA-FY-A4B3 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FY-A4B4                    TCGA-GE-A2C6 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-H2-A26U                    TCGA-H2-A2K9 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-H2-A3RH                    TCGA-H2-A3RI 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-H2-A421                    TCGA-H2-A422 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-IM-A3EB                    TCGA-IM-A3ED 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-IM-A3U2                    TCGA-IM-A3U3 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-IM-A41Y                    TCGA-IM-A41Z 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-IM-A420                    TCGA-IM-A4EB 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-J8-A3NZ                    TCGA-J8-A3O0 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-J8-A3O1                    TCGA-J8-A3O2 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-J8-A3YD                    TCGA-J8-A3YE 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-J8-A3YF                    TCGA-J8-A3YG 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-J8-A3YH                    TCGA-J8-A42S 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-J8-A4HW                    TCGA-J8-A4HY 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-KS-A41F                    TCGA-KS-A41I 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-KS-A41J                    TCGA-KS-A41L 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-KS-A4I1                    TCGA-KS-A4I3 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-KS-A4I5                    TCGA-KS-A4I7 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-KS-A4I9                    TCGA-KS-A4IB 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-KS-A4IC                    TCGA-KS-A4ID 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-L6-A4EP                    TCGA-L6-A4EQ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-L6-A4EU                    TCGA-MK-A4N6 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-MK-A4N7                    TCGA-MK-A4N9 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-QD-A8IV 
"AMP PEAK 20(6P22.3) WILD-TYPE" 
D19V14, binary
                               cls
clus                              0   1
  AMP PEAK 20(6P22.3) MUTATED     0   3
  AMP PEAK 20(6P22.3) WILD-TYPE 225 261
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 20(6P22.3) MUTATED      0    3
  AMP PEAK 20(6P22.3) WILD-TYPE  225  261
            clus
vv           AMP PEAK 20(6P22.3) MUTATED AMP PEAK 20(6P22.3) WILD-TYPE
  MULTIFOCAL                           0                           225
  UNIFOCAL                             3                           261
[1] 2 2
[1] FALSE
D19V15, continuous
[1] "Remove cluster labels:"      "AMP PEAK 20(6P22.3) MUTATED"
clus
  AMP PEAK 20(6P22.3) MUTATED AMP PEAK 20(6P22.3) WILD-TYPE 
                            2                           399 
                   TCGA-4C-A93U                    TCGA-BJ-A0Z2 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A0Z3                    TCGA-BJ-A0Z9 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A0ZA                    TCGA-BJ-A0ZB 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A0ZC                    TCGA-BJ-A0ZE 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A0ZG                    TCGA-BJ-A0ZH 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A0ZJ                    TCGA-BJ-A18Y 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A18Z                    TCGA-BJ-A190 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A191                    TCGA-BJ-A192 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A28R                    TCGA-BJ-A28S 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A28T                    TCGA-BJ-A28V 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A28W                    TCGA-BJ-A28Z 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A290                    TCGA-BJ-A291 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A2N8                    TCGA-BJ-A2N9 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A2P4                    TCGA-BJ-A3PU 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A45C                    TCGA-BJ-A45D 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A45E                    TCGA-BJ-A45F 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A45G                    TCGA-BJ-A45H 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A45I                    TCGA-BJ-A45J 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A45K                    TCGA-BJ-A4O8 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A4O9                    TCGA-CE-A13K 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-CE-A27D                    TCGA-CE-A3MD 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-CE-A3ME                    TCGA-CE-A481 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-CE-A482                    TCGA-CE-A483 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-CE-A484                    TCGA-CE-A485 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DE-A0XZ                    TCGA-DE-A0Y2 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DE-A0Y3                    TCGA-DE-A2OL 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DE-A3KN                    TCGA-DE-A4M8 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DE-A4M9                    TCGA-DE-A4MA 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DE-A4MB                    TCGA-DE-A4MC 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DE-A4MD                    TCGA-DE-A69J 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DE-A69K                    TCGA-DE-A7U5 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A13L                    TCGA-DJ-A13M 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A13O                    TCGA-DJ-A13R 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A13S                    TCGA-DJ-A13U 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A13V                    TCGA-DJ-A13W 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A13X                    TCGA-DJ-A1QD 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A1QE                    TCGA-DJ-A1QF 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A1QG                    TCGA-DJ-A1QH 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A1QI                    TCGA-DJ-A1QL 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A1QM                    TCGA-DJ-A1QN 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A1QO                    TCGA-DJ-A1QQ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PN                    TCGA-DJ-A2PO 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PP                    TCGA-DJ-A2PQ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PR                    TCGA-DJ-A2PS 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PT                    TCGA-DJ-A2PU 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PV                    TCGA-DJ-A2PW 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PY                    TCGA-DJ-A2PZ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q1                    TCGA-DJ-A2Q2 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q3                    TCGA-DJ-A2Q4 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q5                    TCGA-DJ-A2Q6 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q7                    TCGA-DJ-A2Q8 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q9                    TCGA-DJ-A2QA 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2QC                    TCGA-DJ-A3UK 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UM                    TCGA-DJ-A3UN 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UO                    TCGA-DJ-A3UP 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UQ                    TCGA-DJ-A3UR 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3US                    TCGA-DJ-A3UT 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UU                    TCGA-DJ-A3UW 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UX                    TCGA-DJ-A3UY 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3V0                    TCGA-DJ-A3V2 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3V3                    TCGA-DJ-A3V4 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3V5                    TCGA-DJ-A3V7 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3V8                    TCGA-DJ-A3VA 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3VB                    TCGA-DJ-A3VD 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3VE                    TCGA-DJ-A3VF 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3VG                    TCGA-DJ-A3VJ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3VK                    TCGA-DJ-A3VL 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3VM                    TCGA-DJ-A4UL 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A4UP                    TCGA-DJ-A4UQ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A4UT                    TCGA-DJ-A4V0 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A4V2                    TCGA-DJ-A4V4 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A4V5                    TCGA-DO-A1JZ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-DO-A1K0                    TCGA-DO-A2HM 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-E3-A3DY                    TCGA-E3-A3DZ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-E3-A3E0                    TCGA-E3-A3E1 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-E3-A3E2                    TCGA-E3-A3E3 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-E8-A419                    TCGA-EL-A3CN 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3CO                    TCGA-EL-A3CR 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3CS                    TCGA-EL-A3CT 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3CU                    TCGA-EL-A3CV 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3CW                    TCGA-EL-A3CX 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3CY                    TCGA-EL-A3CZ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3D0                    TCGA-EL-A3D1 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3D4                    TCGA-EL-A3D5 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3D6                    TCGA-EL-A3GO 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3GP                    TCGA-EL-A3GQ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3GR                    TCGA-EL-A3GS 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3GU                    TCGA-EL-A3GV 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3GW                    TCGA-EL-A3GX 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3GY                    TCGA-EL-A3GZ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3H2                    TCGA-EL-A3H3 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3H4                    TCGA-EL-A3H5 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3H7                    TCGA-EL-A3H8 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3MW                    TCGA-EL-A3MX 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3MY                    TCGA-EL-A3MZ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3N2                    TCGA-EL-A3N3 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3T1                    TCGA-EL-A3T2 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3T3                    TCGA-EL-A3T6 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3T7                    TCGA-EL-A3T8 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3T9                    TCGA-EL-A3TA 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3TB                    TCGA-EL-A3ZG 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZH                    TCGA-EL-A3ZK 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZL                    TCGA-EL-A3ZM 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZN                    TCGA-EL-A3ZO 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZP                    TCGA-EL-A3ZQ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZR                    TCGA-EL-A3ZS 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZT                    TCGA-EL-A4JV 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A4JW                    TCGA-EL-A4JX 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A4JZ                    TCGA-EL-A4K0 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A4K1                    TCGA-EL-A4K2 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A4K4                    TCGA-EL-A4K6 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A4K7                    TCGA-EL-A4K9 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A4KD                    TCGA-EL-A4KG 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EL-A4KH                    TCGA-EL-A4KI 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A1CS                    TCGA-EM-A1CT 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A1CU                    TCGA-EM-A1CV 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A1CW                    TCGA-EM-A1YA 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A1YB                    TCGA-EM-A1YC 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A1YD                    TCGA-EM-A1YE 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A22I                    TCGA-EM-A22J 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A22K                    TCGA-EM-A22L 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A22N                    TCGA-EM-A22O 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A22P                    TCGA-EM-A22Q 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2CJ                    TCGA-EM-A2CK 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2CL                    TCGA-EM-A2CN 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2CO                    TCGA-EM-A2CP 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2CQ                    TCGA-EM-A2CT 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2CU                    TCGA-EM-A2OW 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2OX                    TCGA-EM-A2OY 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2P0                    TCGA-EM-A2P1 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2P2                    TCGA-EM-A2P3 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3AI                    TCGA-EM-A3AJ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3AK                    TCGA-EM-A3AL 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3AN                    TCGA-EM-A3AO 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3AP                    TCGA-EM-A3AQ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3AR                    TCGA-EM-A3FJ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3FM                    TCGA-EM-A3FN 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3FO                    TCGA-EM-A3FP 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3FR                    TCGA-EM-A3O3 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3O6                    TCGA-EM-A3O7 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3O8                    TCGA-EM-A3O9 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3OA                    TCGA-EM-A3OB 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3ST                    TCGA-EM-A3SU 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3SX                    TCGA-EM-A3SY 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3SZ                    TCGA-EM-A4FF 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A4FH                    TCGA-EM-A4FK 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A4FM                    TCGA-EM-A4FN 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A4FQ                    TCGA-EM-A4FR 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A4FU                    TCGA-EM-A4FV 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-EM-A4G1                    TCGA-ET-A25G 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A25I                    TCGA-ET-A25J 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A25K                    TCGA-ET-A25L 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A25M                    TCGA-ET-A25N 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A25O                    TCGA-ET-A25P 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A25R                    TCGA-ET-A2MY 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A2MZ                    TCGA-ET-A2N0 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A2N5                    TCGA-ET-A39J 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A39M                    TCGA-ET-A39N 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A39O                    TCGA-ET-A39P 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A39T                    TCGA-ET-A3BN 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A3BO                    TCGA-ET-A3BP 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A3BQ                    TCGA-ET-A3BS 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A3BT                    TCGA-ET-A3BU 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A3BV                    TCGA-ET-A3BW 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A3BX                    TCGA-ET-A3DO 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A3DS                    TCGA-ET-A3DT 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A40P                    TCGA-ET-A40Q 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A40R                    TCGA-ET-A40S 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-ET-A4KN                    TCGA-ET-A4KQ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FE-A22Z                    TCGA-FE-A230 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FE-A232                    TCGA-FE-A233 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FE-A234                    TCGA-FE-A235 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FE-A236                    TCGA-FE-A237 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FE-A238                    TCGA-FE-A23A 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FE-A3PA                    TCGA-FE-A3PB 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FE-A3PC                    TCGA-FE-A3PD 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FY-A2QD                    TCGA-FY-A3I4 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FY-A3I5                    TCGA-FY-A3ON 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FY-A3R8                    TCGA-FY-A3TY 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FY-A3W9                    TCGA-FY-A3YR 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FY-A40K                    TCGA-FY-A40L 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FY-A40M                    TCGA-FY-A40N 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-FY-A4B3                    TCGA-FY-A76V 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-GE-A2C6                    TCGA-H2-A421 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-IM-A3EB                    TCGA-IM-A3ED 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-IM-A3U2                    TCGA-IM-A3U3 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-IM-A41Y                    TCGA-IM-A41Z 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-IM-A420                    TCGA-IM-A4EB 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-J8-A3O0                    TCGA-J8-A3YD 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-J8-A3YG                    TCGA-KS-A41F 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-KS-A41I                    TCGA-KS-A41J 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-KS-A41L                    TCGA-KS-A4I3 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-KS-A4I5                    TCGA-KS-A4I7 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-KS-A4I9                    TCGA-KS-A4IB 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-KS-A4IC                    TCGA-KS-A4ID 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-L6-A4EP                    TCGA-L6-A4EQ 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-L6-A4ET                    TCGA-L6-A4EU 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-MK-A4N6                    TCGA-MK-A4N7 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-MK-A4N9                    TCGA-MK-A84Z 
"AMP PEAK 20(6P22.3) WILD-TYPE" "AMP PEAK 20(6P22.3) WILD-TYPE" 
                   TCGA-QD-A8IV 
"AMP PEAK 20(6P22.3) WILD-TYPE" 
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 20(6P22.3) MUTATED                                  0     1
  AMP PEAK 20(6P22.3) WILD-TYPE                                1    51
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(6P22.3) MUTATED                           0     2
  AMP PEAK 20(6P22.3) WILD-TYPE                        27   326
D19V16, multiclass
                                  clus
vv                                 AMP PEAK 20(6P22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      2
                                  clus
vv                                 AMP PEAK 20(6P22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       51
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V17, binary
                               cls
clus                              0   1
  AMP PEAK 20(6P22.3) MUTATED     0   3
  AMP PEAK 20(6P22.3) WILD-TYPE  38 356
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 20(6P22.3) MUTATED      0    3
  AMP PEAK 20(6P22.3) WILD-TYPE   38  356
                        clus
vv                       AMP PEAK 20(6P22.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           3
                        clus
vv                       AMP PEAK 20(6P22.3) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           356
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 21(6P22.2) MUTATION ANALYSIS
D20V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 21(6P22.2) MUTATED     2   2
  AMP PEAK 21(6P22.2) WILD-TYPE 479  14
  AMP PEAK 21(6P22.2) MUTATED AMP PEAK 21(6P22.2) WILD-TYPE 
                            4                           493 
  AMP PEAK 21(6P22.2) MUTATED AMP PEAK 21(6P22.2) WILD-TYPE 
                            2                            14 
$`AMP PEAK 21(6P22.2) MUTATED`
TCGA-DJ-A2Q0 TCGA-EL-A3CW TCGA-EM-A3FP TCGA-FE-A239 
       34.36        57.01        17.39        33.63 

$`AMP PEAK 21(6P22.2) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
       30.58        35.41        27.45        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
       31.99        34.85        28.96         8.78         8.42        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        30.61         0.16         0.23        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        33.50         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
      157.15        37.94       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       47.84        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       78.61        57.01        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       32.32        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       22.52        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       21.01        12.07        17.49        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.06         7.33         0.49         9.24        13.91        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.86        29.95        29.85        13.51        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
      107.41       108.46        84.89       123.32       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       94.13        55.10        98.20        28.24        50.40        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
       76.64         5.79        87.62        77.82        75.42        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
       52.47       116.78        94.59        84.85        80.58        66.84 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       43.73        62.83       166.62        24.72        43.99        46.26 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
       44.38        40.21        37.48        33.17        31.40        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       71.44        31.59        79.69        24.69        68.22       117.40 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       66.77       112.80        39.95        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        13.28 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10       116.09         1.25        20.42        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        7.82         0.99        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08         0.30         0.76        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       15.16         6.58        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83        31.10         8.22        25.64        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        23.93 
TCGA-QD-A8IV 
       12.89 

  AMP PEAK 21(6P22.2) MUTATED AMP PEAK 21(6P22.2) WILD-TYPE 
                        17.39                          0.16 
  AMP PEAK 21(6P22.2) MUTATED AMP PEAK 21(6P22.2) WILD-TYPE 
                        57.01                        169.32 
  AMP PEAK 21(6P22.2) MUTATED AMP PEAK 21(6P22.2) WILD-TYPE 
                       33.995                        30.610 
[1] "17.4 - 57.0 (34.0)" "0.2 - 169.3 (30.6)"
[1] "hr=" "18" 
D20V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 21(6P22.2) MUTATED         0        2         2        0         0
  AMP PEAK 21(6P22.2) WILD-TYPE     282       48       109        2        46
                               vv
clus                            STAGE IVC
  AMP PEAK 21(6P22.2) MUTATED           0
  AMP PEAK 21(6P22.2) WILD-TYPE         6
D20V3, multiclass
           clus
vv          AMP PEAK 21(6P22.2) MUTATED AMP PEAK 21(6P22.2) WILD-TYPE
  STAGE I                             0                           282
  STAGE II                            2                            48
  STAGE III                           2                           109
  STAGE IV                            0                             2
  STAGE IVA                           0                            46
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 21(6P22.2) MUTATED     0   3   1   0
  AMP PEAK 21(6P22.2) WILD-TYPE 142 162 166  23
D20V4, multiclass
    clus
vv   AMP PEAK 21(6P22.2) MUTATED AMP PEAK 21(6P22.2) WILD-TYPE
  T1                           0                           142
  T2                           3                           162
  T3                           1                           166
  T4                           0                            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"
D20V5, binary
                               cls
clus                              0   1
  AMP PEAK 21(6P22.2) MUTATED     3   1
  AMP PEAK 21(6P22.2) WILD-TYPE 222 223
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 21(6P22.2) MUTATED      3    1
  AMP PEAK 21(6P22.2) WILD-TYPE  222  223
   clus
vv  AMP PEAK 21(6P22.2) MUTATED AMP PEAK 21(6P22.2) WILD-TYPE
  0                           3                           222
  1                           1                           223
[1] 2 2
[1] FALSE
D20V6, binary
                               cls
clus                              0   1
  AMP PEAK 21(6P22.2) MUTATED     2   0
  AMP PEAK 21(6P22.2) WILD-TYPE 276   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 21(6P22.2) MUTATED      2    0
  AMP PEAK 21(6P22.2) WILD-TYPE  276    9
   clus
vv  AMP PEAK 21(6P22.2) MUTATED AMP PEAK 21(6P22.2) WILD-TYPE
  0                           2                           276
  1                           0                             9
[1] 2 2
[1] FALSE
D20V7, binary
                               cls
clus                              0   1
  AMP PEAK 21(6P22.2) MUTATED     3   1
  AMP PEAK 21(6P22.2) WILD-TYPE 362 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 21(6P22.2) MUTATED      3    1
  AMP PEAK 21(6P22.2) WILD-TYPE  362  133
        clus
vv       AMP PEAK 21(6P22.2) MUTATED AMP PEAK 21(6P22.2) WILD-TYPE
  FEMALE                           3                           362
  MALE                             1                           133
[1] 2 2
[1] FALSE
D20V8, binary
                               cls
clus                              0   1
  AMP PEAK 21(6P22.2) MUTATED     2   2
  AMP PEAK 21(6P22.2) WILD-TYPE 183 288
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 21(6P22.2) MUTATED      2    2
  AMP PEAK 21(6P22.2) WILD-TYPE  183  288
     clus
vv    AMP PEAK 21(6P22.2) MUTATED AMP PEAK 21(6P22.2) WILD-TYPE
  NO                            2                           183
  YES                           2                           288
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 21(6P22.2) MUTATED                0
  AMP PEAK 21(6P22.2) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 21(6P22.2) MUTATED                                               3
  AMP PEAK 21(6P22.2) WILD-TYPE                                           352
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 21(6P22.2) MUTATED                                                                        1
  AMP PEAK 21(6P22.2) WILD-TYPE                                                                     99
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 21(6P22.2) MUTATED                                                                     0
  AMP PEAK 21(6P22.2) WILD-TYPE                                                                  36
D20V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 21(6P22.2) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       AMP PEAK 21(6P22.2) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            99
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V10, binary
                               cls
clus                              0   1
  AMP PEAK 21(6P22.2) MUTATED     4   0
  AMP PEAK 21(6P22.2) WILD-TYPE 416  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 21(6P22.2) MUTATED      4    0
  AMP PEAK 21(6P22.2) WILD-TYPE  416   17
     clus
vv    AMP PEAK 21(6P22.2) MUTATED AMP PEAK 21(6P22.2) WILD-TYPE
  NO                            4                           416
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 21(6P22.2) MUTATED              0                       0    4
  AMP PEAK 21(6P22.2) WILD-TYPE          132                      18  326
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 21(6P22.2) MUTATED                     0
  AMP PEAK 21(6P22.2) WILD-TYPE                   1
D20V11, multiclass
                         clus
vv                        AMP PEAK 21(6P22.2) MUTATED
  MINIMAL (T3)                                      0
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              4
  VERY ADVANCED (T4B)                               0
                         clus
vv                        AMP PEAK 21(6P22.2) WILD-TYPE
  MINIMAL (T3)                                      132
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              326
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 21(6P22.2) MUTATED     4   0   0   0
  AMP PEAK 21(6P22.2) WILD-TYPE 379  51   4  30
D20V12, multiclass
    clus
vv   AMP PEAK 21(6P22.2) MUTATED AMP PEAK 21(6P22.2) WILD-TYPE
  R0                           4                           379
  R1                           0                            51
  R2                           0                             4
  RX                           0                            30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V13, continuous
D20V14, binary
                               cls
clus                              0   1
  AMP PEAK 21(6P22.2) MUTATED     1   3
  AMP PEAK 21(6P22.2) WILD-TYPE 224 261
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 21(6P22.2) MUTATED      1    3
  AMP PEAK 21(6P22.2) WILD-TYPE  224  261
            clus
vv           AMP PEAK 21(6P22.2) MUTATED AMP PEAK 21(6P22.2) WILD-TYPE
  MULTIFOCAL                           1                           224
  UNIFOCAL                             3                           261
[1] 2 2
[1] FALSE
D20V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 21(6P22.2) MUTATED                                  0     0
  AMP PEAK 21(6P22.2) WILD-TYPE                                1    52
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(6P22.2) MUTATED                           0     3
  AMP PEAK 21(6P22.2) WILD-TYPE                        27   325
D20V16, multiclass
                                  clus
vv                                 AMP PEAK 21(6P22.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      3
                                  clus
vv                                 AMP PEAK 21(6P22.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       52
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V17, binary
                               cls
clus                              0   1
  AMP PEAK 21(6P22.2) MUTATED     0   3
  AMP PEAK 21(6P22.2) WILD-TYPE  38 356
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 21(6P22.2) MUTATED      0    3
  AMP PEAK 21(6P22.2) WILD-TYPE   38  356
                        clus
vv                       AMP PEAK 21(6P22.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           3
                        clus
vv                       AMP PEAK 21(6P22.2) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           356
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 22(6P21.31) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 22(6P21.31) MUTATED     2   1
  AMP PEAK 22(6P21.31) WILD-TYPE 479  15
  AMP PEAK 22(6P21.31) MUTATED AMP PEAK 22(6P21.31) WILD-TYPE 
                             3                            494 
  AMP PEAK 22(6P21.31) MUTATED AMP PEAK 22(6P21.31) WILD-TYPE 
                             1                             15 
$`AMP PEAK 22(6P21.31) MUTATED`
TCGA-DE-A0Y3 TCGA-DJ-A2Q0 TCGA-FE-A239 
       50.17        34.36        33.63 

$`AMP PEAK 22(6P21.31) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       34.85        28.96         8.78         8.42        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24        33.93        37.48        36.46        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        33.53        35.18        15.88        36.92        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       32.42        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        17.69        59.57        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        42.54        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL 
        7.76        35.67         3.12        36.43        24.76        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        21.34        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        52.44        39.95        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       47.84        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       78.61        57.01        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       32.32        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       22.52        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33         0.49         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
      106.09       107.41       108.46        84.89       123.32       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       95.34        94.13        55.10        98.20        28.24        50.40 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
       79.10        76.64         5.79        87.62        77.82        75.42 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
       46.65        52.47       116.78        94.59        84.85        80.58 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
       66.84        43.73        62.83       166.62        24.72        43.99 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
       46.26        44.38        40.21        37.48        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA 
      117.40        66.77       112.80        39.95        81.83       106.36 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD 
       85.15        85.68        78.77        71.08         4.11         1.05 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       13.28         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       17.82         7.82         0.99        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83        31.10         8.22        25.64        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       23.93        12.89 

  AMP PEAK 22(6P21.31) MUTATED AMP PEAK 22(6P21.31) WILD-TYPE 
                         33.63                           0.16 
  AMP PEAK 22(6P21.31) MUTATED AMP PEAK 22(6P21.31) WILD-TYPE 
                         50.17                         169.32 
  AMP PEAK 22(6P21.31) MUTATED AMP PEAK 22(6P21.31) WILD-TYPE 
                        34.360                         30.595 
[1] "33.6 - 50.2 (34.4)" "0.2 - 169.3 (30.6)"
[1] "hr=" "10" 
D21V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 22(6P21.31) MUTATED         0        1         1        0         0
  AMP PEAK 22(6P21.31) WILD-TYPE     282       49       110        2        46
                                vv
clus                             STAGE IVC
  AMP PEAK 22(6P21.31) MUTATED           1
  AMP PEAK 22(6P21.31) WILD-TYPE         5
D21V3, multiclass
           clus
vv          AMP PEAK 22(6P21.31) MUTATED AMP PEAK 22(6P21.31) WILD-TYPE
  STAGE I                              0                            282
  STAGE II                             1                             49
  STAGE III                            1                            110
  STAGE IV                             0                              2
  STAGE IVA                            0                             46
  STAGE IVC                            1                              5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 22(6P21.31) MUTATED     0   1   1   1
  AMP PEAK 22(6P21.31) WILD-TYPE 142 164 166  22
D21V4, multiclass
    clus
vv   AMP PEAK 22(6P21.31) MUTATED AMP PEAK 22(6P21.31) WILD-TYPE
  T1                            0                            142
  T2                            1                            164
  T3                            1                            166
  T4                            1                             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"
D21V5, binary
                                cls
clus                               0   1
  AMP PEAK 22(6P21.31) MUTATED     2   1
  AMP PEAK 22(6P21.31) WILD-TYPE 223 223
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(6P21.31) MUTATED      2    1
  AMP PEAK 22(6P21.31) WILD-TYPE  223  223
   clus
vv  AMP PEAK 22(6P21.31) MUTATED AMP PEAK 22(6P21.31) WILD-TYPE
  0                            2                            223
  1                            1                            223
[1] 2 2
[1] FALSE
D21V6, binary
                                cls
clus                               0   1
  AMP PEAK 22(6P21.31) MUTATED     1   1
  AMP PEAK 22(6P21.31) WILD-TYPE 277   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(6P21.31) MUTATED      1    1
  AMP PEAK 22(6P21.31) WILD-TYPE  277    8
   clus
vv  AMP PEAK 22(6P21.31) MUTATED AMP PEAK 22(6P21.31) WILD-TYPE
  0                            1                            277
  1                            1                              8
[1] 2 2
[1] FALSE
D21V7, binary
                                cls
clus                               0   1
  AMP PEAK 22(6P21.31) MUTATED     2   1
  AMP PEAK 22(6P21.31) WILD-TYPE 363 133
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(6P21.31) MUTATED      2    1
  AMP PEAK 22(6P21.31) WILD-TYPE  363  133
        clus
vv       AMP PEAK 22(6P21.31) MUTATED AMP PEAK 22(6P21.31) WILD-TYPE
  FEMALE                            2                            363
  MALE                              1                            133
[1] 2 2
[1] FALSE
D21V8, binary
                                cls
clus                               0   1
  AMP PEAK 22(6P21.31) MUTATED     1   2
  AMP PEAK 22(6P21.31) WILD-TYPE 184 288
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(6P21.31) MUTATED      1    2
  AMP PEAK 22(6P21.31) WILD-TYPE  184  288
     clus
vv    AMP PEAK 22(6P21.31) MUTATED AMP PEAK 22(6P21.31) WILD-TYPE
  NO                             1                            184
  YES                            2                            288
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 22(6P21.31) MUTATED                0
  AMP PEAK 22(6P21.31) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 22(6P21.31) MUTATED                                               3
  AMP PEAK 22(6P21.31) WILD-TYPE                                           352
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 22(6P21.31) MUTATED                                                                        0
  AMP PEAK 22(6P21.31) WILD-TYPE                                                                    100
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 22(6P21.31) MUTATED                                                                     0
  AMP PEAK 22(6P21.31) WILD-TYPE                                                                  36
D21V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 22(6P21.31) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            0
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       AMP PEAK 22(6P21.31) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            100
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V10, binary
                                cls
clus                               0   1
  AMP PEAK 22(6P21.31) MUTATED     3   0
  AMP PEAK 22(6P21.31) WILD-TYPE 417  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(6P21.31) MUTATED      3    0
  AMP PEAK 22(6P21.31) WILD-TYPE  417   17
     clus
vv    AMP PEAK 22(6P21.31) MUTATED AMP PEAK 22(6P21.31) WILD-TYPE
  NO                             3                            417
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 22(6P21.31) MUTATED              0                       0    2
  AMP PEAK 22(6P21.31) WILD-TYPE          132                      18  328
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 22(6P21.31) MUTATED                     0
  AMP PEAK 22(6P21.31) WILD-TYPE                   1
D21V11, multiclass
[1] "Remove cluster labels:"       "AMP PEAK 22(6P21.31) MUTATED"
clus
  AMP PEAK 22(6P21.31) MUTATED AMP PEAK 22(6P21.31) WILD-TYPE 
                             2                            479 
                    TCGA-4C-A93U                     TCGA-BJ-A0YZ 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A0Z0                     TCGA-BJ-A0Z2 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A0Z3                     TCGA-BJ-A0Z9 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A0ZA                     TCGA-BJ-A0ZB 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A0ZC                     TCGA-BJ-A0ZE 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A0ZG                     TCGA-BJ-A0ZH 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A0ZJ                     TCGA-BJ-A18Y 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A18Z                     TCGA-BJ-A190 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A191                     TCGA-BJ-A192 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A28X                     TCGA-BJ-A28Z 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A290                     TCGA-BJ-A2N7 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A2N9                     TCGA-BJ-A2NA 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A3EZ                     TCGA-BJ-A3F0 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A3PR                     TCGA-BJ-A3PU 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A45C                     TCGA-BJ-A45D 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A45G                     TCGA-BJ-A45H 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A45I                     TCGA-BJ-A45K 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A4O8                     TCGA-BJ-A4O9 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-CE-A13K                     TCGA-CE-A27D 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-CE-A3MD                     TCGA-CE-A3ME 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-CE-A481                     TCGA-CE-A482 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-CE-A483                     TCGA-CE-A484 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-CE-A485                     TCGA-DE-A0XZ 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DE-A0Y2                     TCGA-DE-A2OL 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DE-A3KN                     TCGA-DE-A4M8 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DE-A4M9                     TCGA-DE-A4MA 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DE-A4MB                     TCGA-DE-A4MC 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DE-A4MD                     TCGA-DE-A69J 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DE-A69K                     TCGA-DJ-A13L 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A13M                     TCGA-DJ-A13O 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A13P                     TCGA-DJ-A13R 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A13S                     TCGA-DJ-A13T 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A13U                     TCGA-DJ-A13V 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A13W                     TCGA-DJ-A13X 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A1QD                     TCGA-DJ-A1QE 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A1QF                     TCGA-DJ-A1QG 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A1QH                     TCGA-DJ-A1QI 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A1QL                     TCGA-DJ-A1QM 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A1QN                     TCGA-DJ-A1QO 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A1QQ                     TCGA-DJ-A2PN 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A2PO                     TCGA-DJ-A2PP 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A2PQ                     TCGA-DJ-A2PR 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A2PS                     TCGA-DJ-A2PT 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A2PU                     TCGA-DJ-A2PV 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A2PW                     TCGA-DJ-A2PX 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A2PY                     TCGA-DJ-A2PZ 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A2Q1                     TCGA-DJ-A2Q2 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A2Q3                     TCGA-DJ-A2Q4 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A2Q5                     TCGA-DJ-A2Q6 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A2Q7                     TCGA-DJ-A2Q8 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A2Q9                     TCGA-DJ-A2QA 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A2QB                     TCGA-DJ-A2QC 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3UK                     TCGA-DJ-A3UM 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3UN                     TCGA-DJ-A3UO 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3UP                     TCGA-DJ-A3UQ 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3UR                     TCGA-DJ-A3US 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3UT                     TCGA-DJ-A3UU 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3UW                     TCGA-DJ-A3UX 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3UY                     TCGA-DJ-A3UZ 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3V0                     TCGA-DJ-A3V2 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3V3                     TCGA-DJ-A3V4 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3V5                     TCGA-DJ-A3V7 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3V8                     TCGA-DJ-A3V9 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3VA                     TCGA-DJ-A3VB 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3VD                     TCGA-DJ-A3VE 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3VF                     TCGA-DJ-A3VG 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3VI                     TCGA-DJ-A3VJ 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3VK                     TCGA-DJ-A3VL 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3VM                     TCGA-DJ-A4UL 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A4UP                     TCGA-DJ-A4UQ 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A4UR                     TCGA-DJ-A4UT 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A4UW                     TCGA-DJ-A4V0 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A4V2                     TCGA-DJ-A4V4 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A4V5                     TCGA-DO-A1JZ 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-DO-A1K0                     TCGA-DO-A2HM 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-E3-A3DY                     TCGA-E3-A3DZ 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-E3-A3E0                     TCGA-E3-A3E1 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-E3-A3E2                     TCGA-E3-A3E3 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-E3-A3E5                     TCGA-E8-A242 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-E8-A2EA                     TCGA-E8-A3X7 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-E8-A413                     TCGA-E8-A414 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-E8-A415                     TCGA-E8-A416 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-E8-A417                     TCGA-E8-A418 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-E8-A419                     TCGA-E8-A432 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-E8-A433                     TCGA-E8-A434 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-E8-A436                     TCGA-E8-A437 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-E8-A438                     TCGA-E8-A44K 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-E8-A44M                     TCGA-EL-A3CL 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3CM                     TCGA-EL-A3CN 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3CO                     TCGA-EL-A3CP 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3CR                     TCGA-EL-A3CS 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3CT                     TCGA-EL-A3CU 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3CV                     TCGA-EL-A3CW 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3CX                     TCGA-EL-A3CY 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3CZ                     TCGA-EL-A3D0 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3D1                     TCGA-EL-A3D4 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3D5                     TCGA-EL-A3D6 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3GO                     TCGA-EL-A3GP 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3GQ                     TCGA-EL-A3GR 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3GS                     TCGA-EL-A3GU 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3GV                     TCGA-EL-A3GW 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3GX                     TCGA-EL-A3GY 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3GZ                     TCGA-EL-A3H1 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3H2                     TCGA-EL-A3H3 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3H4                     TCGA-EL-A3H5 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3H7                     TCGA-EL-A3H8 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3MW                     TCGA-EL-A3MX 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3MY                     TCGA-EL-A3MZ 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3N2                     TCGA-EL-A3N3 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3T0                     TCGA-EL-A3T1 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3T2                     TCGA-EL-A3T3 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3T6                     TCGA-EL-A3T7 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3T8                     TCGA-EL-A3T9 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3TA                     TCGA-EL-A3TB 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3ZG                     TCGA-EL-A3ZH 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3ZK                     TCGA-EL-A3ZL 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3ZM                     TCGA-EL-A3ZN 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3ZO                     TCGA-EL-A3ZP 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3ZQ                     TCGA-EL-A3ZR 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3ZS                     TCGA-EL-A3ZT 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A4JV                     TCGA-EL-A4JW 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A4JX                     TCGA-EL-A4JZ 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A4K0                     TCGA-EL-A4K1 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A4K2                     TCGA-EL-A4K4 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A4K6                     TCGA-EL-A4K7 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A4K9                     TCGA-EL-A4KD 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A4KG                     TCGA-EL-A4KH 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EL-A4KI                     TCGA-EM-A1CS 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A1CT                     TCGA-EM-A1CU 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A1CV                     TCGA-EM-A1CW 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A1YA                     TCGA-EM-A1YB 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A1YC                     TCGA-EM-A1YD 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A1YE                     TCGA-EM-A22I 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A22J                     TCGA-EM-A22K 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A22L                     TCGA-EM-A22M 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A22N                     TCGA-EM-A22O 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A22P                     TCGA-EM-A22Q 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A2CJ                     TCGA-EM-A2CK 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A2CL                     TCGA-EM-A2CN 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A2CO                     TCGA-EM-A2CP 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A2CQ                     TCGA-EM-A2CT 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A2CU                     TCGA-EM-A2OV 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A2OW                     TCGA-EM-A2OX 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A2OY                     TCGA-EM-A2OZ 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A2P0                     TCGA-EM-A2P1 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A2P2                     TCGA-EM-A2P3 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3AI                     TCGA-EM-A3AJ 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3AK                     TCGA-EM-A3AL 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3AN                     TCGA-EM-A3AO 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3AP                     TCGA-EM-A3AQ 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3AR                     TCGA-EM-A3FJ 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3FK                     TCGA-EM-A3FL 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3FM                     TCGA-EM-A3FN 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3FO                     TCGA-EM-A3FP 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3FQ                     TCGA-EM-A3FR 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3O3                     TCGA-EM-A3O6 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3O7                     TCGA-EM-A3O8 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3O9                     TCGA-EM-A3OA 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3OB                     TCGA-EM-A3ST 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3SU                     TCGA-EM-A3SX 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3SY                     TCGA-EM-A3SZ 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A4FF                     TCGA-EM-A4FH 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A4FK                     TCGA-EM-A4FM 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A4FN                     TCGA-EM-A4FO 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A4FQ                     TCGA-EM-A4FR 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A4FU                     TCGA-EM-A4FV 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-EM-A4G1                     TCGA-ET-A25G 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-ET-A25I                     TCGA-ET-A25J 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-ET-A25K                     TCGA-ET-A25L 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-ET-A25M                     TCGA-ET-A25N 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-ET-A25O                     TCGA-ET-A25P 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-ET-A25R                     TCGA-ET-A2MX 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-ET-A2MY                     TCGA-ET-A2MZ 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-ET-A2N0                     TCGA-ET-A2N1 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-ET-A2N3                     TCGA-ET-A2N4 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-ET-A2N5                     TCGA-ET-A39I 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-ET-A39J                     TCGA-ET-A39K 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-ET-A39L                     TCGA-ET-A39M 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-ET-A39N                     TCGA-ET-A39O 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-ET-A39P                     TCGA-ET-A39R 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-ET-A39S                     TCGA-ET-A39T 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-ET-A3BN                     TCGA-ET-A3BO 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-ET-A3BP                     TCGA-ET-A3BQ 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-ET-A3BS                     TCGA-ET-A3BT 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-ET-A3BU                     TCGA-ET-A3BV 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-ET-A3BW                     TCGA-ET-A3BX 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-ET-A3DO                     TCGA-ET-A3DP 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-ET-A3DQ                     TCGA-ET-A3DR 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-ET-A3DS                     TCGA-ET-A3DT 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-ET-A3DU                     TCGA-ET-A3DV 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-ET-A3DW                     TCGA-ET-A40P 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-ET-A40Q                     TCGA-ET-A40R 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-ET-A40S                     TCGA-ET-A40T 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-ET-A4KN                     TCGA-ET-A4KQ 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-FE-A22Z                     TCGA-FE-A230 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-FE-A231                     TCGA-FE-A232 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-FE-A233                     TCGA-FE-A234 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-FE-A235                     TCGA-FE-A236 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-FE-A237                     TCGA-FE-A238 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-FE-A23A                     TCGA-FE-A3PA 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-FE-A3PB                     TCGA-FE-A3PC 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-FE-A3PD                     TCGA-FK-A3S3 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-FK-A3SB                     TCGA-FK-A3SE 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-FK-A3SG                     TCGA-FK-A3SH 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-FK-A4UB                     TCGA-FY-A2QD 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-FY-A3BL                     TCGA-FY-A3I4 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-FY-A3I5                     TCGA-FY-A3NM 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-FY-A3NN                     TCGA-FY-A3ON 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-FY-A3R6                     TCGA-FY-A3R7 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-FY-A3R8                     TCGA-FY-A3R9 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-FY-A3RA                     TCGA-FY-A3TY 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-FY-A3W9                     TCGA-FY-A3WA 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-FY-A3YR                     TCGA-FY-A40K 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-FY-A40L                     TCGA-FY-A40M 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-FY-A40N                     TCGA-FY-A4B0 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-FY-A4B3                     TCGA-FY-A4B4 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-FY-A76V                     TCGA-GE-A2C6 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-H2-A26U                     TCGA-H2-A2K9 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-H2-A3RH                     TCGA-H2-A3RI 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-H2-A421                     TCGA-H2-A422 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-IM-A3EB                     TCGA-IM-A3ED 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-IM-A3U2                     TCGA-IM-A3U3 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-IM-A41Y                     TCGA-IM-A41Z 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-IM-A420                     TCGA-IM-A4EB 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-J8-A3NZ                     TCGA-J8-A3O0 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-J8-A3O1                     TCGA-J8-A3O2 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-J8-A3YD                     TCGA-J8-A3YE 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-J8-A3YF                     TCGA-J8-A3YG 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-J8-A3YH                     TCGA-J8-A42S 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-J8-A4HW                     TCGA-J8-A4HY 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-KS-A41F                     TCGA-KS-A41I 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-KS-A41J                     TCGA-KS-A41L 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-KS-A4I1                     TCGA-KS-A4I3 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-KS-A4I5                     TCGA-KS-A4I7 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-KS-A4I9                     TCGA-KS-A4IB 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-KS-A4IC                     TCGA-KS-A4ID 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-L6-A4EP                     TCGA-L6-A4EQ 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-L6-A4ET                     TCGA-L6-A4EU 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-MK-A4N7                     TCGA-MK-A4N9 
"AMP PEAK 22(6P21.31) WILD-TYPE" "AMP PEAK 22(6P21.31) WILD-TYPE" 
                    TCGA-QD-A8IV 
"AMP PEAK 22(6P21.31) WILD-TYPE" 
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 22(6P21.31) MUTATED     2   1   0   0
  AMP PEAK 22(6P21.31) WILD-TYPE 381  50   4  30
D21V12, multiclass
    clus
vv   AMP PEAK 22(6P21.31) MUTATED AMP PEAK 22(6P21.31) WILD-TYPE
  R0                            2                            381
  R1                            1                             50
  R2                            0                              4
  RX                            0                             30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V13, continuous
D21V14, binary
                                cls
clus                               0   1
  AMP PEAK 22(6P21.31) MUTATED     1   2
  AMP PEAK 22(6P21.31) WILD-TYPE 224 262
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(6P21.31) MUTATED      1    2
  AMP PEAK 22(6P21.31) WILD-TYPE  224  262
            clus
vv           AMP PEAK 22(6P21.31) MUTATED AMP PEAK 22(6P21.31) WILD-TYPE
  MULTIFOCAL                            1                            224
  UNIFOCAL                              2                            262
[1] 2 2
[1] FALSE
D21V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 22(6P21.31) MUTATED                                  0     1
  AMP PEAK 22(6P21.31) WILD-TYPE                                1    51
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(6P21.31) MUTATED                           0     2
  AMP PEAK 22(6P21.31) WILD-TYPE                        27   326
D21V16, multiclass
                                  clus
vv                                 AMP PEAK 22(6P21.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       2
                                  clus
vv                                 AMP PEAK 22(6P21.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        51
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V17, binary
                                cls
clus                               0   1
  AMP PEAK 22(6P21.31) MUTATED     0   3
  AMP PEAK 22(6P21.31) WILD-TYPE  38 356
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(6P21.31) MUTATED      0    3
  AMP PEAK 22(6P21.31) WILD-TYPE   38  356
                        clus
vv                       AMP PEAK 22(6P21.31) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            3
                        clus
vv                       AMP PEAK 22(6P21.31) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            356
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 23(6P21.2) MUTATION ANALYSIS
D22V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 23(6P21.2) MUTATED     3   1
  AMP PEAK 23(6P21.2) WILD-TYPE 478  15
  AMP PEAK 23(6P21.2) MUTATED AMP PEAK 23(6P21.2) WILD-TYPE 
                            4                           493 
  AMP PEAK 23(6P21.2) MUTATED AMP PEAK 23(6P21.2) WILD-TYPE 
                            1                            15 
$`AMP PEAK 23(6P21.2) MUTATED`
TCGA-DJ-A2Q0 TCGA-E8-A433 TCGA-EL-A3GS TCGA-FE-A239 
       34.36         0.16        65.39        33.63 

$`AMP PEAK 23(6P21.2) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
       30.58        35.41        27.45        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
       31.99        34.85        28.96         8.78         8.42        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        25.45        30.61         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
       50.24       115.10       136.01        50.37        50.20       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       83.57       139.00       150.48       108.66        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       52.50        29.65       147.42       142.52       129.57        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      132.07        98.24        41.29       107.47         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM 
       82.82        89.56        78.97        51.78        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        65.49        61.22        60.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       34.39        30.51        53.36        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       43.59        24.30        27.06        23.90        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        48.49        18.05        19.79        19.46        78.61 
TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       57.01        54.08        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       14.53        10.65        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
       17.88        13.18        23.51         6.05         2.99        12.30 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       48.46        13.15        22.16        40.34        19.73        32.32 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       33.96        17.59        17.46        17.29        14.60        22.52 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.06         7.33         0.49         9.24        13.91        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.86        29.95        29.85        13.51        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
      107.41       108.46        84.89       123.32       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       94.13        55.10        98.20        28.24        50.40        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
       76.64         5.79        87.62        77.82        75.42        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
       52.47       116.78        94.59        84.85        80.58        66.84 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       43.73        62.83       166.62        24.72        43.99        46.26 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
       44.38        40.21        37.48        33.17        31.40        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       71.44        31.59        79.69        24.69        68.22       117.40 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       66.77       112.80        39.95        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        13.28 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10       116.09         1.25        20.42        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        7.82         0.99        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08         0.30         0.76        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       15.16         6.58        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83        31.10         8.22        25.64        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        23.93 
TCGA-QD-A8IV 
       12.89 

  AMP PEAK 23(6P21.2) MUTATED AMP PEAK 23(6P21.2) WILD-TYPE 
                         0.16                          0.20 
  AMP PEAK 23(6P21.2) MUTATED AMP PEAK 23(6P21.2) WILD-TYPE 
                        65.39                        169.32 
  AMP PEAK 23(6P21.2) MUTATED AMP PEAK 23(6P21.2) WILD-TYPE 
                       33.995                        30.610 
[1] "0.2 - 65.4 (34.0)"  "0.2 - 169.3 (30.6)"
[1] "hr=" "7.2"
D22V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 23(6P21.2) MUTATED         2        1         1        0         0
  AMP PEAK 23(6P21.2) WILD-TYPE     280       49       110        2        46
                               vv
clus                            STAGE IVC
  AMP PEAK 23(6P21.2) MUTATED           0
  AMP PEAK 23(6P21.2) WILD-TYPE         6
D22V3, multiclass
           clus
vv          AMP PEAK 23(6P21.2) MUTATED AMP PEAK 23(6P21.2) WILD-TYPE
  STAGE I                             2                           280
  STAGE II                            1                            49
  STAGE III                           1                           110
  STAGE IV                            0                             2
  STAGE IVA                           0                            46
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 23(6P21.2) MUTATED     0   2   2   0
  AMP PEAK 23(6P21.2) WILD-TYPE 142 163 165  23
D22V4, multiclass
    clus
vv   AMP PEAK 23(6P21.2) MUTATED AMP PEAK 23(6P21.2) WILD-TYPE
  T1                           0                           142
  T2                           2                           163
  T3                           2                           165
  T4                           0                            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"
D22V5, binary
                               cls
clus                              0   1
  AMP PEAK 23(6P21.2) MUTATED     3   1
  AMP PEAK 23(6P21.2) WILD-TYPE 222 223
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 23(6P21.2) MUTATED      3    1
  AMP PEAK 23(6P21.2) WILD-TYPE  222  223
   clus
vv  AMP PEAK 23(6P21.2) MUTATED AMP PEAK 23(6P21.2) WILD-TYPE
  0                           3                           222
  1                           1                           223
[1] 2 2
[1] FALSE
D22V6, binary
                               cls
clus                              0   1
  AMP PEAK 23(6P21.2) MUTATED     3   0
  AMP PEAK 23(6P21.2) WILD-TYPE 275   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 23(6P21.2) MUTATED      3    0
  AMP PEAK 23(6P21.2) WILD-TYPE  275    9
   clus
vv  AMP PEAK 23(6P21.2) MUTATED AMP PEAK 23(6P21.2) WILD-TYPE
  0                           3                           275
  1                           0                             9
[1] 2 2
[1] FALSE
D22V7, binary
                               cls
clus                              0   1
  AMP PEAK 23(6P21.2) MUTATED     3   1
  AMP PEAK 23(6P21.2) WILD-TYPE 362 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 23(6P21.2) MUTATED      3    1
  AMP PEAK 23(6P21.2) WILD-TYPE  362  133
        clus
vv       AMP PEAK 23(6P21.2) MUTATED AMP PEAK 23(6P21.2) WILD-TYPE
  FEMALE                           3                           362
  MALE                             1                           133
[1] 2 2
[1] FALSE
D22V8, binary
                               cls
clus                              0   1
  AMP PEAK 23(6P21.2) MUTATED     3   1
  AMP PEAK 23(6P21.2) WILD-TYPE 182 289
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 23(6P21.2) MUTATED      3    1
  AMP PEAK 23(6P21.2) WILD-TYPE  182  289
     clus
vv    AMP PEAK 23(6P21.2) MUTATED AMP PEAK 23(6P21.2) WILD-TYPE
  NO                            3                           182
  YES                           1                           289
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 23(6P21.2) MUTATED                0
  AMP PEAK 23(6P21.2) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 23(6P21.2) MUTATED                                               4
  AMP PEAK 23(6P21.2) WILD-TYPE                                           351
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 23(6P21.2) MUTATED                                                                        0
  AMP PEAK 23(6P21.2) WILD-TYPE                                                                    100
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 23(6P21.2) MUTATED                                                                     0
  AMP PEAK 23(6P21.2) WILD-TYPE                                                                  36
D22V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 23(6P21.2) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           0
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       AMP PEAK 23(6P21.2) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           100
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V10, binary
                               cls
clus                              0   1
  AMP PEAK 23(6P21.2) MUTATED     4   0
  AMP PEAK 23(6P21.2) WILD-TYPE 416  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 23(6P21.2) MUTATED      4    0
  AMP PEAK 23(6P21.2) WILD-TYPE  416   17
     clus
vv    AMP PEAK 23(6P21.2) MUTATED AMP PEAK 23(6P21.2) WILD-TYPE
  NO                            4                           416
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 23(6P21.2) MUTATED              1                       0    3
  AMP PEAK 23(6P21.2) WILD-TYPE          131                      18  327
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 23(6P21.2) MUTATED                     0
  AMP PEAK 23(6P21.2) WILD-TYPE                   1
D22V11, multiclass
                         clus
vv                        AMP PEAK 23(6P21.2) MUTATED
  MINIMAL (T3)                                      1
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              3
  VERY ADVANCED (T4B)                               0
                         clus
vv                        AMP PEAK 23(6P21.2) WILD-TYPE
  MINIMAL (T3)                                      131
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              327
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 23(6P21.2) MUTATED     4   0   0   0
  AMP PEAK 23(6P21.2) WILD-TYPE 379  51   4  30
D22V12, multiclass
    clus
vv   AMP PEAK 23(6P21.2) MUTATED AMP PEAK 23(6P21.2) WILD-TYPE
  R0                           4                           379
  R1                           0                            51
  R2                           0                             4
  RX                           0                            30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V13, continuous
D22V14, binary
                               cls
clus                              0   1
  AMP PEAK 23(6P21.2) MUTATED     1   3
  AMP PEAK 23(6P21.2) WILD-TYPE 224 261
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 23(6P21.2) MUTATED      1    3
  AMP PEAK 23(6P21.2) WILD-TYPE  224  261
            clus
vv           AMP PEAK 23(6P21.2) MUTATED AMP PEAK 23(6P21.2) WILD-TYPE
  MULTIFOCAL                           1                           224
  UNIFOCAL                             3                           261
[1] 2 2
[1] FALSE
D22V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 23(6P21.2) MUTATED                                  0     1
  AMP PEAK 23(6P21.2) WILD-TYPE                                1    51
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(6P21.2) MUTATED                           0     3
  AMP PEAK 23(6P21.2) WILD-TYPE                        27   325
D22V16, multiclass
                                  clus
vv                                 AMP PEAK 23(6P21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      3
                                  clus
vv                                 AMP PEAK 23(6P21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       51
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V17, binary
                               cls
clus                              0   1
  AMP PEAK 23(6P21.2) MUTATED     1   3
  AMP PEAK 23(6P21.2) WILD-TYPE  37 356
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 23(6P21.2) MUTATED      1    3
  AMP PEAK 23(6P21.2) WILD-TYPE   37  356
                        clus
vv                       AMP PEAK 23(6P21.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                           3
                        clus
vv                       AMP PEAK 23(6P21.2) WILD-TYPE
  HISPANIC OR LATINO                                37
  NOT HISPANIC OR LATINO                           356
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 24(6P12.2) MUTATION ANALYSIS
D23V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 24(6P12.2) MUTATED     2   1
  AMP PEAK 24(6P12.2) WILD-TYPE 479  15
  AMP PEAK 24(6P12.2) MUTATED AMP PEAK 24(6P12.2) WILD-TYPE 
                            3                           494 
  AMP PEAK 24(6P12.2) MUTATED AMP PEAK 24(6P12.2) WILD-TYPE 
                            1                            15 
$`AMP PEAK 24(6P12.2) MUTATED`
TCGA-DJ-A2Q0 TCGA-ET-A25J TCGA-FE-A239 
       34.36        77.56        33.63 

$`AMP PEAK 24(6P12.2) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
       30.58        35.41        27.45        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
       31.99        34.85        28.96         8.78         8.42        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        30.61         0.16         0.23        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        33.50         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        69.57        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       49.51        50.24       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       150.48       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        89.56        78.97        51.78 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        47.38        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       60.16         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        47.84        43.59        24.30        27.06        23.90 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J 
       19.46        78.61        57.01        54.08        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P 
       15.75        10.45        14.53        10.65        44.19        41.29 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        47.57        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        32.32        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        29.72        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 
       15.02        14.50        15.06         7.33         0.49         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       13.91        38.66        38.86        29.95        29.85        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        84.59        29.33        21.34         5.33        26.37 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
       26.37        22.45        21.53        60.49        24.46        13.68 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.93        81.70        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
      106.09       107.41       108.46        84.89       123.32       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       95.34        94.13        55.10        98.20        28.24        50.40 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
       79.10        76.64         5.79        87.62        77.82        75.42 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
       46.65        52.47       116.78        94.59        84.85        80.58 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
       66.84        43.73        62.83       166.62        24.72        43.99 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
       46.26        44.38        40.21        37.48        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA 
      117.40        66.77       112.80        39.95        81.83       106.36 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD 
       85.15        85.68        78.77        71.08         4.11         1.05 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       13.28         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       17.82         7.82         0.99        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83        31.10         8.22        25.64        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       23.93        12.89 

  AMP PEAK 24(6P12.2) MUTATED AMP PEAK 24(6P12.2) WILD-TYPE 
                        33.63                          0.16 
  AMP PEAK 24(6P12.2) MUTATED AMP PEAK 24(6P12.2) WILD-TYPE 
                        77.56                        169.32 
  AMP PEAK 24(6P12.2) MUTATED AMP PEAK 24(6P12.2) WILD-TYPE 
                       34.360                        30.595 
[1] "33.6 - 77.6 (34.4)" "0.2 - 169.3 (30.6)"
[1] "hr=" "7.2"
D23V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 24(6P12.2) MUTATED         1        1         1        0         0
  AMP PEAK 24(6P12.2) WILD-TYPE     281       49       110        2        46
                               vv
clus                            STAGE IVC
  AMP PEAK 24(6P12.2) MUTATED           0
  AMP PEAK 24(6P12.2) WILD-TYPE         6
D23V3, multiclass
           clus
vv          AMP PEAK 24(6P12.2) MUTATED AMP PEAK 24(6P12.2) WILD-TYPE
  STAGE I                             1                           281
  STAGE II                            1                            49
  STAGE III                           1                           110
  STAGE IV                            0                             2
  STAGE IVA                           0                            46
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 24(6P12.2) MUTATED     0   2   1   0
  AMP PEAK 24(6P12.2) WILD-TYPE 142 163 166  23
D23V4, multiclass
    clus
vv   AMP PEAK 24(6P12.2) MUTATED AMP PEAK 24(6P12.2) WILD-TYPE
  T1                           0                           142
  T2                           2                           163
  T3                           1                           166
  T4                           0                            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"
D23V5, binary
                               cls
clus                              0   1
  AMP PEAK 24(6P12.2) MUTATED     2   1
  AMP PEAK 24(6P12.2) WILD-TYPE 223 223
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 24(6P12.2) MUTATED      2    1
  AMP PEAK 24(6P12.2) WILD-TYPE  223  223
   clus
vv  AMP PEAK 24(6P12.2) MUTATED AMP PEAK 24(6P12.2) WILD-TYPE
  0                           2                           223
  1                           1                           223
[1] 2 2
[1] FALSE
D23V6, binary
                               cls
clus                              0   1
  AMP PEAK 24(6P12.2) MUTATED     1   0
  AMP PEAK 24(6P12.2) WILD-TYPE 277   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 24(6P12.2) MUTATED      1    0
  AMP PEAK 24(6P12.2) WILD-TYPE  277    9
   clus
vv  AMP PEAK 24(6P12.2) MUTATED AMP PEAK 24(6P12.2) WILD-TYPE
  0                           1                           277
  1                           0                             9
[1] 2 2
[1] FALSE
D23V7, binary
                               cls
clus                              0   1
  AMP PEAK 24(6P12.2) MUTATED     2   1
  AMP PEAK 24(6P12.2) WILD-TYPE 363 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 24(6P12.2) MUTATED      2    1
  AMP PEAK 24(6P12.2) WILD-TYPE  363  133
        clus
vv       AMP PEAK 24(6P12.2) MUTATED AMP PEAK 24(6P12.2) WILD-TYPE
  FEMALE                           2                           363
  MALE                             1                           133
[1] 2 2
[1] FALSE
D23V8, binary
                               cls
clus                              0   1
  AMP PEAK 24(6P12.2) MUTATED     1   2
  AMP PEAK 24(6P12.2) WILD-TYPE 184 288
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 24(6P12.2) MUTATED      1    2
  AMP PEAK 24(6P12.2) WILD-TYPE  184  288
     clus
vv    AMP PEAK 24(6P12.2) MUTATED AMP PEAK 24(6P12.2) WILD-TYPE
  NO                            1                           184
  YES                           2                           288
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 24(6P12.2) MUTATED                0
  AMP PEAK 24(6P12.2) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 24(6P12.2) MUTATED                                               3
  AMP PEAK 24(6P12.2) WILD-TYPE                                           352
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 24(6P12.2) MUTATED                                                                        0
  AMP PEAK 24(6P12.2) WILD-TYPE                                                                    100
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 24(6P12.2) MUTATED                                                                     0
  AMP PEAK 24(6P12.2) WILD-TYPE                                                                  36
D23V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 24(6P12.2) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           0
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       AMP PEAK 24(6P12.2) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           100
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V10, binary
                               cls
clus                              0   1
  AMP PEAK 24(6P12.2) MUTATED     3   0
  AMP PEAK 24(6P12.2) WILD-TYPE 417  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 24(6P12.2) MUTATED      3    0
  AMP PEAK 24(6P12.2) WILD-TYPE  417   17
     clus
vv    AMP PEAK 24(6P12.2) MUTATED AMP PEAK 24(6P12.2) WILD-TYPE
  NO                            3                           417
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 24(6P12.2) MUTATED              0                       0    3
  AMP PEAK 24(6P12.2) WILD-TYPE          132                      18  327
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 24(6P12.2) MUTATED                     0
  AMP PEAK 24(6P12.2) WILD-TYPE                   1
D23V11, multiclass
                         clus
vv                        AMP PEAK 24(6P12.2) MUTATED
  MINIMAL (T3)                                      0
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              3
  VERY ADVANCED (T4B)                               0
                         clus
vv                        AMP PEAK 24(6P12.2) WILD-TYPE
  MINIMAL (T3)                                      132
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              327
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 24(6P12.2) MUTATED     3   0   0   0
  AMP PEAK 24(6P12.2) WILD-TYPE 380  51   4  30
D23V12, multiclass
    clus
vv   AMP PEAK 24(6P12.2) MUTATED AMP PEAK 24(6P12.2) WILD-TYPE
  R0                           3                           380
  R1                           0                            51
  R2                           0                             4
  RX                           0                            30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V13, continuous
D23V14, binary
                               cls
clus                              0   1
  AMP PEAK 24(6P12.2) MUTATED     0   3
  AMP PEAK 24(6P12.2) WILD-TYPE 225 261
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 24(6P12.2) MUTATED      0    3
  AMP PEAK 24(6P12.2) WILD-TYPE  225  261
            clus
vv           AMP PEAK 24(6P12.2) MUTATED AMP PEAK 24(6P12.2) WILD-TYPE
  MULTIFOCAL                           0                           225
  UNIFOCAL                             3                           261
[1] 2 2
[1] FALSE
D23V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 24(6P12.2) MUTATED                                  0     0
  AMP PEAK 24(6P12.2) WILD-TYPE                                1    52
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(6P12.2) MUTATED                           0     3
  AMP PEAK 24(6P12.2) WILD-TYPE                        27   325
D23V16, multiclass
                                  clus
vv                                 AMP PEAK 24(6P12.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      3
                                  clus
vv                                 AMP PEAK 24(6P12.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       52
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V17, binary
                               cls
clus                              0   1
  AMP PEAK 24(6P12.2) MUTATED     0   3
  AMP PEAK 24(6P12.2) WILD-TYPE  38 356
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 24(6P12.2) MUTATED      0    3
  AMP PEAK 24(6P12.2) WILD-TYPE   38  356
                        clus
vv                       AMP PEAK 24(6P12.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           3
                        clus
vv                       AMP PEAK 24(6P12.2) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           356
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 25(6Q12) MUTATION ANALYSIS
D24V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 25(6Q12) MUTATED     3   0
  AMP PEAK 25(6Q12) WILD-TYPE 478  16
  AMP PEAK 25(6Q12) MUTATED AMP PEAK 25(6Q12) WILD-TYPE 
                          3                         494 
  AMP PEAK 25(6Q12) MUTATED AMP PEAK 25(6Q12) WILD-TYPE 
                          0                          16 
$`AMP PEAK 25(6Q12) MUTATED`
TCGA-DJ-A2Q0 TCGA-EL-A3ZS TCGA-J8-A3YE 
       34.36         7.07        27.85 

$`AMP PEAK 25(6Q12) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
       30.58        35.41        27.45        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
       31.99        34.85        28.96         8.78         8.42        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        30.61         0.16         0.23        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        33.50         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        69.57        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       49.51        50.24       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       150.48       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        89.56        78.97        51.78 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        47.38        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
       60.16        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       47.84        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       78.61        57.01        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       32.32        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       22.52        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33         0.49         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
      106.09       107.41       108.46        84.89       123.32       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       95.34        94.13        55.10        98.20        28.24        50.40 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
       79.10        76.64         5.79        87.62        77.82        75.42 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
       46.65        52.47       116.78        94.59        84.85        80.58 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
       66.84        43.73        62.83       166.62        24.72        43.99 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
       46.26        44.38        40.21        37.48        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      117.40        66.77       112.80        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        1.05        13.28         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
       20.42        17.82         7.82         0.99        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08         0.30         0.76 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16         6.58        22.49        19.04 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35        21.60         1.68        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46         2.99        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       18.51        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YF 
       17.23        43.17        27.19        11.24        31.82        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       23.93        12.89 

  AMP PEAK 25(6Q12) MUTATED AMP PEAK 25(6Q12) WILD-TYPE 
                       7.07                        0.16 
  AMP PEAK 25(6Q12) MUTATED AMP PEAK 25(6Q12) WILD-TYPE 
                      34.36                      169.32 
  AMP PEAK 25(6Q12) MUTATED AMP PEAK 25(6Q12) WILD-TYPE 
                      27.85                       30.61 
[1] "7.1 - 34.4 (27.9)"  "0.2 - 169.3 (30.6)"
[1] "hr="     "1200000"
D24V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 25(6Q12) MUTATED         2        1         0        0         0
  AMP PEAK 25(6Q12) WILD-TYPE     280       49       111        2        46
                             vv
clus                          STAGE IVC
  AMP PEAK 25(6Q12) MUTATED           0
  AMP PEAK 25(6Q12) WILD-TYPE         6
D24V3, multiclass
           clus
vv          AMP PEAK 25(6Q12) MUTATED AMP PEAK 25(6Q12) WILD-TYPE
  STAGE I                           2                         280
  STAGE II                          1                          49
  STAGE III                         0                         111
  STAGE IV                          0                           2
  STAGE IVA                         0                          46
  STAGE IVC                         0                           6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK 25(6Q12) MUTATED     1   1   1   0
  AMP PEAK 25(6Q12) WILD-TYPE 141 164 166  23
D24V4, multiclass
    clus
vv   AMP PEAK 25(6Q12) MUTATED AMP PEAK 25(6Q12) WILD-TYPE
  T1                         1                         141
  T2                         1                         164
  T3                         1                         166
  T4                         0                          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"
D24V5, binary
                             cls
clus                            0   1
  AMP PEAK 25(6Q12) MUTATED     1   2
  AMP PEAK 25(6Q12) WILD-TYPE 224 222
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 25(6Q12) MUTATED      1    2
  AMP PEAK 25(6Q12) WILD-TYPE  224  222
   clus
vv  AMP PEAK 25(6Q12) MUTATED AMP PEAK 25(6Q12) WILD-TYPE
  0                         1                         224
  1                         2                         222
[1] 2 2
[1] FALSE
D24V6, binary
                             cls
clus                            0   1
  AMP PEAK 25(6Q12) MUTATED     3   0
  AMP PEAK 25(6Q12) WILD-TYPE 275   9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 25(6Q12) MUTATED      3    0
  AMP PEAK 25(6Q12) WILD-TYPE  275    9
   clus
vv  AMP PEAK 25(6Q12) MUTATED AMP PEAK 25(6Q12) WILD-TYPE
  0                         3                         275
  1                         0                           9
[1] 2 2
[1] FALSE
D24V7, binary
                             cls
clus                            0   1
  AMP PEAK 25(6Q12) MUTATED     3   0
  AMP PEAK 25(6Q12) WILD-TYPE 362 134
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 25(6Q12) MUTATED      3    0
  AMP PEAK 25(6Q12) WILD-TYPE  362  134
        clus
vv       AMP PEAK 25(6Q12) MUTATED AMP PEAK 25(6Q12) WILD-TYPE
  FEMALE                         3                         362
  MALE                           0                         134
[1] 2 2
[1] FALSE
D24V8, binary
                             cls
clus                            0   1
  AMP PEAK 25(6Q12) MUTATED     1   2
  AMP PEAK 25(6Q12) WILD-TYPE 184 288
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 25(6Q12) MUTATED      1    2
  AMP PEAK 25(6Q12) WILD-TYPE  184  288
     clus
vv    AMP PEAK 25(6Q12) MUTATED AMP PEAK 25(6Q12) WILD-TYPE
  NO                          1                         184
  YES                         2                         288
[1] 2 2
[1] FALSE
                             vv
clus                          OTHER  SPECIFY
  AMP PEAK 25(6Q12) MUTATED                0
  AMP PEAK 25(6Q12) WILD-TYPE              8
                             vv
clus                          THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 25(6Q12) MUTATED                                               3
  AMP PEAK 25(6Q12) WILD-TYPE                                           352
                             vv
clus                          THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 25(6Q12) MUTATED                                                                        0
  AMP PEAK 25(6Q12) WILD-TYPE                                                                    100
                             vv
clus                          THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 25(6Q12) MUTATED                                                                     0
  AMP PEAK 25(6Q12) WILD-TYPE                                                                  36
D24V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 25(6Q12) MUTATED
  OTHER  SPECIFY                                                                                 0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                         0
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                            0
                                                                        clus
vv                                                                       AMP PEAK 25(6Q12) WILD-TYPE
  OTHER  SPECIFY                                                                                   8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                         100
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                             36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V10, binary
                             cls
clus                            0   1
  AMP PEAK 25(6Q12) MUTATED     3   0
  AMP PEAK 25(6Q12) WILD-TYPE 417  17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 25(6Q12) MUTATED      3    0
  AMP PEAK 25(6Q12) WILD-TYPE  417   17
     clus
vv    AMP PEAK 25(6Q12) MUTATED AMP PEAK 25(6Q12) WILD-TYPE
  NO                          3                         417
  YES                         0                          17
[1] 2 2
[1] FALSE
                             vv
clus                          MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 25(6Q12) MUTATED              1                       0    2
  AMP PEAK 25(6Q12) WILD-TYPE          131                      18  328
                             vv
clus                          VERY ADVANCED (T4B)
  AMP PEAK 25(6Q12) MUTATED                     0
  AMP PEAK 25(6Q12) WILD-TYPE                   1
D24V11, multiclass
                         clus
vv                        AMP PEAK 25(6Q12) MUTATED AMP PEAK 25(6Q12) WILD-TYPE
  MINIMAL (T3)                                    1                         131
  MODERATE/ADVANCED (T4A)                         0                          18
  NONE                                            2                         328
  VERY ADVANCED (T4B)                             0                           1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK 25(6Q12) MUTATED     3   0   0   0
  AMP PEAK 25(6Q12) WILD-TYPE 380  51   4  30
D24V12, multiclass
    clus
vv   AMP PEAK 25(6Q12) MUTATED AMP PEAK 25(6Q12) WILD-TYPE
  R0                         3                         380
  R1                         0                          51
  R2                         0                           4
  RX                         0                          30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V13, continuous
D24V14, binary
                             cls
clus                            0   1
  AMP PEAK 25(6Q12) MUTATED     0   3
  AMP PEAK 25(6Q12) WILD-TYPE 225 261
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 25(6Q12) MUTATED      0    3
  AMP PEAK 25(6Q12) WILD-TYPE  225  261
            clus
vv           AMP PEAK 25(6Q12) MUTATED AMP PEAK 25(6Q12) WILD-TYPE
  MULTIFOCAL                         0                         225
  UNIFOCAL                           3                         261
[1] 2 2
[1] FALSE
D24V15, continuous
[1] "Remove cluster labels:"    "AMP PEAK 25(6Q12) MUTATED"
clus
  AMP PEAK 25(6Q12) MUTATED AMP PEAK 25(6Q12) WILD-TYPE 
                          2                         399 
                 TCGA-4C-A93U                  TCGA-BJ-A0Z2 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-BJ-A0Z3                  TCGA-BJ-A0Z9 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-BJ-A0ZA                  TCGA-BJ-A0ZB 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-BJ-A0ZC                  TCGA-BJ-A0ZE 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-BJ-A0ZG                  TCGA-BJ-A0ZH 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-BJ-A0ZJ                  TCGA-BJ-A18Y 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-BJ-A18Z                  TCGA-BJ-A190 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-BJ-A191                  TCGA-BJ-A192 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-BJ-A28R                  TCGA-BJ-A28S 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-BJ-A28T                  TCGA-BJ-A28V 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-BJ-A28W                  TCGA-BJ-A28Z 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-BJ-A290                  TCGA-BJ-A291 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-BJ-A2N8                  TCGA-BJ-A2N9 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-BJ-A2P4                  TCGA-BJ-A3PU 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-BJ-A45C                  TCGA-BJ-A45D 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-BJ-A45E                  TCGA-BJ-A45F 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-BJ-A45G                  TCGA-BJ-A45H 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-BJ-A45I                  TCGA-BJ-A45J 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-BJ-A45K                  TCGA-BJ-A4O8 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-BJ-A4O9                  TCGA-CE-A13K 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-CE-A27D                  TCGA-CE-A3MD 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-CE-A3ME                  TCGA-CE-A481 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-CE-A482                  TCGA-CE-A483 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-CE-A484                  TCGA-CE-A485 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DE-A0XZ                  TCGA-DE-A0Y2 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DE-A0Y3                  TCGA-DE-A2OL 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DE-A3KN                  TCGA-DE-A4M8 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DE-A4M9                  TCGA-DE-A4MA 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DE-A4MB                  TCGA-DE-A4MC 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DE-A4MD                  TCGA-DE-A69J 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DE-A69K                  TCGA-DE-A7U5 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A13L                  TCGA-DJ-A13M 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A13O                  TCGA-DJ-A13R 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A13S                  TCGA-DJ-A13U 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A13V                  TCGA-DJ-A13W 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A13X                  TCGA-DJ-A1QD 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A1QE                  TCGA-DJ-A1QF 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A1QG                  TCGA-DJ-A1QH 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A1QI                  TCGA-DJ-A1QL 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A1QM                  TCGA-DJ-A1QN 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A1QO                  TCGA-DJ-A1QQ 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A2PN                  TCGA-DJ-A2PO 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A2PP                  TCGA-DJ-A2PQ 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A2PR                  TCGA-DJ-A2PS 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A2PT                  TCGA-DJ-A2PU 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A2PV                  TCGA-DJ-A2PW 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A2PY                  TCGA-DJ-A2PZ 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A2Q1                  TCGA-DJ-A2Q2 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A2Q3                  TCGA-DJ-A2Q4 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A2Q5                  TCGA-DJ-A2Q6 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A2Q7                  TCGA-DJ-A2Q8 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A2Q9                  TCGA-DJ-A2QA 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A2QC                  TCGA-DJ-A3UK 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A3UM                  TCGA-DJ-A3UN 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A3UO                  TCGA-DJ-A3UP 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A3UQ                  TCGA-DJ-A3UR 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A3US                  TCGA-DJ-A3UT 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A3UU                  TCGA-DJ-A3UW 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A3UX                  TCGA-DJ-A3UY 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A3V0                  TCGA-DJ-A3V2 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A3V3                  TCGA-DJ-A3V4 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A3V5                  TCGA-DJ-A3V7 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A3V8                  TCGA-DJ-A3VA 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A3VB                  TCGA-DJ-A3VD 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A3VE                  TCGA-DJ-A3VF 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A3VG                  TCGA-DJ-A3VJ 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A3VK                  TCGA-DJ-A3VL 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A3VM                  TCGA-DJ-A4UL 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A4UP                  TCGA-DJ-A4UQ 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A4UT                  TCGA-DJ-A4V0 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A4V2                  TCGA-DJ-A4V4 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DJ-A4V5                  TCGA-DO-A1JZ 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-DO-A1K0                  TCGA-DO-A2HM 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-E3-A3DY                  TCGA-E3-A3DZ 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-E3-A3E0                  TCGA-E3-A3E1 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-E3-A3E2                  TCGA-E3-A3E3 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-E8-A419                  TCGA-EL-A3CN 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A3CO                  TCGA-EL-A3CR 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A3CS                  TCGA-EL-A3CT 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A3CU                  TCGA-EL-A3CV 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A3CW                  TCGA-EL-A3CX 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A3CY                  TCGA-EL-A3CZ 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A3D0                  TCGA-EL-A3D1 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A3D4                  TCGA-EL-A3D5 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A3D6                  TCGA-EL-A3GO 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A3GP                  TCGA-EL-A3GQ 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A3GR                  TCGA-EL-A3GS 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A3GU                  TCGA-EL-A3GV 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A3GW                  TCGA-EL-A3GX 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A3GY                  TCGA-EL-A3GZ 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A3H2                  TCGA-EL-A3H3 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A3H4                  TCGA-EL-A3H5 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A3H7                  TCGA-EL-A3H8 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A3MW                  TCGA-EL-A3MX 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A3MY                  TCGA-EL-A3MZ 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A3N2                  TCGA-EL-A3N3 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A3T1                  TCGA-EL-A3T2 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A3T3                  TCGA-EL-A3T6 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A3T7                  TCGA-EL-A3T8 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A3T9                  TCGA-EL-A3TA 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A3TB                  TCGA-EL-A3ZG 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A3ZH                  TCGA-EL-A3ZK 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A3ZL                  TCGA-EL-A3ZM 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A3ZN                  TCGA-EL-A3ZO 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A3ZP                  TCGA-EL-A3ZQ 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A3ZR                  TCGA-EL-A3ZT 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A4JV                  TCGA-EL-A4JW 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A4JX                  TCGA-EL-A4JZ 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A4K0                  TCGA-EL-A4K1 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A4K2                  TCGA-EL-A4K4 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A4K6                  TCGA-EL-A4K7 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A4K9                  TCGA-EL-A4KD 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A4KG                  TCGA-EL-A4KH 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EL-A4KI                  TCGA-EM-A1CS 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A1CT                  TCGA-EM-A1CU 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A1CV                  TCGA-EM-A1CW 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A1YA                  TCGA-EM-A1YB 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A1YC                  TCGA-EM-A1YD 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A1YE                  TCGA-EM-A22I 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A22J                  TCGA-EM-A22K 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A22L                  TCGA-EM-A22N 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A22O                  TCGA-EM-A22P 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A22Q                  TCGA-EM-A2CJ 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A2CK                  TCGA-EM-A2CL 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A2CN                  TCGA-EM-A2CO 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A2CP                  TCGA-EM-A2CQ 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A2CT                  TCGA-EM-A2CU 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A2OW                  TCGA-EM-A2OX 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A2OY                  TCGA-EM-A2P0 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A2P1                  TCGA-EM-A2P2 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A2P3                  TCGA-EM-A3AI 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A3AJ                  TCGA-EM-A3AK 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A3AL                  TCGA-EM-A3AN 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A3AO                  TCGA-EM-A3AP 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A3AQ                  TCGA-EM-A3AR 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A3FJ                  TCGA-EM-A3FM 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A3FN                  TCGA-EM-A3FO 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A3FP                  TCGA-EM-A3FR 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A3O3                  TCGA-EM-A3O6 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A3O7                  TCGA-EM-A3O8 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A3O9                  TCGA-EM-A3OA 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A3OB                  TCGA-EM-A3ST 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A3SU                  TCGA-EM-A3SX 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A3SY                  TCGA-EM-A3SZ 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A4FF                  TCGA-EM-A4FH 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A4FK                  TCGA-EM-A4FM 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A4FN                  TCGA-EM-A4FQ 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A4FR                  TCGA-EM-A4FU 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-EM-A4FV                  TCGA-EM-A4G1 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-ET-A25G                  TCGA-ET-A25I 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-ET-A25J                  TCGA-ET-A25K 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-ET-A25L                  TCGA-ET-A25M 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-ET-A25N                  TCGA-ET-A25O 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-ET-A25P                  TCGA-ET-A25R 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-ET-A2MY                  TCGA-ET-A2MZ 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-ET-A2N0                  TCGA-ET-A2N5 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-ET-A39J                  TCGA-ET-A39M 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-ET-A39N                  TCGA-ET-A39O 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-ET-A39P                  TCGA-ET-A39T 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-ET-A3BN                  TCGA-ET-A3BO 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-ET-A3BP                  TCGA-ET-A3BQ 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-ET-A3BS                  TCGA-ET-A3BT 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-ET-A3BU                  TCGA-ET-A3BV 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-ET-A3BW                  TCGA-ET-A3BX 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-ET-A3DO                  TCGA-ET-A3DS 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-ET-A3DT                  TCGA-ET-A40P 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-ET-A40Q                  TCGA-ET-A40R 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-ET-A40S                  TCGA-ET-A4KN 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-ET-A4KQ                  TCGA-FE-A22Z 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-FE-A230                  TCGA-FE-A232 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-FE-A233                  TCGA-FE-A234 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-FE-A235                  TCGA-FE-A236 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-FE-A237                  TCGA-FE-A238 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-FE-A239                  TCGA-FE-A23A 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-FE-A3PA                  TCGA-FE-A3PB 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-FE-A3PC                  TCGA-FE-A3PD 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-FY-A2QD                  TCGA-FY-A3I4 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-FY-A3I5                  TCGA-FY-A3ON 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-FY-A3R8                  TCGA-FY-A3TY 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-FY-A3W9                  TCGA-FY-A3YR 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-FY-A40K                  TCGA-FY-A40L 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-FY-A40M                  TCGA-FY-A40N 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-FY-A4B3                  TCGA-FY-A76V 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-GE-A2C6                  TCGA-H2-A421 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-IM-A3EB                  TCGA-IM-A3ED 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-IM-A3U2                  TCGA-IM-A3U3 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-IM-A41Y                  TCGA-IM-A41Z 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-IM-A420                  TCGA-IM-A4EB 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-J8-A3O0                  TCGA-J8-A3YD 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-J8-A3YG                  TCGA-KS-A41F 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-KS-A41I                  TCGA-KS-A41J 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-KS-A41L                  TCGA-KS-A4I3 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-KS-A4I5                  TCGA-KS-A4I7 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-KS-A4I9                  TCGA-KS-A4IB 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-KS-A4IC                  TCGA-KS-A4ID 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-L6-A4EP                  TCGA-L6-A4EQ 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-L6-A4ET                  TCGA-L6-A4EU 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-MK-A4N6                  TCGA-MK-A4N7 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-MK-A4N9                  TCGA-MK-A84Z 
"AMP PEAK 25(6Q12) WILD-TYPE" "AMP PEAK 25(6Q12) WILD-TYPE" 
                 TCGA-QD-A8IV 
"AMP PEAK 25(6Q12) WILD-TYPE" 
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 25(6Q12) MUTATED                                  0     0
  AMP PEAK 25(6Q12) WILD-TYPE                                1    52
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(6Q12) MUTATED                           0     3
  AMP PEAK 25(6Q12) WILD-TYPE                        27   325
D24V16, multiclass
                                  clus
vv                                 AMP PEAK 25(6Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                0
  WHITE                                                    3
                                  clus
vv                                 AMP PEAK 25(6Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     52
  BLACK OR AFRICAN AMERICAN                                 27
  WHITE                                                    325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V17, binary
                             cls
clus                            0   1
  AMP PEAK 25(6Q12) MUTATED     0   2
  AMP PEAK 25(6Q12) WILD-TYPE  38 357
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 25(6Q12) MUTATED      0    2
  AMP PEAK 25(6Q12) WILD-TYPE   38  357
                        clus
vv                       AMP PEAK 25(6Q12) MUTATED AMP PEAK 25(6Q12) WILD-TYPE
  HISPANIC OR LATINO                             0                          38
  NOT HISPANIC OR LATINO                         2                         357
[1] 2 2
[1] FALSE

Clustering(25) Variable = AMP PEAK 26(6Q27) MUTATION ANALYSIS
D25V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 26(6Q27) MUTATED     4   0
  AMP PEAK 26(6Q27) WILD-TYPE 477  16
  AMP PEAK 26(6Q27) MUTATED AMP PEAK 26(6Q27) WILD-TYPE 
                          4                         493 
  AMP PEAK 26(6Q27) MUTATED AMP PEAK 26(6Q27) WILD-TYPE 
                          0                          16 
$`AMP PEAK 26(6Q27) MUTATED`
TCGA-DJ-A2Q0 TCGA-EM-A22J TCGA-ET-A39N TCGA-FE-A22Z 
       34.36        14.50       123.32        73.74 

$`AMP PEAK 26(6Q27) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
       30.58        35.41        27.45        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
       31.99        34.85        28.96         8.78         8.42        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        30.61         0.16         0.23        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        33.50         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        69.57        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       49.51        50.24       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       150.48       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        89.56        78.97        51.78 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        47.38        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       60.16         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        47.84        43.59        24.30        27.06        23.90 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22K 
       19.46        78.61        57.01        54.08        14.73        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       32.32        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       22.52        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33         0.49         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
      106.09       107.41       108.46        84.89       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       94.13        55.10        98.20        28.24        50.40        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
       76.64         5.79        87.62        77.82        75.42        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
       52.47       116.78        94.59        84.85        80.58        66.84 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       43.73        62.83       166.62        24.72        43.99        46.26 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A230 
       44.38        40.21        37.48        33.17        31.40        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
      112.80        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        13.28 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10       116.09         1.25        20.42        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        7.82         0.99        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08         0.30         0.76        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       15.16         6.58        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83        31.10         8.22        25.64        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        23.93 
TCGA-QD-A8IV 
       12.89 

  AMP PEAK 26(6Q27) MUTATED AMP PEAK 26(6Q27) WILD-TYPE 
                      14.50                        0.16 
  AMP PEAK 26(6Q27) MUTATED AMP PEAK 26(6Q27) WILD-TYPE 
                     123.32                      169.32 
  AMP PEAK 26(6Q27) MUTATED AMP PEAK 26(6Q27) WILD-TYPE 
                      54.05                       30.61 
[1] "14.5 - 123.3 (54.0)" "0.2 - 169.3 (30.6)" 
[1] "hr="     "9100000"
D25V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 26(6Q27) MUTATED         1        2         0        0         1
  AMP PEAK 26(6Q27) WILD-TYPE     281       48       111        2        45
                             vv
clus                          STAGE IVC
  AMP PEAK 26(6Q27) MUTATED           0
  AMP PEAK 26(6Q27) WILD-TYPE         6
D25V3, multiclass
           clus
vv          AMP PEAK 26(6Q27) MUTATED AMP PEAK 26(6Q27) WILD-TYPE
  STAGE I                           1                         281
  STAGE II                          2                          48
  STAGE III                         0                         111
  STAGE IV                          0                           2
  STAGE IVA                         1                          45
  STAGE IVC                         0                           6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK 26(6Q27) MUTATED     0   2   1   1
  AMP PEAK 26(6Q27) WILD-TYPE 142 163 166  22
D25V4, multiclass
    clus
vv   AMP PEAK 26(6Q27) MUTATED AMP PEAK 26(6Q27) WILD-TYPE
  T1                         0                         142
  T2                         2                         163
  T3                         1                         166
  T4                         1                          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"
D25V5, binary
                             cls
clus                            0   1
  AMP PEAK 26(6Q27) MUTATED     2   1
  AMP PEAK 26(6Q27) WILD-TYPE 223 223
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 26(6Q27) MUTATED      2    1
  AMP PEAK 26(6Q27) WILD-TYPE  223  223
   clus
vv  AMP PEAK 26(6Q27) MUTATED AMP PEAK 26(6Q27) WILD-TYPE
  0                         2                         223
  1                         1                         223
[1] 2 2
[1] FALSE
D25V6, binary
                             cls
clus                            0   1
  AMP PEAK 26(6Q27) MUTATED     1   0
  AMP PEAK 26(6Q27) WILD-TYPE 277   9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 26(6Q27) MUTATED      1    0
  AMP PEAK 26(6Q27) WILD-TYPE  277    9
   clus
vv  AMP PEAK 26(6Q27) MUTATED AMP PEAK 26(6Q27) WILD-TYPE
  0                         1                         277
  1                         0                           9
[1] 2 2
[1] FALSE
D25V7, binary
                             cls
clus                            0   1
  AMP PEAK 26(6Q27) MUTATED     4   0
  AMP PEAK 26(6Q27) WILD-TYPE 361 134
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 26(6Q27) MUTATED      4    0
  AMP PEAK 26(6Q27) WILD-TYPE  361  134
        clus
vv       AMP PEAK 26(6Q27) MUTATED AMP PEAK 26(6Q27) WILD-TYPE
  FEMALE                         4                         361
  MALE                           0                         134
[1] 2 2
[1] FALSE
D25V8, binary
                             cls
clus                            0   1
  AMP PEAK 26(6Q27) MUTATED     2   2
  AMP PEAK 26(6Q27) WILD-TYPE 183 288
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 26(6Q27) MUTATED      2    2
  AMP PEAK 26(6Q27) WILD-TYPE  183  288
     clus
vv    AMP PEAK 26(6Q27) MUTATED AMP PEAK 26(6Q27) WILD-TYPE
  NO                          2                         183
  YES                         2                         288
[1] 2 2
[1] FALSE
                             vv
clus                          OTHER  SPECIFY
  AMP PEAK 26(6Q27) MUTATED                0
  AMP PEAK 26(6Q27) WILD-TYPE              8
                             vv
clus                          THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 26(6Q27) MUTATED                                               2
  AMP PEAK 26(6Q27) WILD-TYPE                                           353
                             vv
clus                          THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 26(6Q27) MUTATED                                                                        2
  AMP PEAK 26(6Q27) WILD-TYPE                                                                     98
                             vv
clus                          THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 26(6Q27) MUTATED                                                                     0
  AMP PEAK 26(6Q27) WILD-TYPE                                                                  36
D25V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 26(6Q27) MUTATED
  OTHER  SPECIFY                                                                                 0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                         2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                            0
                                                                        clus
vv                                                                       AMP PEAK 26(6Q27) WILD-TYPE
  OTHER  SPECIFY                                                                                   8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                             36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V10, binary
                             cls
clus                            0   1
  AMP PEAK 26(6Q27) MUTATED     3   1
  AMP PEAK 26(6Q27) WILD-TYPE 417  16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 26(6Q27) MUTATED      3    1
  AMP PEAK 26(6Q27) WILD-TYPE  417   16
     clus
vv    AMP PEAK 26(6Q27) MUTATED AMP PEAK 26(6Q27) WILD-TYPE
  NO                          3                         417
  YES                         1                          16
[1] 2 2
[1] FALSE
                             vv
clus                          MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 26(6Q27) MUTATED              0                       1    3
  AMP PEAK 26(6Q27) WILD-TYPE          132                      17  327
                             vv
clus                          VERY ADVANCED (T4B)
  AMP PEAK 26(6Q27) MUTATED                     0
  AMP PEAK 26(6Q27) WILD-TYPE                   1
D25V11, multiclass
                         clus
vv                        AMP PEAK 26(6Q27) MUTATED AMP PEAK 26(6Q27) WILD-TYPE
  MINIMAL (T3)                                    0                         132
  MODERATE/ADVANCED (T4A)                         1                          17
  NONE                                            3                         327
  VERY ADVANCED (T4B)                             0                           1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK 26(6Q27) MUTATED     3   0   0   1
  AMP PEAK 26(6Q27) WILD-TYPE 380  51   4  29
D25V12, multiclass
    clus
vv   AMP PEAK 26(6Q27) MUTATED AMP PEAK 26(6Q27) WILD-TYPE
  R0                         3                         380
  R1                         0                          51
  R2                         0                           4
  RX                         1                          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"
D25V13, continuous
D25V14, binary
                             cls
clus                            0   1
  AMP PEAK 26(6Q27) MUTATED     0   4
  AMP PEAK 26(6Q27) WILD-TYPE 225 260
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 26(6Q27) MUTATED      0    4
  AMP PEAK 26(6Q27) WILD-TYPE  225  260
            clus
vv           AMP PEAK 26(6Q27) MUTATED AMP PEAK 26(6Q27) WILD-TYPE
  MULTIFOCAL                         0                         225
  UNIFOCAL                           4                         260
[1] 2 2
[1] FALSE
D25V15, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 26(6Q27) MUTATED                                  0     0
  AMP PEAK 26(6Q27) WILD-TYPE                                1    52
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 26(6Q27) MUTATED                           0     3
  AMP PEAK 26(6Q27) WILD-TYPE                        27   325
D25V16, multiclass
                                  clus
vv                                 AMP PEAK 26(6Q27) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                0
  WHITE                                                    3
                                  clus
vv                                 AMP PEAK 26(6Q27) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     52
  BLACK OR AFRICAN AMERICAN                                 27
  WHITE                                                    325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V17, binary
                             cls
clus                            0   1
  AMP PEAK 26(6Q27) MUTATED     0   3
  AMP PEAK 26(6Q27) WILD-TYPE  38 356
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 26(6Q27) MUTATED      0    3
  AMP PEAK 26(6Q27) WILD-TYPE   38  356
                        clus
vv                       AMP PEAK 26(6Q27) MUTATED AMP PEAK 26(6Q27) WILD-TYPE
  HISPANIC OR LATINO                             0                          38
  NOT HISPANIC OR LATINO                         3                         356
[1] 2 2
[1] FALSE

Clustering(26) Variable = AMP PEAK 27(7Q11.21) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 27(7Q11.21) MUTATED    19   1
  AMP PEAK 27(7Q11.21) WILD-TYPE 462  15
  AMP PEAK 27(7Q11.21) MUTATED AMP PEAK 27(7Q11.21) WILD-TYPE 
                            20                            477 
  AMP PEAK 27(7Q11.21) MUTATED AMP PEAK 27(7Q11.21) WILD-TYPE 
                             1                             15 
$`AMP PEAK 27(7Q11.21) MUTATED`
TCGA-BJ-A190 TCGA-BJ-A2N9 TCGA-BJ-A45E TCGA-DJ-A2Q0 TCGA-E8-A416 TCGA-EL-A3T9 
       20.58        20.48        21.01        34.36         0.72         5.72 
TCGA-EL-A3ZM TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY 
       36.03        78.61        57.01        10.65         6.05        32.32 
TCGA-EM-A3AI TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FY-A3BL 
       22.52         9.24        13.51        37.25       123.32        20.42 
TCGA-FY-A3I5 TCGA-FY-A3NM 
        7.82         0.99 

$`AMP PEAK 27(7Q11.21) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        42.08        51.39        41.52         4.83        44.35 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
       42.15        21.04        35.54        32.45        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
       11.08        30.21        22.88        18.38        16.57        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
        7.99        10.88         3.45        23.84        28.44        15.45 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
       21.63        23.18        19.43        23.47        12.66        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.66        35.84        21.63        50.17        37.64        15.85 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O 
       14.70        14.27         2.76         9.96        48.79        38.17 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      169.32        18.58         8.71        56.19        23.38        43.17 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       52.37         8.32        11.01       135.91        30.61        44.98 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
       42.51        14.96        17.59         6.02        42.58        47.41 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
       17.56        10.09         7.82        30.58        35.41        27.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
       26.20        38.83        33.96        31.99        34.85        28.96 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.78         8.42        37.74         6.77        40.24        33.93 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
       37.48        36.46        35.11        39.09        35.90        33.53 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       35.18        15.88        36.92        31.04        32.42        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU 
       16.41        19.56        36.33        32.81        36.33        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       59.57        11.34        35.87        40.96        36.99        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        42.54        19.20        23.21        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       24.82        22.92        21.01        18.97         7.76        35.67 
TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        3.12        36.43        24.76        17.23        27.62        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       21.34        33.04        34.78        27.06        26.93        35.54 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        35.38        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       92.55        47.21        66.38        80.52        63.19        52.44 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       39.95        31.23        35.67        31.27        29.98        31.50 
TCGA-E8-A415 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 
       31.04         0.26         3.02        25.45        30.61         0.16 
TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M 
        0.23        14.96         7.69        33.50         0.39         0.39 
TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR 
       31.66        26.73       155.54        97.74       158.83         7.66 
TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX 
       45.53        60.95       157.15        37.94        57.01       106.62 
TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 
        4.18        79.50       139.86        98.53        69.57        57.11 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS 
      108.36        64.87        49.51        50.24       115.10        65.39 
TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
      136.01        50.37        50.20       147.75       101.13       139.99 
TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
       49.32        33.50        43.36        49.71        83.57       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 
      150.48       108.66        57.63        17.52        52.50        29.65 
TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
      147.42       142.52       129.57        32.48       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
       41.29       107.47        66.90        82.82        89.56        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       51.78        62.30        53.06        47.38        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       60.16         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        47.84        43.59        24.30        27.06        23.90 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       19.46        54.08        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       14.53        44.19        41.29        14.24        47.57        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU 
       13.18        23.51         2.99        12.30        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        40.34        19.73        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       17.29        14.60        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        29.72        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA 
       15.02        14.50        15.06         7.33         0.49        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.66        38.86        29.95        29.85        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        63.45        88.41        58.75        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       83.34         2.66        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
      108.46        84.89       100.57        95.34        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       98.20        28.24        50.40        79.10        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       87.62        77.82        75.42        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       94.59        84.85        80.58        66.84        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      166.62        24.72        43.99        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        13.28         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 
       48.10       116.09         1.25        17.82        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08         0.30         0.76 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16         6.58        22.49        19.04 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35        21.60         1.68        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46         2.99        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       18.51        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       17.23        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY 
       24.69        22.29         5.75         2.47         2.60         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.40        40.37        21.83         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       30.21        23.93        12.89 

  AMP PEAK 27(7Q11.21) MUTATED AMP PEAK 27(7Q11.21) WILD-TYPE 
                          0.72                           0.16 
  AMP PEAK 27(7Q11.21) MUTATED AMP PEAK 27(7Q11.21) WILD-TYPE 
                        123.32                         169.32 
  AMP PEAK 27(7Q11.21) MUTATED AMP PEAK 27(7Q11.21) WILD-TYPE 
                         20.53                          30.94 
[1] "0.7 - 123.3 (20.5)" "0.2 - 169.3 (30.9)"
[1] "hr=" "2.3"
D26V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 27(7Q11.21) MUTATED         9        6         3        1         1
  AMP PEAK 27(7Q11.21) WILD-TYPE     273       44       108        1        45
                                vv
clus                             STAGE IVC
  AMP PEAK 27(7Q11.21) MUTATED           0
  AMP PEAK 27(7Q11.21) WILD-TYPE         6
D26V3, multiclass
           clus
vv          AMP PEAK 27(7Q11.21) MUTATED AMP PEAK 27(7Q11.21) WILD-TYPE
  STAGE I                              9                            273
  STAGE II                             6                             44
  STAGE III                            3                            108
  STAGE IV                             1                              1
  STAGE IVA                            1                             45
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 27(7Q11.21) MUTATED     6   7   5   2
  AMP PEAK 27(7Q11.21) WILD-TYPE 136 158 162  21
D26V4, multiclass
    clus
vv   AMP PEAK 27(7Q11.21) MUTATED AMP PEAK 27(7Q11.21) WILD-TYPE
  T1                            6                            136
  T2                            7                            158
  T3                            5                            162
  T4                            2                             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"
D26V5, binary
                                cls
clus                               0   1
  AMP PEAK 27(7Q11.21) MUTATED    13   2
  AMP PEAK 27(7Q11.21) WILD-TYPE 212 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(7Q11.21) MUTATED     13    2
  AMP PEAK 27(7Q11.21) WILD-TYPE  212  222
   clus
vv  AMP PEAK 27(7Q11.21) MUTATED AMP PEAK 27(7Q11.21) WILD-TYPE
  0                           13                            212
  1                            2                            222
[1] 2 2
[1] FALSE
D26V6, binary
                                cls
clus                               0   1
  AMP PEAK 27(7Q11.21) MUTATED     6   0
  AMP PEAK 27(7Q11.21) WILD-TYPE 272   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(7Q11.21) MUTATED      6    0
  AMP PEAK 27(7Q11.21) WILD-TYPE  272    9
   clus
vv  AMP PEAK 27(7Q11.21) MUTATED AMP PEAK 27(7Q11.21) WILD-TYPE
  0                            6                            272
  1                            0                              9
[1] 2 2
[1] FALSE
D26V7, binary
                                cls
clus                               0   1
  AMP PEAK 27(7Q11.21) MUTATED    14   6
  AMP PEAK 27(7Q11.21) WILD-TYPE 351 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(7Q11.21) MUTATED     14    6
  AMP PEAK 27(7Q11.21) WILD-TYPE  351  128
        clus
vv       AMP PEAK 27(7Q11.21) MUTATED AMP PEAK 27(7Q11.21) WILD-TYPE
  FEMALE                           14                            351
  MALE                              6                            128
[1] 2 2
[1] FALSE
D26V8, binary
                                cls
clus                               0   1
  AMP PEAK 27(7Q11.21) MUTATED     7   9
  AMP PEAK 27(7Q11.21) WILD-TYPE 178 281
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(7Q11.21) MUTATED      7    9
  AMP PEAK 27(7Q11.21) WILD-TYPE  178  281
     clus
vv    AMP PEAK 27(7Q11.21) MUTATED AMP PEAK 27(7Q11.21) WILD-TYPE
  NO                             7                            178
  YES                            9                            281
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 27(7Q11.21) MUTATED                0
  AMP PEAK 27(7Q11.21) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 27(7Q11.21) MUTATED                                              11
  AMP PEAK 27(7Q11.21) WILD-TYPE                                           344
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 27(7Q11.21) MUTATED                                                                        9
  AMP PEAK 27(7Q11.21) WILD-TYPE                                                                     91
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 27(7Q11.21) MUTATED                                                                     0
  AMP PEAK 27(7Q11.21) WILD-TYPE                                                                  36
D26V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 27(7Q11.21) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    11
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            9
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       AMP PEAK 27(7Q11.21) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     344
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             91
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V10, binary
                                cls
clus                               0   1
  AMP PEAK 27(7Q11.21) MUTATED    16   0
  AMP PEAK 27(7Q11.21) WILD-TYPE 404  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(7Q11.21) MUTATED     16    0
  AMP PEAK 27(7Q11.21) WILD-TYPE  404   17
     clus
vv    AMP PEAK 27(7Q11.21) MUTATED AMP PEAK 27(7Q11.21) WILD-TYPE
  NO                            16                            404
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 27(7Q11.21) MUTATED              1                       1   16
  AMP PEAK 27(7Q11.21) WILD-TYPE          131                      17  314
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 27(7Q11.21) MUTATED                     1
  AMP PEAK 27(7Q11.21) WILD-TYPE                   0
D26V11, multiclass
                         clus
vv                        AMP PEAK 27(7Q11.21) MUTATED
  MINIMAL (T3)                                       1
  MODERATE/ADVANCED (T4A)                            1
  NONE                                              16
  VERY ADVANCED (T4B)                                1
                         clus
vv                        AMP PEAK 27(7Q11.21) WILD-TYPE
  MINIMAL (T3)                                       131
  MODERATE/ADVANCED (T4A)                             17
  NONE                                               314
  VERY ADVANCED (T4B)                                  0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 27(7Q11.21) MUTATED    14   3   0   2
  AMP PEAK 27(7Q11.21) WILD-TYPE 369  48   4  28
D26V12, multiclass
    clus
vv   AMP PEAK 27(7Q11.21) MUTATED AMP PEAK 27(7Q11.21) WILD-TYPE
  R0                           14                            369
  R1                            3                             48
  R2                            0                              4
  RX                            2                             28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V13, continuous
D26V14, binary
                                cls
clus                               0   1
  AMP PEAK 27(7Q11.21) MUTATED     8  11
  AMP PEAK 27(7Q11.21) WILD-TYPE 217 253
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(7Q11.21) MUTATED      8   11
  AMP PEAK 27(7Q11.21) WILD-TYPE  217  253
            clus
vv           AMP PEAK 27(7Q11.21) MUTATED AMP PEAK 27(7Q11.21) WILD-TYPE
  MULTIFOCAL                            8                            217
  UNIFOCAL                             11                            253
[1] 2 2
[1] FALSE
D26V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 27(7Q11.21) MUTATED                                  0     1
  AMP PEAK 27(7Q11.21) WILD-TYPE                                1    51
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 27(7Q11.21) MUTATED                           0    11
  AMP PEAK 27(7Q11.21) WILD-TYPE                        27   317
D26V16, multiclass
                                  clus
vv                                 AMP PEAK 27(7Q11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                      11
                                  clus
vv                                 AMP PEAK 27(7Q11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        51
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       317
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V17, binary
                                cls
clus                               0   1
  AMP PEAK 27(7Q11.21) MUTATED     0  12
  AMP PEAK 27(7Q11.21) WILD-TYPE  38 347
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(7Q11.21) MUTATED      0   12
  AMP PEAK 27(7Q11.21) WILD-TYPE   38  347
                        clus
vv                       AMP PEAK 27(7Q11.21) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           12
                        clus
vv                       AMP PEAK 27(7Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            347
[1] 2 2
[1] FALSE

Clustering(27) Variable = AMP PEAK 28(7Q21.11) MUTATION ANALYSIS
D27V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 28(7Q21.11) MUTATED    20   1
  AMP PEAK 28(7Q21.11) WILD-TYPE 461  15
  AMP PEAK 28(7Q21.11) MUTATED AMP PEAK 28(7Q21.11) WILD-TYPE 
                            21                            476 
  AMP PEAK 28(7Q21.11) MUTATED AMP PEAK 28(7Q21.11) WILD-TYPE 
                             1                             15 
$`AMP PEAK 28(7Q21.11) MUTATED`
TCGA-BJ-A190 TCGA-BJ-A2N9 TCGA-BJ-A45E TCGA-DJ-A2PN TCGA-DJ-A2Q0 TCGA-EL-A3T9 
       20.58        20.48        21.01        10.09        34.36         5.72 
TCGA-EL-A3ZM TCGA-EL-A4K7 TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO 
       36.03        41.13        78.61        57.01        10.65         6.05 
TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N 
       32.32        22.52         9.24        13.51        37.25       123.32 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3WA 
        7.82         0.99        17.06 

$`AMP PEAK 28(7Q21.11) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        42.08        51.39        41.52         4.83        44.35 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
       42.15        21.04        35.54        32.45        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
       11.08        30.21        22.88        18.38        16.57        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
        7.99        10.88         3.45        23.84        28.44        15.45 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
       21.63        23.18        19.43        23.47        12.66        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.66        35.84        21.63        50.17        37.64        15.85 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O 
       14.70        14.27         2.76         9.96        48.79        38.17 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      169.32        18.58         8.71        56.19        23.38        43.17 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       52.37         8.32        11.01       135.91        30.61        44.98 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
       42.51        14.96        17.59         6.02        42.58        47.41 
TCGA-DJ-A1QQ TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS 
       17.56         7.82        30.58        35.41        27.45        26.20 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY 
       38.83        33.96        31.99        34.85        28.96         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
        8.42        37.74         6.77        40.24        33.93        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        35.11        39.09        35.90        33.53        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       15.88        36.92        31.04        32.42        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW 
       19.56        36.33        32.81        36.33        17.69        59.57 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       11.34        35.87        40.96        36.99        20.22        30.61 
TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       42.54        19.20        23.21        21.27        20.48        24.82 
TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI 
       22.92        21.01        18.97         7.76        35.67         3.12 
TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       36.43        24.76        17.23        27.62        30.87        21.34 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       47.21        66.38        80.52        63.19        52.44        39.95 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
       31.23        35.67        31.27        29.98        31.50        31.04 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 
        0.72         0.26         3.02        25.45        30.61         0.16 
TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M 
        0.23        14.96         7.69        33.50         0.39         0.39 
TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR 
       31.66        26.73       155.54        97.74       158.83         7.66 
TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX 
       45.53        60.95       157.15        37.94        57.01       106.62 
TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 
        4.18        79.50       139.86        98.53        69.57        57.11 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS 
      108.36        64.87        49.51        50.24       115.10        65.39 
TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
      136.01        50.37        50.20       147.75       101.13       139.99 
TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
       49.32        33.50        43.36        49.71        83.57       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 
      150.48       108.66        57.63        17.52        52.50        29.65 
TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
      147.42       142.52       129.57        32.48       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
       41.29       107.47        66.90        82.82        89.56        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       51.78        62.30        53.06        47.38        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       60.16         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       47.84        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       54.08        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       44.19        41.29        14.24        47.57        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
       23.51         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       40.34        19.73        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       14.60        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB 
       14.50        15.06         7.33         0.49        13.91        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       38.86        29.95        29.85        12.79        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
       21.34         5.33        26.37        26.37        22.45        21.53 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       60.49        24.46        13.68        81.93        81.70        77.56 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       70.42        56.58        60.20        63.39        65.29        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       63.45        88.41        58.75        52.60        54.35        83.34 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89       100.57        95.34        94.13        55.10        98.20 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24        50.40        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       77.82        75.42        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       71.08         4.11         1.05        13.28         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 
      116.09         1.25        20.42        17.82        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08         0.30         0.76 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83        31.10         8.22        25.64        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       23.93        12.89 

  AMP PEAK 28(7Q21.11) MUTATED AMP PEAK 28(7Q21.11) WILD-TYPE 
                          0.99                           0.16 
  AMP PEAK 28(7Q21.11) MUTATED AMP PEAK 28(7Q21.11) WILD-TYPE 
                        123.32                         169.32 
  AMP PEAK 28(7Q21.11) MUTATED AMP PEAK 28(7Q21.11) WILD-TYPE 
                        20.580                         30.905 
[1] "1.0 - 123.3 (20.6)" "0.2 - 169.3 (30.9)"
[1] "hr=" "2.1"
D27V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 28(7Q21.11) MUTATED         9        6         4        1         1
  AMP PEAK 28(7Q21.11) WILD-TYPE     273       44       107        1        45
                                vv
clus                             STAGE IVC
  AMP PEAK 28(7Q21.11) MUTATED           0
  AMP PEAK 28(7Q21.11) WILD-TYPE         6
D27V3, multiclass
           clus
vv          AMP PEAK 28(7Q21.11) MUTATED AMP PEAK 28(7Q21.11) WILD-TYPE
  STAGE I                              9                            273
  STAGE II                             6                             44
  STAGE III                            4                            107
  STAGE IV                             1                              1
  STAGE IVA                            1                             45
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 28(7Q21.11) MUTATED     6   8   5   2
  AMP PEAK 28(7Q21.11) WILD-TYPE 136 157 162  21
D27V4, multiclass
    clus
vv   AMP PEAK 28(7Q21.11) MUTATED AMP PEAK 28(7Q21.11) WILD-TYPE
  T1                            6                            136
  T2                            8                            157
  T3                            5                            162
  T4                            2                             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"
D27V5, binary
                                cls
clus                               0   1
  AMP PEAK 28(7Q21.11) MUTATED    13   3
  AMP PEAK 28(7Q21.11) WILD-TYPE 212 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(7Q21.11) MUTATED     13    3
  AMP PEAK 28(7Q21.11) WILD-TYPE  212  221
   clus
vv  AMP PEAK 28(7Q21.11) MUTATED AMP PEAK 28(7Q21.11) WILD-TYPE
  0                           13                            212
  1                            3                            221
[1] 2 2
[1] FALSE
D27V6, binary
                                cls
clus                               0   1
  AMP PEAK 28(7Q21.11) MUTATED     6   0
  AMP PEAK 28(7Q21.11) WILD-TYPE 272   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(7Q21.11) MUTATED      6    0
  AMP PEAK 28(7Q21.11) WILD-TYPE  272    9
   clus
vv  AMP PEAK 28(7Q21.11) MUTATED AMP PEAK 28(7Q21.11) WILD-TYPE
  0                            6                            272
  1                            0                              9
[1] 2 2
[1] FALSE
D27V7, binary
                                cls
clus                               0   1
  AMP PEAK 28(7Q21.11) MUTATED    15   6
  AMP PEAK 28(7Q21.11) WILD-TYPE 350 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(7Q21.11) MUTATED     15    6
  AMP PEAK 28(7Q21.11) WILD-TYPE  350  128
        clus
vv       AMP PEAK 28(7Q21.11) MUTATED AMP PEAK 28(7Q21.11) WILD-TYPE
  FEMALE                           15                            350
  MALE                              6                            128
[1] 2 2
[1] FALSE
D27V8, binary
                                cls
clus                               0   1
  AMP PEAK 28(7Q21.11) MUTATED     9   9
  AMP PEAK 28(7Q21.11) WILD-TYPE 176 281
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(7Q21.11) MUTATED      9    9
  AMP PEAK 28(7Q21.11) WILD-TYPE  176  281
     clus
vv    AMP PEAK 28(7Q21.11) MUTATED AMP PEAK 28(7Q21.11) WILD-TYPE
  NO                             9                            176
  YES                            9                            281
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 28(7Q21.11) MUTATED                0
  AMP PEAK 28(7Q21.11) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 28(7Q21.11) MUTATED                                              11
  AMP PEAK 28(7Q21.11) WILD-TYPE                                           344
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 28(7Q21.11) MUTATED                                                                       10
  AMP PEAK 28(7Q21.11) WILD-TYPE                                                                     90
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 28(7Q21.11) MUTATED                                                                     0
  AMP PEAK 28(7Q21.11) WILD-TYPE                                                                  36
D27V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 28(7Q21.11) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    11
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           10
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       AMP PEAK 28(7Q21.11) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     344
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             90
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V10, binary
                                cls
clus                               0   1
  AMP PEAK 28(7Q21.11) MUTATED    19   0
  AMP PEAK 28(7Q21.11) WILD-TYPE 401  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(7Q21.11) MUTATED     19    0
  AMP PEAK 28(7Q21.11) WILD-TYPE  401   17
     clus
vv    AMP PEAK 28(7Q21.11) MUTATED AMP PEAK 28(7Q21.11) WILD-TYPE
  NO                            19                            401
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 28(7Q21.11) MUTATED              2                       1   16
  AMP PEAK 28(7Q21.11) WILD-TYPE          130                      17  314
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 28(7Q21.11) MUTATED                     1
  AMP PEAK 28(7Q21.11) WILD-TYPE                   0
D27V11, multiclass
                         clus
vv                        AMP PEAK 28(7Q21.11) MUTATED
  MINIMAL (T3)                                       2
  MODERATE/ADVANCED (T4A)                            1
  NONE                                              16
  VERY ADVANCED (T4B)                                1
                         clus
vv                        AMP PEAK 28(7Q21.11) WILD-TYPE
  MINIMAL (T3)                                       130
  MODERATE/ADVANCED (T4A)                             17
  NONE                                               314
  VERY ADVANCED (T4B)                                  0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 28(7Q21.11) MUTATED    15   3   0   2
  AMP PEAK 28(7Q21.11) WILD-TYPE 368  48   4  28
D27V12, multiclass
    clus
vv   AMP PEAK 28(7Q21.11) MUTATED AMP PEAK 28(7Q21.11) WILD-TYPE
  R0                           15                            368
  R1                            3                             48
  R2                            0                              4
  RX                            2                             28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V13, continuous
D27V14, binary
                                cls
clus                               0   1
  AMP PEAK 28(7Q21.11) MUTATED     8  13
  AMP PEAK 28(7Q21.11) WILD-TYPE 217 251
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(7Q21.11) MUTATED      8   13
  AMP PEAK 28(7Q21.11) WILD-TYPE  217  251
            clus
vv           AMP PEAK 28(7Q21.11) MUTATED AMP PEAK 28(7Q21.11) WILD-TYPE
  MULTIFOCAL                            8                            217
  UNIFOCAL                             13                            251
[1] 2 2
[1] FALSE
D27V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 28(7Q21.11) MUTATED                                  0     0
  AMP PEAK 28(7Q21.11) WILD-TYPE                                1    52
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 28(7Q21.11) MUTATED                           0    13
  AMP PEAK 28(7Q21.11) WILD-TYPE                        27   315
D27V16, multiclass
                                  clus
vv                                 AMP PEAK 28(7Q21.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                      13
                                  clus
vv                                 AMP PEAK 28(7Q21.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        52
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       315
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V17, binary
                                cls
clus                               0   1
  AMP PEAK 28(7Q21.11) MUTATED     0  13
  AMP PEAK 28(7Q21.11) WILD-TYPE  38 346
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(7Q21.11) MUTATED      0   13
  AMP PEAK 28(7Q21.11) WILD-TYPE   38  346
                        clus
vv                       AMP PEAK 28(7Q21.11) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           13
                        clus
vv                       AMP PEAK 28(7Q21.11) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            346
[1] 2 2
[1] FALSE

Clustering(28) Variable = AMP PEAK 29(7Q31.1) MUTATION ANALYSIS
D28V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 29(7Q31.1) MUTATED    21   1
  AMP PEAK 29(7Q31.1) WILD-TYPE 460  15
  AMP PEAK 29(7Q31.1) MUTATED AMP PEAK 29(7Q31.1) WILD-TYPE 
                           22                           475 
  AMP PEAK 29(7Q31.1) MUTATED AMP PEAK 29(7Q31.1) WILD-TYPE 
                            1                            15 
$`AMP PEAK 29(7Q31.1) MUTATED`
TCGA-BJ-A190 TCGA-BJ-A192 TCGA-BJ-A2N9 TCGA-BJ-A45E TCGA-DJ-A2Q0 TCGA-EL-A3T9 
       20.58        44.35        20.48        21.01        34.36         5.72 
TCGA-EL-A3ZM TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CJ TCGA-EM-A2CO 
       36.03        78.61        57.01        10.65        47.57         6.05 
TCGA-EM-A2CQ TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A2MZ 
       12.30        32.32        22.52         9.24        13.51        37.25 
TCGA-ET-A39N TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-KS-A4I3 
      123.32         7.82         0.99        43.69 

$`AMP PEAK 29(7Q31.1) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A28R 
       15.12        42.08        51.39        41.52         4.83        42.15 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04        35.54        32.45        11.31        30.97        11.08 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA TCGA-BJ-A2P4 
       30.21        22.88        18.38        16.57        18.97         7.04 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.01        13.94        36.39        23.31        18.64         7.99 
TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J 
       10.88         3.45        23.84        28.44        15.45        21.63 
TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD 
       23.18        19.43        23.47        12.66        12.30        12.79 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 
       12.46        11.38        10.68        15.02        12.43        12.66 
TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       35.84        21.63        50.17        37.64        15.85        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.27         2.76         9.96        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        23.38        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        11.01       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS 
       10.09         7.82        30.58        35.41        27.45        26.20 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY 
       38.83        33.96        31.99        34.85        28.96         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
        8.42        37.74         6.77        40.24        33.93        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        35.11        39.09        35.90        33.53        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       15.88        36.92        31.04        32.42        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW 
       19.56        36.33        32.81        36.33        17.69        59.57 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       11.34        35.87        40.96        36.99        20.22        30.61 
TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       42.54        19.20        23.21        21.27        20.48        24.82 
TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI 
       22.92        21.01        18.97         7.76        35.67         3.12 
TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       36.43        24.76        17.23        27.62        30.87        21.34 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       47.21        66.38        80.52        63.19        52.44        39.95 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
       31.23        35.67        31.27        29.98        31.50        31.04 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 
        0.72         0.26         3.02        25.45        30.61         0.16 
TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M 
        0.23        14.96         7.69        33.50         0.39         0.39 
TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR 
       31.66        26.73       155.54        97.74       158.83         7.66 
TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX 
       45.53        60.95       157.15        37.94        57.01       106.62 
TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 
        4.18        79.50       139.86        98.53        69.57        57.11 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS 
      108.36        64.87        49.51        50.24       115.10        65.39 
TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
      136.01        50.37        50.20       147.75       101.13       139.99 
TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
       49.32        33.50        43.36        49.71        83.57       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 
      150.48       108.66        57.63        17.52        52.50        29.65 
TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
      147.42       142.52       129.57        32.48       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
       41.29       107.47        66.90        82.82        89.56        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       51.78        62.30        53.06        47.38        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       60.16         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        47.84        43.59        24.30        27.06        23.90 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       19.46        54.08        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CK TCGA-EM-A2CL 
       14.53        44.19        41.29        14.24        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
       23.51         2.99        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       19.73        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
       15.06         7.33         0.49        13.91        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       29.95        29.85        12.79        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        5.33        26.37        26.37        22.45        21.53        60.49 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       24.46        13.68        81.93        81.70        77.56        70.42 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       56.58        60.20        63.39        65.29        18.38        63.45 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       88.41        58.75        52.60        54.35        83.34         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       80.88        33.24       106.09       107.41       108.46        84.89 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
      100.57        95.34        94.13        55.10        98.20        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
       50.40        79.10        76.64         5.79        87.62        77.82 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       75.42        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       117.40        66.77       112.80        39.95        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.11         1.05        13.28         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        1.25        20.42        17.82        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83        31.10         8.22        25.64        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.98        15.68       113.85        26.70        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        23.93 
TCGA-QD-A8IV 
       12.89 

  AMP PEAK 29(7Q31.1) MUTATED AMP PEAK 29(7Q31.1) WILD-TYPE 
                         0.99                          0.16 
  AMP PEAK 29(7Q31.1) MUTATED AMP PEAK 29(7Q31.1) WILD-TYPE 
                       123.32                        169.32 
  AMP PEAK 29(7Q31.1) MUTATED AMP PEAK 29(7Q31.1) WILD-TYPE 
                       21.765                        30.610 
[1] "1.0 - 123.3 (21.8)" "0.2 - 169.3 (30.6)"
[1] "hr=" "1.9"
D28V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 29(7Q31.1) MUTATED        10        6         4        1         1
  AMP PEAK 29(7Q31.1) WILD-TYPE     272       44       107        1        45
                               vv
clus                            STAGE IVC
  AMP PEAK 29(7Q31.1) MUTATED           0
  AMP PEAK 29(7Q31.1) WILD-TYPE         6
D28V3, multiclass
           clus
vv          AMP PEAK 29(7Q31.1) MUTATED AMP PEAK 29(7Q31.1) WILD-TYPE
  STAGE I                            10                           272
  STAGE II                            6                            44
  STAGE III                           4                           107
  STAGE IV                            1                             1
  STAGE IVA                           1                            45
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 29(7Q31.1) MUTATED     6   7   7   2
  AMP PEAK 29(7Q31.1) WILD-TYPE 136 158 160  21
D28V4, multiclass
    clus
vv   AMP PEAK 29(7Q31.1) MUTATED AMP PEAK 29(7Q31.1) WILD-TYPE
  T1                           6                           136
  T2                           7                           158
  T3                           7                           160
  T4                           2                            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"
D28V5, binary
                               cls
clus                              0   1
  AMP PEAK 29(7Q31.1) MUTATED    12   4
  AMP PEAK 29(7Q31.1) WILD-TYPE 213 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 29(7Q31.1) MUTATED     12    4
  AMP PEAK 29(7Q31.1) WILD-TYPE  213  220
   clus
vv  AMP PEAK 29(7Q31.1) MUTATED AMP PEAK 29(7Q31.1) WILD-TYPE
  0                          12                           213
  1                           4                           220
[1] 2 2
[1] FALSE
D28V6, binary
                               cls
clus                              0   1
  AMP PEAK 29(7Q31.1) MUTATED     6   0
  AMP PEAK 29(7Q31.1) WILD-TYPE 272   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 29(7Q31.1) MUTATED      6    0
  AMP PEAK 29(7Q31.1) WILD-TYPE  272    9
   clus
vv  AMP PEAK 29(7Q31.1) MUTATED AMP PEAK 29(7Q31.1) WILD-TYPE
  0                           6                           272
  1                           0                             9
[1] 2 2
[1] FALSE
D28V7, binary
                               cls
clus                              0   1
  AMP PEAK 29(7Q31.1) MUTATED    16   6
  AMP PEAK 29(7Q31.1) WILD-TYPE 349 128
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 29(7Q31.1) MUTATED     16    6
  AMP PEAK 29(7Q31.1) WILD-TYPE  349  128
        clus
vv       AMP PEAK 29(7Q31.1) MUTATED AMP PEAK 29(7Q31.1) WILD-TYPE
  FEMALE                          16                           349
  MALE                             6                           128
[1] 2 2
[1] FALSE
D28V8, binary
                               cls
clus                              0   1
  AMP PEAK 29(7Q31.1) MUTATED     9  10
  AMP PEAK 29(7Q31.1) WILD-TYPE 176 280
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 29(7Q31.1) MUTATED      9   10
  AMP PEAK 29(7Q31.1) WILD-TYPE  176  280
     clus
vv    AMP PEAK 29(7Q31.1) MUTATED AMP PEAK 29(7Q31.1) WILD-TYPE
  NO                            9                           176
  YES                          10                           280
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 29(7Q31.1) MUTATED                0
  AMP PEAK 29(7Q31.1) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 29(7Q31.1) MUTATED                                              11
  AMP PEAK 29(7Q31.1) WILD-TYPE                                           344
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 29(7Q31.1) MUTATED                                                                       11
  AMP PEAK 29(7Q31.1) WILD-TYPE                                                                     89
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 29(7Q31.1) MUTATED                                                                     0
  AMP PEAK 29(7Q31.1) WILD-TYPE                                                                  36
D28V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 29(7Q31.1) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   11
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          11
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       AMP PEAK 29(7Q31.1) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    344
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            89
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V10, binary
                               cls
clus                              0   1
  AMP PEAK 29(7Q31.1) MUTATED    20   0
  AMP PEAK 29(7Q31.1) WILD-TYPE 400  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 29(7Q31.1) MUTATED     20    0
  AMP PEAK 29(7Q31.1) WILD-TYPE  400   17
     clus
vv    AMP PEAK 29(7Q31.1) MUTATED AMP PEAK 29(7Q31.1) WILD-TYPE
  NO                           20                           400
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 29(7Q31.1) MUTATED              3                       1   16
  AMP PEAK 29(7Q31.1) WILD-TYPE          129                      17  314
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 29(7Q31.1) MUTATED                     1
  AMP PEAK 29(7Q31.1) WILD-TYPE                   0
D28V11, multiclass
                         clus
vv                        AMP PEAK 29(7Q31.1) MUTATED
  MINIMAL (T3)                                      3
  MODERATE/ADVANCED (T4A)                           1
  NONE                                             16
  VERY ADVANCED (T4B)                               1
                         clus
vv                        AMP PEAK 29(7Q31.1) WILD-TYPE
  MINIMAL (T3)                                      129
  MODERATE/ADVANCED (T4A)                            17
  NONE                                              314
  VERY ADVANCED (T4B)                                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 29(7Q31.1) MUTATED    14   4   0   3
  AMP PEAK 29(7Q31.1) WILD-TYPE 369  47   4  27
D28V12, multiclass
    clus
vv   AMP PEAK 29(7Q31.1) MUTATED AMP PEAK 29(7Q31.1) WILD-TYPE
  R0                          14                           369
  R1                           4                            47
  R2                           0                             4
  RX                           3                            27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V13, continuous
D28V14, binary
                               cls
clus                              0   1
  AMP PEAK 29(7Q31.1) MUTATED    10  12
  AMP PEAK 29(7Q31.1) WILD-TYPE 215 252
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 29(7Q31.1) MUTATED     10   12
  AMP PEAK 29(7Q31.1) WILD-TYPE  215  252
            clus
vv           AMP PEAK 29(7Q31.1) MUTATED AMP PEAK 29(7Q31.1) WILD-TYPE
  MULTIFOCAL                          10                           215
  UNIFOCAL                            12                           252
[1] 2 2
[1] FALSE
D28V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 29(7Q31.1) MUTATED                                  0     1
  AMP PEAK 29(7Q31.1) WILD-TYPE                                1    51
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 29(7Q31.1) MUTATED                           0    11
  AMP PEAK 29(7Q31.1) WILD-TYPE                        27   317
D28V16, multiclass
                                  clus
vv                                 AMP PEAK 29(7Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                     11
                                  clus
vv                                 AMP PEAK 29(7Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       51
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      317
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V17, binary
                               cls
clus                              0   1
  AMP PEAK 29(7Q31.1) MUTATED     0  10
  AMP PEAK 29(7Q31.1) WILD-TYPE  38 349
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 29(7Q31.1) MUTATED      0   10
  AMP PEAK 29(7Q31.1) WILD-TYPE   38  349
                        clus
vv                       AMP PEAK 29(7Q31.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          10
                        clus
vv                       AMP PEAK 29(7Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           349
[1] 2 2
[1] FALSE

Clustering(29) Variable = AMP PEAK 30(7Q34) MUTATION ANALYSIS
D29V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 30(7Q34) MUTATED    21   1
  AMP PEAK 30(7Q34) WILD-TYPE 460  15
  AMP PEAK 30(7Q34) MUTATED AMP PEAK 30(7Q34) WILD-TYPE 
                         22                         475 
  AMP PEAK 30(7Q34) MUTATED AMP PEAK 30(7Q34) WILD-TYPE 
                          1                          15 
$`AMP PEAK 30(7Q34) MUTATED`
TCGA-BJ-A190 TCGA-BJ-A192 TCGA-BJ-A2N9 TCGA-BJ-A45E TCGA-DJ-A2Q0 TCGA-EL-A3T9 
       20.58        44.35        20.48        21.01        34.36         5.72 
TCGA-EL-A3ZM TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CJ TCGA-EM-A2CO 
       36.03        78.61        57.01        10.65        47.57         6.05 
TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N 
       32.32        22.52         9.24        13.51        37.25       123.32 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-J8-A3O1 TCGA-KS-A4ID 
        7.82         0.99        27.19        33.24 

$`AMP PEAK 30(7Q34) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A28R 
       15.12        42.08        51.39        41.52         4.83        42.15 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04        35.54        32.45        11.31        30.97        11.08 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA TCGA-BJ-A2P4 
       30.21        22.88        18.38        16.57        18.97         7.04 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.01        13.94        36.39        23.31        18.64         7.99 
TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J 
       10.88         3.45        23.84        28.44        15.45        21.63 
TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD 
       23.18        19.43        23.47        12.66        12.30        12.79 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 
       12.46        11.38        10.68        15.02        12.43        12.66 
TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       35.84        21.63        50.17        37.64        15.85        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.27         2.76         9.96        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        23.38        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        11.01       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS 
       10.09         7.82        30.58        35.41        27.45        26.20 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY 
       38.83        33.96        31.99        34.85        28.96         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
        8.42        37.74         6.77        40.24        33.93        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        35.11        39.09        35.90        33.53        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       15.88        36.92        31.04        32.42        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW 
       19.56        36.33        32.81        36.33        17.69        59.57 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       11.34        35.87        40.96        36.99        20.22        30.61 
TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       42.54        19.20        23.21        21.27        20.48        24.82 
TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI 
       22.92        21.01        18.97         7.76        35.67         3.12 
TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       36.43        24.76        17.23        27.62        30.87        21.34 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       47.21        66.38        80.52        63.19        52.44        39.95 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
       31.23        35.67        31.27        29.98        31.50        31.04 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 
        0.72         0.26         3.02        25.45        30.61         0.16 
TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M 
        0.23        14.96         7.69        33.50         0.39         0.39 
TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR 
       31.66        26.73       155.54        97.74       158.83         7.66 
TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX 
       45.53        60.95       157.15        37.94        57.01       106.62 
TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 
        4.18        79.50       139.86        98.53        69.57        57.11 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS 
      108.36        64.87        49.51        50.24       115.10        65.39 
TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
      136.01        50.37        50.20       147.75       101.13       139.99 
TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
       49.32        33.50        43.36        49.71        83.57       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 
      150.48       108.66        57.63        17.52        52.50        29.65 
TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
      147.42       142.52       129.57        32.48       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
       41.29       107.47        66.90        82.82        89.56        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       51.78        62.30        53.06        47.38        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       60.16         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        47.84        43.59        24.30        27.06        23.90 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       19.46        54.08        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CK TCGA-EM-A2CL 
       14.53        44.19        41.29        14.24        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
       23.51         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       40.34        19.73        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       14.60        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB 
       14.50        15.06         7.33         0.49        13.91        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       38.86        29.95        29.85        12.79        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
       21.34         5.33        26.37        26.37        22.45        21.53 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       60.49        24.46        13.68        81.93        81.70        77.56 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       70.42        56.58        60.20        63.39        65.29        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       63.45        88.41        58.75        52.60        54.35        83.34 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89       100.57        95.34        94.13        55.10        98.20 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24        50.40        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       77.82        75.42        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       71.08         4.11         1.05        13.28         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 
      116.09         1.25        20.42        17.82        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08         0.30         0.76 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16         6.58        22.49        19.04 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35        21.60         1.68        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46         2.99        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       18.51        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       17.23        43.17        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-L6-A4EP TCGA-L6-A4EQ 
       32.45        87.39        84.72        35.28        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        23.93 
TCGA-QD-A8IV 
       12.89 

  AMP PEAK 30(7Q34) MUTATED AMP PEAK 30(7Q34) WILD-TYPE 
                       0.99                        0.16 
  AMP PEAK 30(7Q34) MUTATED AMP PEAK 30(7Q34) WILD-TYPE 
                     123.32                      169.32 
  AMP PEAK 30(7Q34) MUTATED AMP PEAK 30(7Q34) WILD-TYPE 
                     24.855                      30.610 
[1] "1.0 - 123.3 (24.9)" "0.2 - 169.3 (30.6)"
[1] "hr=" "1.9"
D29V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 30(7Q34) MUTATED        10        6         4        1         1
  AMP PEAK 30(7Q34) WILD-TYPE     272       44       107        1        45
                             vv
clus                          STAGE IVC
  AMP PEAK 30(7Q34) MUTATED           0
  AMP PEAK 30(7Q34) WILD-TYPE         6
D29V3, multiclass
           clus
vv          AMP PEAK 30(7Q34) MUTATED AMP PEAK 30(7Q34) WILD-TYPE
  STAGE I                          10                         272
  STAGE II                          6                          44
  STAGE III                         4                         107
  STAGE IV                          1                           1
  STAGE IVA                         1                          45
  STAGE IVC                         0                           6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK 30(7Q34) MUTATED     6   7   7   2
  AMP PEAK 30(7Q34) WILD-TYPE 136 158 160  21
D29V4, multiclass
    clus
vv   AMP PEAK 30(7Q34) MUTATED AMP PEAK 30(7Q34) WILD-TYPE
  T1                         6                         136
  T2                         7                         158
  T3                         7                         160
  T4                         2                          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"
D29V5, binary
                             cls
clus                            0   1
  AMP PEAK 30(7Q34) MUTATED    13   3
  AMP PEAK 30(7Q34) WILD-TYPE 212 221
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 30(7Q34) MUTATED     13    3
  AMP PEAK 30(7Q34) WILD-TYPE  212  221
   clus
vv  AMP PEAK 30(7Q34) MUTATED AMP PEAK 30(7Q34) WILD-TYPE
  0                        13                         212
  1                         3                         221
[1] 2 2
[1] FALSE
D29V6, binary
                             cls
clus                            0   1
  AMP PEAK 30(7Q34) MUTATED     7   0
  AMP PEAK 30(7Q34) WILD-TYPE 271   9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 30(7Q34) MUTATED      7    0
  AMP PEAK 30(7Q34) WILD-TYPE  271    9
   clus
vv  AMP PEAK 30(7Q34) MUTATED AMP PEAK 30(7Q34) WILD-TYPE
  0                         7                         271
  1                         0                           9
[1] 2 2
[1] FALSE
D29V7, binary
                             cls
clus                            0   1
  AMP PEAK 30(7Q34) MUTATED    17   5
  AMP PEAK 30(7Q34) WILD-TYPE 348 129
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 30(7Q34) MUTATED     17    5
  AMP PEAK 30(7Q34) WILD-TYPE  348  129
        clus
vv       AMP PEAK 30(7Q34) MUTATED AMP PEAK 30(7Q34) WILD-TYPE
  FEMALE                        17                         348
  MALE                           5                         129
[1] 2 2
[1] FALSE
D29V8, binary
                             cls
clus                            0   1
  AMP PEAK 30(7Q34) MUTATED     9  10
  AMP PEAK 30(7Q34) WILD-TYPE 176 280
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 30(7Q34) MUTATED      9   10
  AMP PEAK 30(7Q34) WILD-TYPE  176  280
     clus
vv    AMP PEAK 30(7Q34) MUTATED AMP PEAK 30(7Q34) WILD-TYPE
  NO                          9                         176
  YES                        10                         280
[1] 2 2
[1] FALSE
                             vv
clus                          OTHER  SPECIFY
  AMP PEAK 30(7Q34) MUTATED                0
  AMP PEAK 30(7Q34) WILD-TYPE              8
                             vv
clus                          THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 30(7Q34) MUTATED                                              11
  AMP PEAK 30(7Q34) WILD-TYPE                                           344
                             vv
clus                          THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 30(7Q34) MUTATED                                                                       11
  AMP PEAK 30(7Q34) WILD-TYPE                                                                     89
                             vv
clus                          THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 30(7Q34) MUTATED                                                                     0
  AMP PEAK 30(7Q34) WILD-TYPE                                                                  36
D29V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 30(7Q34) MUTATED
  OTHER  SPECIFY                                                                                 0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                 11
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                        11
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                            0
                                                                        clus
vv                                                                       AMP PEAK 30(7Q34) WILD-TYPE
  OTHER  SPECIFY                                                                                   8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  344
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          89
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                             36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V10, binary
                             cls
clus                            0   1
  AMP PEAK 30(7Q34) MUTATED    20   0
  AMP PEAK 30(7Q34) WILD-TYPE 400  17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 30(7Q34) MUTATED     20    0
  AMP PEAK 30(7Q34) WILD-TYPE  400   17
     clus
vv    AMP PEAK 30(7Q34) MUTATED AMP PEAK 30(7Q34) WILD-TYPE
  NO                         20                         400
  YES                         0                          17
[1] 2 2
[1] FALSE
                             vv
clus                          MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 30(7Q34) MUTATED              2                       1   17
  AMP PEAK 30(7Q34) WILD-TYPE          130                      17  313
                             vv
clus                          VERY ADVANCED (T4B)
  AMP PEAK 30(7Q34) MUTATED                     1
  AMP PEAK 30(7Q34) WILD-TYPE                   0
D29V11, multiclass
                         clus
vv                        AMP PEAK 30(7Q34) MUTATED AMP PEAK 30(7Q34) WILD-TYPE
  MINIMAL (T3)                                    2                         130
  MODERATE/ADVANCED (T4A)                         1                          17
  NONE                                           17                         313
  VERY ADVANCED (T4B)                             1                           0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK 30(7Q34) MUTATED    15   3   0   3
  AMP PEAK 30(7Q34) WILD-TYPE 368  48   4  27
D29V12, multiclass
    clus
vv   AMP PEAK 30(7Q34) MUTATED AMP PEAK 30(7Q34) WILD-TYPE
  R0                        15                         368
  R1                         3                          48
  R2                         0                           4
  RX                         3                          27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V13, continuous
D29V14, binary
                             cls
clus                            0   1
  AMP PEAK 30(7Q34) MUTATED     9  13
  AMP PEAK 30(7Q34) WILD-TYPE 216 251
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 30(7Q34) MUTATED      9   13
  AMP PEAK 30(7Q34) WILD-TYPE  216  251
            clus
vv           AMP PEAK 30(7Q34) MUTATED AMP PEAK 30(7Q34) WILD-TYPE
  MULTIFOCAL                         9                         216
  UNIFOCAL                          13                         251
[1] 2 2
[1] FALSE
D29V15, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 30(7Q34) MUTATED                                  0     0
  AMP PEAK 30(7Q34) WILD-TYPE                                1    52
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 30(7Q34) MUTATED                           0    13
  AMP PEAK 30(7Q34) WILD-TYPE                        27   315
D29V16, multiclass
                                  clus
vv                                 AMP PEAK 30(7Q34) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                0
  WHITE                                                   13
                                  clus
vv                                 AMP PEAK 30(7Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     52
  BLACK OR AFRICAN AMERICAN                                 27
  WHITE                                                    315
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V17, binary
                             cls
clus                            0   1
  AMP PEAK 30(7Q34) MUTATED     1  10
  AMP PEAK 30(7Q34) WILD-TYPE  37 349
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 30(7Q34) MUTATED      1   10
  AMP PEAK 30(7Q34) WILD-TYPE   37  349
                        clus
vv                       AMP PEAK 30(7Q34) MUTATED AMP PEAK 30(7Q34) WILD-TYPE
  HISPANIC OR LATINO                             1                          37
  NOT HISPANIC OR LATINO                        10                         349
[1] 2 2
[1] FALSE

Clustering(30) Variable = AMP PEAK 31(9Q22.31) MUTATION ANALYSIS
D30V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 31(9Q22.31) MUTATED     6   0
  AMP PEAK 31(9Q22.31) WILD-TYPE 475  16
  AMP PEAK 31(9Q22.31) MUTATED AMP PEAK 31(9Q22.31) WILD-TYPE 
                             6                            491 
  AMP PEAK 31(9Q22.31) MUTATED AMP PEAK 31(9Q22.31) WILD-TYPE 
                             0                             16 
$`AMP PEAK 31(9Q22.31) MUTATED`
TCGA-DJ-A2PW TCGA-EL-A4K9 TCGA-EM-A1YD TCGA-ET-A2N4 TCGA-ET-A40Q TCGA-FY-A3I5 
       34.85        47.84        57.01         2.66        46.26         7.82 

$`AMP PEAK 31(9Q22.31) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
       30.58        35.41        27.45        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       31.99        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        30.61         0.16         0.23        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        33.50         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        69.57        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       49.51        50.24       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       150.48       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        89.56        78.97        51.78 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        47.38        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       60.16         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       41.13        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       78.61        54.08        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       14.53        10.65        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
       17.88        13.18        23.51         6.05         2.99        12.30 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       48.46        13.15        22.16        40.34        19.73        32.32 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       33.96        17.59        17.46        17.29        14.60        22.52 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.06         7.33         0.49         9.24        13.91        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.86        29.95        29.85        13.51        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       54.35        83.34        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      108.46        84.89       123.32       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        98.20        28.24        50.40        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.79        87.62        77.82        75.42        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40R TCGA-ET-A40S 
       62.83       166.62        24.72        43.99        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        13.28         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM 
       48.10       116.09         1.25        20.42        17.82         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
        0.30         0.76        17.06        17.36        15.16         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
       22.49        19.04         1.35        21.60         1.68        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46         2.99        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        8.22        25.64        17.23        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
       26.70        43.69        18.64        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       36.10        32.45        30.21        23.93        12.89 

  AMP PEAK 31(9Q22.31) MUTATED AMP PEAK 31(9Q22.31) WILD-TYPE 
                          2.66                           0.16 
  AMP PEAK 31(9Q22.31) MUTATED AMP PEAK 31(9Q22.31) WILD-TYPE 
                         57.01                         169.32 
  AMP PEAK 31(9Q22.31) MUTATED AMP PEAK 31(9Q22.31) WILD-TYPE 
                        40.555                         30.610 
[1] "2.7 - 57.0 (40.6)"  "0.2 - 169.3 (30.6)"
[1] "hr="     "9100000"
D30V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 31(9Q22.31) MUTATED         1        2         3        0         0
  AMP PEAK 31(9Q22.31) WILD-TYPE     281       48       108        2        46
                                vv
clus                             STAGE IVC
  AMP PEAK 31(9Q22.31) MUTATED           0
  AMP PEAK 31(9Q22.31) WILD-TYPE         6
D30V3, multiclass
           clus
vv          AMP PEAK 31(9Q22.31) MUTATED AMP PEAK 31(9Q22.31) WILD-TYPE
  STAGE I                              1                            281
  STAGE II                             2                             48
  STAGE III                            3                            108
  STAGE IV                             0                              2
  STAGE IVA                            0                             46
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 31(9Q22.31) MUTATED     0   2   4   0
  AMP PEAK 31(9Q22.31) WILD-TYPE 142 163 163  23
D30V4, multiclass
    clus
vv   AMP PEAK 31(9Q22.31) MUTATED AMP PEAK 31(9Q22.31) WILD-TYPE
  T1                            0                            142
  T2                            2                            163
  T3                            4                            163
  T4                            0                             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"
D30V5, binary
                                cls
clus                               0   1
  AMP PEAK 31(9Q22.31) MUTATED     4   2
  AMP PEAK 31(9Q22.31) WILD-TYPE 221 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(9Q22.31) MUTATED      4    2
  AMP PEAK 31(9Q22.31) WILD-TYPE  221  222
   clus
vv  AMP PEAK 31(9Q22.31) MUTATED AMP PEAK 31(9Q22.31) WILD-TYPE
  0                            4                            221
  1                            2                            222
[1] 2 2
[1] FALSE
D30V6, binary
                                cls
clus                               0   1
  AMP PEAK 31(9Q22.31) MUTATED     2   0
  AMP PEAK 31(9Q22.31) WILD-TYPE 276   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(9Q22.31) MUTATED      2    0
  AMP PEAK 31(9Q22.31) WILD-TYPE  276    9
   clus
vv  AMP PEAK 31(9Q22.31) MUTATED AMP PEAK 31(9Q22.31) WILD-TYPE
  0                            2                            276
  1                            0                              9
[1] 2 2
[1] FALSE
D30V7, binary
                                cls
clus                               0   1
  AMP PEAK 31(9Q22.31) MUTATED     3   3
  AMP PEAK 31(9Q22.31) WILD-TYPE 362 131
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(9Q22.31) MUTATED      3    3
  AMP PEAK 31(9Q22.31) WILD-TYPE  362  131
        clus
vv       AMP PEAK 31(9Q22.31) MUTATED AMP PEAK 31(9Q22.31) WILD-TYPE
  FEMALE                            3                            362
  MALE                              3                            131
[1] 2 2
[1] FALSE
D30V8, binary
                                cls
clus                               0   1
  AMP PEAK 31(9Q22.31) MUTATED     1   4
  AMP PEAK 31(9Q22.31) WILD-TYPE 184 286
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(9Q22.31) MUTATED      1    4
  AMP PEAK 31(9Q22.31) WILD-TYPE  184  286
     clus
vv    AMP PEAK 31(9Q22.31) MUTATED AMP PEAK 31(9Q22.31) WILD-TYPE
  NO                             1                            184
  YES                            4                            286
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 31(9Q22.31) MUTATED                0
  AMP PEAK 31(9Q22.31) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 31(9Q22.31) MUTATED                                               2
  AMP PEAK 31(9Q22.31) WILD-TYPE                                           353
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 31(9Q22.31) MUTATED                                                                        3
  AMP PEAK 31(9Q22.31) WILD-TYPE                                                                     97
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 31(9Q22.31) MUTATED                                                                     1
  AMP PEAK 31(9Q22.31) WILD-TYPE                                                                  35
D30V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 31(9Q22.31) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               1
                                                                        clus
vv                                                                       AMP PEAK 31(9Q22.31) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             97
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V10, binary
                                cls
clus                               0   1
  AMP PEAK 31(9Q22.31) MUTATED     4   1
  AMP PEAK 31(9Q22.31) WILD-TYPE 416  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(9Q22.31) MUTATED      4    1
  AMP PEAK 31(9Q22.31) WILD-TYPE  416   16
     clus
vv    AMP PEAK 31(9Q22.31) MUTATED AMP PEAK 31(9Q22.31) WILD-TYPE
  NO                             4                            416
  YES                            1                             16
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 31(9Q22.31) MUTATED              3                       0    3
  AMP PEAK 31(9Q22.31) WILD-TYPE          129                      18  327
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 31(9Q22.31) MUTATED                     0
  AMP PEAK 31(9Q22.31) WILD-TYPE                   1
D30V11, multiclass
                         clus
vv                        AMP PEAK 31(9Q22.31) MUTATED
  MINIMAL (T3)                                       3
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               3
  VERY ADVANCED (T4B)                                0
                         clus
vv                        AMP PEAK 31(9Q22.31) WILD-TYPE
  MINIMAL (T3)                                       129
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               327
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 31(9Q22.31) MUTATED     5   0   0   1
  AMP PEAK 31(9Q22.31) WILD-TYPE 378  51   4  29
D30V12, multiclass
    clus
vv   AMP PEAK 31(9Q22.31) MUTATED AMP PEAK 31(9Q22.31) WILD-TYPE
  R0                            5                            378
  R1                            0                             51
  R2                            0                              4
  RX                            1                             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"
D30V13, continuous
D30V14, binary
                                cls
clus                               0   1
  AMP PEAK 31(9Q22.31) MUTATED     5   1
  AMP PEAK 31(9Q22.31) WILD-TYPE 220 263
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(9Q22.31) MUTATED      5    1
  AMP PEAK 31(9Q22.31) WILD-TYPE  220  263
            clus
vv           AMP PEAK 31(9Q22.31) MUTATED AMP PEAK 31(9Q22.31) WILD-TYPE
  MULTIFOCAL                            5                            220
  UNIFOCAL                              1                            263
[1] 2 2
[1] FALSE
D30V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 31(9Q22.31) MUTATED                                  0     0
  AMP PEAK 31(9Q22.31) WILD-TYPE                                1    52
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 31(9Q22.31) MUTATED                           0     5
  AMP PEAK 31(9Q22.31) WILD-TYPE                        27   323
D30V16, multiclass
                                  clus
vv                                 AMP PEAK 31(9Q22.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       5
                                  clus
vv                                 AMP PEAK 31(9Q22.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        52
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       323
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V17, binary
                                cls
clus                               0   1
  AMP PEAK 31(9Q22.31) MUTATED     0   5
  AMP PEAK 31(9Q22.31) WILD-TYPE  38 354
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(9Q22.31) MUTATED      0    5
  AMP PEAK 31(9Q22.31) WILD-TYPE   38  354
                        clus
vv                       AMP PEAK 31(9Q22.31) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            5
                        clus
vv                       AMP PEAK 31(9Q22.31) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            354
[1] 2 2
[1] FALSE

Clustering(31) Variable = AMP PEAK 32(9Q31.1) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 32(9Q31.1) MUTATED     5   1
  AMP PEAK 32(9Q31.1) WILD-TYPE 476  15
  AMP PEAK 32(9Q31.1) MUTATED AMP PEAK 32(9Q31.1) WILD-TYPE 
                            6                           491 
  AMP PEAK 32(9Q31.1) MUTATED AMP PEAK 32(9Q31.1) WILD-TYPE 
                            1                            15 
$`AMP PEAK 32(9Q31.1) MUTATED`
TCGA-DJ-A2PW TCGA-EL-A3CW TCGA-EL-A4K9 TCGA-EM-A1YD TCGA-ET-A40P TCGA-FY-A3I5 
       34.85        57.01        47.84        57.01        43.99         7.82 

$`AMP PEAK 32(9Q31.1) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
       30.58        35.41        27.45        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       31.99        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        30.61         0.16         0.23        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        33.50         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
      157.15        37.94       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       43.59        24.30        27.06        23.90        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        48.49        18.05        19.79        19.46        78.61 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       54.08        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.65        44.19        41.29        14.24        47.57        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       13.18        23.51         6.05         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        40.34        19.73        32.32        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ 
       17.59        17.46        17.29        14.60        22.52        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        33.07        13.38         8.35        29.72 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        47.38        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 
       17.49        17.39        16.18        15.02        14.50        15.06 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33         0.49         9.24        13.91        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       29.95        29.85        13.51        12.79        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
       21.34         5.33        26.37        26.37        22.45        21.53 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       60.49        24.46        13.68        81.93        81.70        77.56 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       70.42        56.58        60.20        63.39        65.29        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       63.45        88.41        58.75        37.25        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       83.34         2.66        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      108.46        84.89       123.32       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        98.20        28.24        50.40        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.79        87.62        77.82        75.42        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
       62.83       166.62        24.72        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        13.28         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM 
       48.10       116.09         1.25        20.42        17.82         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
        0.30         0.76        17.06        17.36        15.16         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
       22.49        19.04         1.35        21.60         1.68        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46         2.99        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        8.22        25.64        17.23        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
       26.70        43.69        18.64        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       36.10        32.45        30.21        23.93        12.89 

  AMP PEAK 32(9Q31.1) MUTATED AMP PEAK 32(9Q31.1) WILD-TYPE 
                         7.82                          0.16 
  AMP PEAK 32(9Q31.1) MUTATED AMP PEAK 32(9Q31.1) WILD-TYPE 
                        57.01                        169.32 
  AMP PEAK 32(9Q31.1) MUTATED AMP PEAK 32(9Q31.1) WILD-TYPE 
                       45.915                        30.580 
[1] "7.8 - 57.0 (45.9)"  "0.2 - 169.3 (30.6)"
[1] "hr=" "4.6"
D31V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 32(9Q31.1) MUTATED         1        2         3        0         0
  AMP PEAK 32(9Q31.1) WILD-TYPE     281       48       108        2        46
                               vv
clus                            STAGE IVC
  AMP PEAK 32(9Q31.1) MUTATED           0
  AMP PEAK 32(9Q31.1) WILD-TYPE         6
D31V3, multiclass
           clus
vv          AMP PEAK 32(9Q31.1) MUTATED AMP PEAK 32(9Q31.1) WILD-TYPE
  STAGE I                             1                           281
  STAGE II                            2                            48
  STAGE III                           3                           108
  STAGE IV                            0                             2
  STAGE IVA                           0                            46
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 32(9Q31.1) MUTATED     0   4   2   0
  AMP PEAK 32(9Q31.1) WILD-TYPE 142 161 165  23
D31V4, multiclass
    clus
vv   AMP PEAK 32(9Q31.1) MUTATED AMP PEAK 32(9Q31.1) WILD-TYPE
  T1                           0                           142
  T2                           4                           161
  T3                           2                           165
  T4                           0                            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"
D31V5, binary
                               cls
clus                              0   1
  AMP PEAK 32(9Q31.1) MUTATED     4   2
  AMP PEAK 32(9Q31.1) WILD-TYPE 221 222
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 32(9Q31.1) MUTATED      4    2
  AMP PEAK 32(9Q31.1) WILD-TYPE  221  222
   clus
vv  AMP PEAK 32(9Q31.1) MUTATED AMP PEAK 32(9Q31.1) WILD-TYPE
  0                           4                           221
  1                           2                           222
[1] 2 2
[1] FALSE
D31V6, binary
                               cls
clus                              0   1
  AMP PEAK 32(9Q31.1) MUTATED     3   0
  AMP PEAK 32(9Q31.1) WILD-TYPE 275   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 32(9Q31.1) MUTATED      3    0
  AMP PEAK 32(9Q31.1) WILD-TYPE  275    9
   clus
vv  AMP PEAK 32(9Q31.1) MUTATED AMP PEAK 32(9Q31.1) WILD-TYPE
  0                           3                           275
  1                           0                             9
[1] 2 2
[1] FALSE
D31V7, binary
                               cls
clus                              0   1
  AMP PEAK 32(9Q31.1) MUTATED     4   2
  AMP PEAK 32(9Q31.1) WILD-TYPE 361 132
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 32(9Q31.1) MUTATED      4    2
  AMP PEAK 32(9Q31.1) WILD-TYPE  361  132
        clus
vv       AMP PEAK 32(9Q31.1) MUTATED AMP PEAK 32(9Q31.1) WILD-TYPE
  FEMALE                           4                           361
  MALE                             2                           132
[1] 2 2
[1] FALSE
D31V8, binary
                               cls
clus                              0   1
  AMP PEAK 32(9Q31.1) MUTATED     2   3
  AMP PEAK 32(9Q31.1) WILD-TYPE 183 287
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 32(9Q31.1) MUTATED      2    3
  AMP PEAK 32(9Q31.1) WILD-TYPE  183  287
     clus
vv    AMP PEAK 32(9Q31.1) MUTATED AMP PEAK 32(9Q31.1) WILD-TYPE
  NO                            2                           183
  YES                           3                           287
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 32(9Q31.1) MUTATED                0
  AMP PEAK 32(9Q31.1) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 32(9Q31.1) MUTATED                                               3
  AMP PEAK 32(9Q31.1) WILD-TYPE                                           352
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 32(9Q31.1) MUTATED                                                                        3
  AMP PEAK 32(9Q31.1) WILD-TYPE                                                                     97
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 32(9Q31.1) MUTATED                                                                     0
  AMP PEAK 32(9Q31.1) WILD-TYPE                                                                  36
D31V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 32(9Q31.1) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       AMP PEAK 32(9Q31.1) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            97
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V10, binary
                               cls
clus                              0   1
  AMP PEAK 32(9Q31.1) MUTATED     5   0
  AMP PEAK 32(9Q31.1) WILD-TYPE 415  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 32(9Q31.1) MUTATED      5    0
  AMP PEAK 32(9Q31.1) WILD-TYPE  415   17
     clus
vv    AMP PEAK 32(9Q31.1) MUTATED AMP PEAK 32(9Q31.1) WILD-TYPE
  NO                            5                           415
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 32(9Q31.1) MUTATED              1                       0    5
  AMP PEAK 32(9Q31.1) WILD-TYPE          131                      18  325
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 32(9Q31.1) MUTATED                     0
  AMP PEAK 32(9Q31.1) WILD-TYPE                   1
D31V11, multiclass
                         clus
vv                        AMP PEAK 32(9Q31.1) MUTATED
  MINIMAL (T3)                                      1
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              5
  VERY ADVANCED (T4B)                               0
                         clus
vv                        AMP PEAK 32(9Q31.1) WILD-TYPE
  MINIMAL (T3)                                      131
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              325
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 32(9Q31.1) MUTATED     6   0   0   0
  AMP PEAK 32(9Q31.1) WILD-TYPE 377  51   4  30
D31V12, multiclass
    clus
vv   AMP PEAK 32(9Q31.1) MUTATED AMP PEAK 32(9Q31.1) WILD-TYPE
  R0                           6                           377
  R1                           0                            51
  R2                           0                             4
  RX                           0                            30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V13, continuous
D31V14, binary
                               cls
clus                              0   1
  AMP PEAK 32(9Q31.1) MUTATED     3   3
  AMP PEAK 32(9Q31.1) WILD-TYPE 222 261
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 32(9Q31.1) MUTATED      3    3
  AMP PEAK 32(9Q31.1) WILD-TYPE  222  261
            clus
vv           AMP PEAK 32(9Q31.1) MUTATED AMP PEAK 32(9Q31.1) WILD-TYPE
  MULTIFOCAL                           3                           222
  UNIFOCAL                             3                           261
[1] 2 2
[1] FALSE
D31V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 32(9Q31.1) MUTATED                                  0     0
  AMP PEAK 32(9Q31.1) WILD-TYPE                                1    52
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 32(9Q31.1) MUTATED                           0     5
  AMP PEAK 32(9Q31.1) WILD-TYPE                        27   323
D31V16, multiclass
                                  clus
vv                                 AMP PEAK 32(9Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      5
                                  clus
vv                                 AMP PEAK 32(9Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       52
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      323
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V17, binary
                               cls
clus                              0   1
  AMP PEAK 32(9Q31.1) MUTATED     0   5
  AMP PEAK 32(9Q31.1) WILD-TYPE  38 354
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 32(9Q31.1) MUTATED      0    5
  AMP PEAK 32(9Q31.1) WILD-TYPE   38  354
                        clus
vv                       AMP PEAK 32(9Q31.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           5
                        clus
vv                       AMP PEAK 32(9Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           354
[1] 2 2
[1] FALSE

Clustering(32) Variable = AMP PEAK 33(9Q34.3) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 33(9Q34.3) MUTATED     7   0
  AMP PEAK 33(9Q34.3) WILD-TYPE 474  16
  AMP PEAK 33(9Q34.3) MUTATED AMP PEAK 33(9Q34.3) WILD-TYPE 
                            7                           490 
  AMP PEAK 33(9Q34.3) MUTATED AMP PEAK 33(9Q34.3) WILD-TYPE 
                            0                            16 
$`AMP PEAK 33(9Q34.3) MUTATED`
TCGA-DJ-A13M TCGA-DJ-A2PW TCGA-EL-A4K9 TCGA-EM-A1YD TCGA-EM-A22Q TCGA-FE-A22Z 
       48.79        34.85        47.84        57.01        14.24        73.74 
TCGA-FY-A3I5 
        7.82 

$`AMP PEAK 33(9Q34.3) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
        9.96        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       28.96         8.78         8.42        34.36        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24        33.93        37.48        36.46        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        33.53        35.18        15.88        36.92        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       32.42        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        17.69        59.57        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        42.54        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL 
        7.76        35.67         3.12        36.43        24.76        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        21.34        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        52.44        39.95        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       43.59        24.30        27.06        23.90        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        48.49        18.05        19.79        19.46        78.61 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       54.08        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       10.65        44.19        41.29        47.57        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         6.05         2.99        12.30        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        40.34        19.73        32.32        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.46        17.29        14.60        22.52        30.94        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR 
       14.14        33.07        13.38         8.35        29.72        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        47.38        21.01        12.07        17.49 
TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 
       17.39        16.18        15.02        14.50        15.06         7.33 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
        0.49         9.24        13.91        38.66        38.86        29.95 
TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       29.85        13.51        12.79        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        5.33        26.37        26.37        22.45        21.53        60.49 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       24.46        13.68        81.93        81.70        77.56        70.42 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       56.58        60.20        63.39        65.29        18.38        63.45 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       88.41        58.75        37.25        52.60        54.35        83.34 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       84.89       123.32       100.57        95.34        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       98.20        28.24        50.40        79.10        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       87.62        77.82        75.42        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       94.59        84.85        80.58        66.84        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      166.62        24.72        43.99        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       37.48        33.17        31.40        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       71.08         4.11         1.05        13.28         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON 
      116.09         1.25        20.42        17.82         0.99        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
       13.91        16.27        15.68        16.57        18.08         0.30 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
        0.76        17.06        17.36        15.16         6.58        22.49 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04         1.35        21.60         1.68        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46         2.99        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        18.51        16.90        21.83        31.10         8.22 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
       25.64        17.23        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW 
       27.85        24.69        22.29         5.75         2.47         2.60 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       43.69        18.64        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       33.24        33.40        40.37        21.83         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45        30.21        23.93        12.89 

  AMP PEAK 33(9Q34.3) MUTATED AMP PEAK 33(9Q34.3) WILD-TYPE 
                         7.82                          0.16 
  AMP PEAK 33(9Q34.3) MUTATED AMP PEAK 33(9Q34.3) WILD-TYPE 
                        73.74                        169.32 
  AMP PEAK 33(9Q34.3) MUTATED AMP PEAK 33(9Q34.3) WILD-TYPE 
                       47.840                        30.595 
[1] "7.8 - 73.7 (47.8)"  "0.2 - 169.3 (30.6)"
[1] "hr="     "9200000"
D32V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 33(9Q34.3) MUTATED         2        2         2        0         1
  AMP PEAK 33(9Q34.3) WILD-TYPE     280       48       109        2        45
                               vv
clus                            STAGE IVC
  AMP PEAK 33(9Q34.3) MUTATED           0
  AMP PEAK 33(9Q34.3) WILD-TYPE         6
D32V3, multiclass
           clus
vv          AMP PEAK 33(9Q34.3) MUTATED AMP PEAK 33(9Q34.3) WILD-TYPE
  STAGE I                             2                           280
  STAGE II                            2                            48
  STAGE III                           2                           109
  STAGE IV                            0                             2
  STAGE IVA                           1                            45
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 33(9Q34.3) MUTATED     1   2   3   1
  AMP PEAK 33(9Q34.3) WILD-TYPE 141 163 164  22
D32V4, multiclass
    clus
vv   AMP PEAK 33(9Q34.3) MUTATED AMP PEAK 33(9Q34.3) WILD-TYPE
  T1                           1                           141
  T2                           2                           163
  T3                           3                           164
  T4                           1                            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"
D32V5, binary
                               cls
clus                              0   1
  AMP PEAK 33(9Q34.3) MUTATED     5   2
  AMP PEAK 33(9Q34.3) WILD-TYPE 220 222
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 33(9Q34.3) MUTATED      5    2
  AMP PEAK 33(9Q34.3) WILD-TYPE  220  222
   clus
vv  AMP PEAK 33(9Q34.3) MUTATED AMP PEAK 33(9Q34.3) WILD-TYPE
  0                           5                           220
  1                           2                           222
[1] 2 2
[1] FALSE
D32V6, binary
                               cls
clus                              0   1
  AMP PEAK 33(9Q34.3) MUTATED     3   0
  AMP PEAK 33(9Q34.3) WILD-TYPE 275   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 33(9Q34.3) MUTATED      3    0
  AMP PEAK 33(9Q34.3) WILD-TYPE  275    9
   clus
vv  AMP PEAK 33(9Q34.3) MUTATED AMP PEAK 33(9Q34.3) WILD-TYPE
  0                           3                           275
  1                           0                             9
[1] 2 2
[1] FALSE
D32V7, binary
                               cls
clus                              0   1
  AMP PEAK 33(9Q34.3) MUTATED     4   3
  AMP PEAK 33(9Q34.3) WILD-TYPE 361 131
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 33(9Q34.3) MUTATED      4    3
  AMP PEAK 33(9Q34.3) WILD-TYPE  361  131
        clus
vv       AMP PEAK 33(9Q34.3) MUTATED AMP PEAK 33(9Q34.3) WILD-TYPE
  FEMALE                           4                           361
  MALE                             3                           131
[1] 2 2
[1] FALSE
D32V8, binary
                               cls
clus                              0   1
  AMP PEAK 33(9Q34.3) MUTATED     3   3
  AMP PEAK 33(9Q34.3) WILD-TYPE 182 287
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 33(9Q34.3) MUTATED      3    3
  AMP PEAK 33(9Q34.3) WILD-TYPE  182  287
     clus
vv    AMP PEAK 33(9Q34.3) MUTATED AMP PEAK 33(9Q34.3) WILD-TYPE
  NO                            3                           182
  YES                           3                           287
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 33(9Q34.3) MUTATED                0
  AMP PEAK 33(9Q34.3) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 33(9Q34.3) MUTATED                                               2
  AMP PEAK 33(9Q34.3) WILD-TYPE                                           353
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 33(9Q34.3) MUTATED                                                                        5
  AMP PEAK 33(9Q34.3) WILD-TYPE                                                                     95
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 33(9Q34.3) MUTATED                                                                     0
  AMP PEAK 33(9Q34.3) WILD-TYPE                                                                  36
D32V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 33(9Q34.3) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           5
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       AMP PEAK 33(9Q34.3) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            95
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V10, binary
                               cls
clus                              0   1
  AMP PEAK 33(9Q34.3) MUTATED     6   0
  AMP PEAK 33(9Q34.3) WILD-TYPE 414  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 33(9Q34.3) MUTATED      6    0
  AMP PEAK 33(9Q34.3) WILD-TYPE  414   17
     clus
vv    AMP PEAK 33(9Q34.3) MUTATED AMP PEAK 33(9Q34.3) WILD-TYPE
  NO                            6                           414
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 33(9Q34.3) MUTATED              1                       1    5
  AMP PEAK 33(9Q34.3) WILD-TYPE          131                      17  325
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 33(9Q34.3) MUTATED                     0
  AMP PEAK 33(9Q34.3) WILD-TYPE                   1
D32V11, multiclass
                         clus
vv                        AMP PEAK 33(9Q34.3) MUTATED
  MINIMAL (T3)                                      1
  MODERATE/ADVANCED (T4A)                           1
  NONE                                              5
  VERY ADVANCED (T4B)                               0
                         clus
vv                        AMP PEAK 33(9Q34.3) WILD-TYPE
  MINIMAL (T3)                                      131
  MODERATE/ADVANCED (T4A)                            17
  NONE                                              325
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 33(9Q34.3) MUTATED     7   0   0   0
  AMP PEAK 33(9Q34.3) WILD-TYPE 376  51   4  30
D32V12, multiclass
    clus
vv   AMP PEAK 33(9Q34.3) MUTATED AMP PEAK 33(9Q34.3) WILD-TYPE
  R0                           7                           376
  R1                           0                            51
  R2                           0                             4
  RX                           0                            30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V13, continuous
D32V14, binary
                               cls
clus                              0   1
  AMP PEAK 33(9Q34.3) MUTATED     4   3
  AMP PEAK 33(9Q34.3) WILD-TYPE 221 261
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 33(9Q34.3) MUTATED      4    3
  AMP PEAK 33(9Q34.3) WILD-TYPE  221  261
            clus
vv           AMP PEAK 33(9Q34.3) MUTATED AMP PEAK 33(9Q34.3) WILD-TYPE
  MULTIFOCAL                           4                           221
  UNIFOCAL                             3                           261
[1] 2 2
[1] FALSE
D32V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 33(9Q34.3) MUTATED                                  0     0
  AMP PEAK 33(9Q34.3) WILD-TYPE                                1    52
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 33(9Q34.3) MUTATED                           0     5
  AMP PEAK 33(9Q34.3) WILD-TYPE                        27   323
D32V16, multiclass
                                  clus
vv                                 AMP PEAK 33(9Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      5
                                  clus
vv                                 AMP PEAK 33(9Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       52
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      323
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V17, binary
                               cls
clus                              0   1
  AMP PEAK 33(9Q34.3) MUTATED     0   5
  AMP PEAK 33(9Q34.3) WILD-TYPE  38 354
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 33(9Q34.3) MUTATED      0    5
  AMP PEAK 33(9Q34.3) WILD-TYPE   38  354
                        clus
vv                       AMP PEAK 33(9Q34.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           5
                        clus
vv                       AMP PEAK 33(9Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           354
[1] 2 2
[1] FALSE

Clustering(33) Variable = AMP PEAK 34(10Q24.2) MUTATION ANALYSIS
D33V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 34(10Q24.2) MUTATED     2   1
  AMP PEAK 34(10Q24.2) WILD-TYPE 479  15
  AMP PEAK 34(10Q24.2) MUTATED AMP PEAK 34(10Q24.2) WILD-TYPE 
                             3                            494 
  AMP PEAK 34(10Q24.2) MUTATED AMP PEAK 34(10Q24.2) WILD-TYPE 
                             1                             15 
$`AMP PEAK 34(10Q24.2) MUTATED`
TCGA-EM-A1YC TCGA-EM-A22N TCGA-ET-A39I 
       78.61        10.65        33.24 

$`AMP PEAK 34(10Q24.2) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
       30.58        35.41        27.45        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74         6.77        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        36.33        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       35.87        40.96        36.99        20.22        30.61        42.54 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20        23.21        21.27        20.48        24.82        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ 
       21.01        18.97         7.76        35.67         3.12        36.43 
TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       24.76        17.23        27.62        30.87        21.34        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        80.52        63.19        52.44        39.95        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04         0.72 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
        0.26         3.02        25.45        30.61         0.16         0.23 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        33.50         0.39         0.39        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS 
       26.73       155.54        97.74       158.83         7.66        45.53 
TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY 
       60.95       157.15        37.94        57.01       106.62         4.18 
TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 
       79.50       139.86        98.53        69.57        57.11       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
       64.87        49.51        50.24       115.10        65.39       136.01 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        50.20       147.75       101.13       139.99        49.32 
TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 
       33.50        43.36        49.71        83.57       139.00       150.48 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 
      108.66        57.63        17.52        52.50        29.65       147.42 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        47.38        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        37.94        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J 
       19.79        19.46        57.01        54.08        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       15.75        10.45        14.53        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       32.32        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       22.52        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33         0.49         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39J 
       52.60        54.35        83.34         2.66        80.88       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
      107.41       108.46        84.89       123.32       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       94.13        55.10        98.20        28.24        50.40        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
       76.64         5.79        87.62        77.82        75.42        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
       52.47       116.78        94.59        84.85        80.58        66.84 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       43.73        62.83       166.62        24.72        43.99        46.26 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
       44.38        40.21        37.48        33.17        31.40        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       71.44        31.59        79.69        24.69        68.22       117.40 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77       112.80        39.95        33.63        81.83       106.36 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD 
       85.15        85.68        78.77        71.08         4.11         1.05 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       13.28         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       17.82         7.82         0.99        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83        31.10         8.22        25.64        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       23.93        12.89 

  AMP PEAK 34(10Q24.2) MUTATED AMP PEAK 34(10Q24.2) WILD-TYPE 
                         10.65                           0.16 
  AMP PEAK 34(10Q24.2) MUTATED AMP PEAK 34(10Q24.2) WILD-TYPE 
                         78.61                         169.32 
  AMP PEAK 34(10Q24.2) MUTATED AMP PEAK 34(10Q24.2) WILD-TYPE 
                         33.24                          30.61 
[1] "10.7 - 78.6 (33.2)" "0.2 - 169.3 (30.6)"
[1] "hr=" "9.4"
D33V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 34(10Q24.2) MUTATED         2        0         1        0         0
  AMP PEAK 34(10Q24.2) WILD-TYPE     280       50       110        2        46
                                vv
clus                             STAGE IVC
  AMP PEAK 34(10Q24.2) MUTATED           0
  AMP PEAK 34(10Q24.2) WILD-TYPE         6
D33V3, multiclass
           clus
vv          AMP PEAK 34(10Q24.2) MUTATED AMP PEAK 34(10Q24.2) WILD-TYPE
  STAGE I                              2                            280
  STAGE II                             0                             50
  STAGE III                            1                            110
  STAGE IV                             0                              2
  STAGE IVA                            0                             46
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 34(10Q24.2) MUTATED     2   0   1   0
  AMP PEAK 34(10Q24.2) WILD-TYPE 140 165 166  23
D33V4, multiclass
    clus
vv   AMP PEAK 34(10Q24.2) MUTATED AMP PEAK 34(10Q24.2) WILD-TYPE
  T1                            2                            140
  T2                            0                            165
  T3                            1                            166
  T4                            0                             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"
D33V5, binary
                                cls
clus                               0   1
  AMP PEAK 34(10Q24.2) MUTATED     2   0
  AMP PEAK 34(10Q24.2) WILD-TYPE 223 224
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 34(10Q24.2) MUTATED      2    0
  AMP PEAK 34(10Q24.2) WILD-TYPE  223  224
   clus
vv  AMP PEAK 34(10Q24.2) MUTATED AMP PEAK 34(10Q24.2) WILD-TYPE
  0                            2                            223
  1                            0                            224
[1] 2 2
[1] FALSE
D33V6, binary
                                cls
clus                               0   1
  AMP PEAK 34(10Q24.2) MUTATED     0   0
  AMP PEAK 34(10Q24.2) WILD-TYPE 278   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 34(10Q24.2) MUTATED      0    0
  AMP PEAK 34(10Q24.2) WILD-TYPE  278    9
D33V7, binary
                                cls
clus                               0   1
  AMP PEAK 34(10Q24.2) MUTATED     3   0
  AMP PEAK 34(10Q24.2) WILD-TYPE 362 134
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 34(10Q24.2) MUTATED      3    0
  AMP PEAK 34(10Q24.2) WILD-TYPE  362  134
        clus
vv       AMP PEAK 34(10Q24.2) MUTATED AMP PEAK 34(10Q24.2) WILD-TYPE
  FEMALE                            3                            362
  MALE                              0                            134
[1] 2 2
[1] FALSE
D33V8, binary
                                cls
clus                               0   1
  AMP PEAK 34(10Q24.2) MUTATED     0   2
  AMP PEAK 34(10Q24.2) WILD-TYPE 185 288
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 34(10Q24.2) MUTATED      0    2
  AMP PEAK 34(10Q24.2) WILD-TYPE  185  288
     clus
vv    AMP PEAK 34(10Q24.2) MUTATED AMP PEAK 34(10Q24.2) WILD-TYPE
  NO                             0                            185
  YES                            2                            288
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 34(10Q24.2) MUTATED                0
  AMP PEAK 34(10Q24.2) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 34(10Q24.2) MUTATED                                               0
  AMP PEAK 34(10Q24.2) WILD-TYPE                                           355
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 34(10Q24.2) MUTATED                                                                        3
  AMP PEAK 34(10Q24.2) WILD-TYPE                                                                     97
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 34(10Q24.2) MUTATED                                                                     0
  AMP PEAK 34(10Q24.2) WILD-TYPE                                                                  36
D33V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 34(10Q24.2) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     0
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       AMP PEAK 34(10Q24.2) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     355
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             97
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V10, binary
                                cls
clus                               0   1
  AMP PEAK 34(10Q24.2) MUTATED     3   0
  AMP PEAK 34(10Q24.2) WILD-TYPE 417  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 34(10Q24.2) MUTATED      3    0
  AMP PEAK 34(10Q24.2) WILD-TYPE  417   17
     clus
vv    AMP PEAK 34(10Q24.2) MUTATED AMP PEAK 34(10Q24.2) WILD-TYPE
  NO                             3                            417
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 34(10Q24.2) MUTATED              0                       0    3
  AMP PEAK 34(10Q24.2) WILD-TYPE          132                      18  327
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 34(10Q24.2) MUTATED                     0
  AMP PEAK 34(10Q24.2) WILD-TYPE                   1
D33V11, multiclass
                         clus
vv                        AMP PEAK 34(10Q24.2) MUTATED
  MINIMAL (T3)                                       0
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               3
  VERY ADVANCED (T4B)                                0
                         clus
vv                        AMP PEAK 34(10Q24.2) WILD-TYPE
  MINIMAL (T3)                                       132
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               327
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 34(10Q24.2) MUTATED     2   0   0   1
  AMP PEAK 34(10Q24.2) WILD-TYPE 381  51   4  29
D33V12, multiclass
    clus
vv   AMP PEAK 34(10Q24.2) MUTATED AMP PEAK 34(10Q24.2) WILD-TYPE
  R0                            2                            381
  R1                            0                             51
  R2                            0                              4
  RX                            1                             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"
D33V13, continuous
[1] "Remove cluster labels:"       "AMP PEAK 34(10Q24.2) MUTATED"
clus
  AMP PEAK 34(10Q24.2) MUTATED AMP PEAK 34(10Q24.2) WILD-TYPE 
                             2                            383 
                    TCGA-4C-A93U                     TCGA-BJ-A0Z0 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A0Z3                     TCGA-BJ-A0Z9 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A0ZA                     TCGA-BJ-A0ZB 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A0ZH                     TCGA-BJ-A0ZJ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A18Y                     TCGA-BJ-A18Z 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A190                     TCGA-BJ-A191 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A28R                     TCGA-BJ-A28T 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A28W                     TCGA-BJ-A28X 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A28Z                     TCGA-BJ-A290 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A291                     TCGA-BJ-A2N8 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A2N9                     TCGA-BJ-A2NA 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A3EZ                     TCGA-BJ-A3PR 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A3PU                     TCGA-BJ-A45C 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A45D                     TCGA-BJ-A45E 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A45G                     TCGA-BJ-A45I 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A45J                     TCGA-BJ-A45K 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A4O8                     TCGA-BJ-A4O9 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-CE-A13K                     TCGA-CE-A3MD 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-CE-A483                     TCGA-CE-A484 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-CE-A485                     TCGA-DE-A0XZ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A0Y2                     TCGA-DE-A0Y3 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A3KN                     TCGA-DE-A4M8 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A4MA                     TCGA-DE-A4MB 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A4MC                     TCGA-DE-A4MD 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A69K                     TCGA-DE-A7U5 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A13M                     TCGA-DJ-A13O 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A13R                     TCGA-DJ-A13T 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A13V                     TCGA-DJ-A13W 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A13X                     TCGA-DJ-A1QG 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A1QH                     TCGA-DJ-A1QM 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PO                     TCGA-DJ-A2PP 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PQ                     TCGA-DJ-A2PR 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PS                     TCGA-DJ-A2PT 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PU                     TCGA-DJ-A2PV 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PW                     TCGA-DJ-A2PX 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PY                     TCGA-DJ-A2PZ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2Q0                     TCGA-DJ-A2Q1 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2Q2                     TCGA-DJ-A2Q3 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2Q4                     TCGA-DJ-A2Q5 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2Q6                     TCGA-DJ-A2Q7 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2Q8                     TCGA-DJ-A2Q9 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2QA                     TCGA-DJ-A2QB 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UK                     TCGA-DJ-A3UM 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UN                     TCGA-DJ-A3UO 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UP                     TCGA-DJ-A3UQ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UR                     TCGA-DJ-A3UU 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UW                     TCGA-DJ-A3UX 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UZ                     TCGA-DJ-A3V0 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3V2                     TCGA-DJ-A3V3 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3V4                     TCGA-DJ-A3V5 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3V7                     TCGA-DJ-A3V8 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3V9                     TCGA-DJ-A3VA 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3VB                     TCGA-DJ-A3VD 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3VF                     TCGA-DJ-A3VG 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3VI                     TCGA-DJ-A3VJ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3VK                     TCGA-DJ-A3VL 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A4UL                     TCGA-DJ-A4UP 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A4UQ                     TCGA-DJ-A4UR 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A4UW                     TCGA-DJ-A4V2 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A4V5                     TCGA-DO-A1K0 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DO-A2HM                     TCGA-E3-A3DY 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-E3-A3DZ                     TCGA-E3-A3E0 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-E3-A3E1                     TCGA-E3-A3E2 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-E3-A3E3                     TCGA-E3-A3E5 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-E8-A242                     TCGA-E8-A2EA 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-E8-A414                     TCGA-E8-A415 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-E8-A417                     TCGA-E8-A419 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-E8-A433                     TCGA-E8-A436 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-E8-A438                     TCGA-E8-A44K 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CM                     TCGA-EL-A3CN 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CO                     TCGA-EL-A3CR 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CS                     TCGA-EL-A3CT 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CU                     TCGA-EL-A3CV 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CW                     TCGA-EL-A3CX 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CY                     TCGA-EL-A3CZ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3D0                     TCGA-EL-A3D1 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3D4                     TCGA-EL-A3D5 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3D6                     TCGA-EL-A3GO 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3GP                     TCGA-EL-A3GQ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3GS                     TCGA-EL-A3GU 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3GV                     TCGA-EL-A3GX 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3H3                     TCGA-EL-A3H4 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3H5                     TCGA-EL-A3H7 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3H8                     TCGA-EL-A3MW 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3MX                     TCGA-EL-A3MZ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3N2                     TCGA-EL-A3T0 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3T1                     TCGA-EL-A3T2 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3TB                     TCGA-EL-A3ZH 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZK                     TCGA-EL-A3ZL 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZM                     TCGA-EL-A3ZN 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZO                     TCGA-EL-A3ZP 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZS                     TCGA-EL-A4JV 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4JW                     TCGA-EL-A4JX 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4JZ                     TCGA-EL-A4K0 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4K1                     TCGA-EL-A4K2 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4K4                     TCGA-EL-A4K6 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4K7                     TCGA-EL-A4KD 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4KG                     TCGA-EL-A4KI 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A1CS                     TCGA-EM-A1CT 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A1CU                     TCGA-EM-A1CV 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A1CW                     TCGA-EM-A1YD 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A1YE                     TCGA-EM-A22I 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A22J                     TCGA-EM-A22K 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A22L                     TCGA-EM-A22M 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A22O                     TCGA-EM-A22P 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A22Q                     TCGA-EM-A2CK 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2CN                     TCGA-EM-A2CP 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2CQ                     TCGA-EM-A2CT 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2CU                     TCGA-EM-A2OV 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2OX                     TCGA-EM-A2OY 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2OZ                     TCGA-EM-A2P0 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2P1                     TCGA-EM-A2P2 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3AJ                     TCGA-EM-A3AK 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3AL                     TCGA-EM-A3AN 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3AO                     TCGA-EM-A3AQ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3AR                     TCGA-EM-A3FJ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3FK                     TCGA-EM-A3FM 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3FN                     TCGA-EM-A3FO 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3FP                     TCGA-EM-A3FQ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3FR                     TCGA-EM-A3O3 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3O8                     TCGA-EM-A3O9 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3OA                     TCGA-EM-A3OB 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3ST                     TCGA-EM-A3SU 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3SX                     TCGA-EM-A3SZ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A4FF                     TCGA-EM-A4FM 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A4FN                     TCGA-EM-A4FO 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A4FQ                     TCGA-EM-A4FR 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A4FV                     TCGA-EM-A4G1 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25G                     TCGA-ET-A25I 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25J                     TCGA-ET-A25K 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25L                     TCGA-ET-A25M 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25N                     TCGA-ET-A25O 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25P                     TCGA-ET-A2MX 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A2MZ                     TCGA-ET-A2N0 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A2N1                     TCGA-ET-A2N4 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A39K                     TCGA-ET-A39L 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A39O                     TCGA-ET-A39P 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A39R                     TCGA-ET-A39S 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A39T                     TCGA-ET-A3BO 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3BP                     TCGA-ET-A3BQ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3BS                     TCGA-ET-A3BT 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3BU                     TCGA-ET-A3BV 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3BX                     TCGA-ET-A3DQ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3DR                     TCGA-ET-A3DS 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3DT                     TCGA-ET-A3DU 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3DV                     TCGA-ET-A3DW 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A40P                     TCGA-ET-A40Q 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A40R                     TCGA-ET-A40S 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A40T                     TCGA-ET-A4KN 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A22Z                     TCGA-FE-A230 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A231                     TCGA-FE-A232 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A233                     TCGA-FE-A234 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A235                     TCGA-FE-A236 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A237                     TCGA-FE-A238 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A239                     TCGA-FE-A23A 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A3PB                     TCGA-FE-A3PC 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A3PD                     TCGA-FK-A3S3 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FK-A3SB                     TCGA-FK-A3SE 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FK-A3SG                     TCGA-FK-A3SH 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FK-A4UB                     TCGA-FY-A2QD 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3I4                     TCGA-FY-A3I5 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3NM                     TCGA-FY-A3NN 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3ON                     TCGA-FY-A3R6 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3R7                     TCGA-FY-A3R9 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3TY                     TCGA-FY-A3W9 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3YR                     TCGA-FY-A40K 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A40L                     TCGA-FY-A40M 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A40N                     TCGA-FY-A4B3 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A4B4                     TCGA-GE-A2C6 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-H2-A26U                     TCGA-H2-A2K9 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-H2-A3RH                     TCGA-H2-A3RI 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-H2-A421                     TCGA-H2-A422 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-IM-A3EB                     TCGA-IM-A3ED 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-IM-A3U2                     TCGA-IM-A3U3 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-IM-A41Y                     TCGA-IM-A41Z 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-IM-A420                     TCGA-IM-A4EB 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-J8-A3NZ                     TCGA-J8-A3O0 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-J8-A3O1                     TCGA-J8-A3O2 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-J8-A3YD                     TCGA-J8-A3YE 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-J8-A3YF                     TCGA-J8-A3YG 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-J8-A3YH                     TCGA-J8-A42S 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-J8-A4HW                     TCGA-J8-A4HY 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A41F                     TCGA-KS-A41I 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A41J                     TCGA-KS-A41L 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A4I1                     TCGA-KS-A4I3 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A4I5                     TCGA-KS-A4I7 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A4I9                     TCGA-KS-A4IB 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A4IC                     TCGA-KS-A4ID 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-L6-A4EP                     TCGA-L6-A4EQ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-L6-A4EU                     TCGA-MK-A4N6 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-MK-A4N7                     TCGA-MK-A4N9 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-QD-A8IV 
"AMP PEAK 34(10Q24.2) WILD-TYPE" 
D33V14, binary
                                cls
clus                               0   1
  AMP PEAK 34(10Q24.2) MUTATED     1   2
  AMP PEAK 34(10Q24.2) WILD-TYPE 224 262
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 34(10Q24.2) MUTATED      1    2
  AMP PEAK 34(10Q24.2) WILD-TYPE  224  262
            clus
vv           AMP PEAK 34(10Q24.2) MUTATED AMP PEAK 34(10Q24.2) WILD-TYPE
  MULTIFOCAL                            1                            224
  UNIFOCAL                              2                            262
[1] 2 2
[1] FALSE
D33V15, continuous
[1] "Remove cluster labels:"       "AMP PEAK 34(10Q24.2) MUTATED"
clus
  AMP PEAK 34(10Q24.2) MUTATED AMP PEAK 34(10Q24.2) WILD-TYPE 
                             2                            399 
                    TCGA-4C-A93U                     TCGA-BJ-A0Z2 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A0Z3                     TCGA-BJ-A0Z9 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A0ZA                     TCGA-BJ-A0ZB 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A0ZC                     TCGA-BJ-A0ZE 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A0ZG                     TCGA-BJ-A0ZH 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A0ZJ                     TCGA-BJ-A18Y 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A18Z                     TCGA-BJ-A190 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A191                     TCGA-BJ-A192 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A28R                     TCGA-BJ-A28S 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A28T                     TCGA-BJ-A28V 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A28W                     TCGA-BJ-A28Z 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A290                     TCGA-BJ-A291 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A2N8                     TCGA-BJ-A2N9 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A2P4                     TCGA-BJ-A3PU 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A45C                     TCGA-BJ-A45D 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A45E                     TCGA-BJ-A45F 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A45G                     TCGA-BJ-A45H 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A45I                     TCGA-BJ-A45J 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A45K                     TCGA-BJ-A4O8 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A4O9                     TCGA-CE-A13K 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-CE-A27D                     TCGA-CE-A3MD 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-CE-A3ME                     TCGA-CE-A481 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-CE-A482                     TCGA-CE-A483 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-CE-A484                     TCGA-CE-A485 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A0XZ                     TCGA-DE-A0Y2 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A0Y3                     TCGA-DE-A2OL 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A3KN                     TCGA-DE-A4M8 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A4M9                     TCGA-DE-A4MA 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A4MB                     TCGA-DE-A4MC 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A4MD                     TCGA-DE-A69J 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A69K                     TCGA-DE-A7U5 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A13L                     TCGA-DJ-A13M 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A13O                     TCGA-DJ-A13R 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A13S                     TCGA-DJ-A13U 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A13V                     TCGA-DJ-A13W 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A13X                     TCGA-DJ-A1QD 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A1QE                     TCGA-DJ-A1QF 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A1QG                     TCGA-DJ-A1QH 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A1QI                     TCGA-DJ-A1QL 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A1QM                     TCGA-DJ-A1QN 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A1QO                     TCGA-DJ-A1QQ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PN                     TCGA-DJ-A2PO 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PP                     TCGA-DJ-A2PQ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PR                     TCGA-DJ-A2PS 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PT                     TCGA-DJ-A2PU 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PV                     TCGA-DJ-A2PW 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PY                     TCGA-DJ-A2PZ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2Q0                     TCGA-DJ-A2Q1 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2Q2                     TCGA-DJ-A2Q3 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2Q4                     TCGA-DJ-A2Q5 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2Q6                     TCGA-DJ-A2Q7 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2Q8                     TCGA-DJ-A2Q9 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2QA                     TCGA-DJ-A2QC 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UK                     TCGA-DJ-A3UM 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UN                     TCGA-DJ-A3UO 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UP                     TCGA-DJ-A3UQ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UR                     TCGA-DJ-A3US 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UT                     TCGA-DJ-A3UU 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UW                     TCGA-DJ-A3UX 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UY                     TCGA-DJ-A3V0 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3V2                     TCGA-DJ-A3V3 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3V4                     TCGA-DJ-A3V5 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3V7                     TCGA-DJ-A3V8 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3VA                     TCGA-DJ-A3VB 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3VD                     TCGA-DJ-A3VE 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3VF                     TCGA-DJ-A3VG 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3VJ                     TCGA-DJ-A3VK 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3VL                     TCGA-DJ-A3VM 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A4UL                     TCGA-DJ-A4UP 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A4UQ                     TCGA-DJ-A4UT 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A4V0                     TCGA-DJ-A4V2 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A4V4                     TCGA-DJ-A4V5 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DO-A1JZ                     TCGA-DO-A1K0 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DO-A2HM                     TCGA-E3-A3DY 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-E3-A3DZ                     TCGA-E3-A3E0 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-E3-A3E1                     TCGA-E3-A3E2 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-E3-A3E3                     TCGA-E8-A419 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CN                     TCGA-EL-A3CO 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CR                     TCGA-EL-A3CS 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CT                     TCGA-EL-A3CU 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CV                     TCGA-EL-A3CW 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CX                     TCGA-EL-A3CY 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CZ                     TCGA-EL-A3D0 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3D1                     TCGA-EL-A3D4 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3D5                     TCGA-EL-A3D6 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3GO                     TCGA-EL-A3GP 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3GQ                     TCGA-EL-A3GR 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3GS                     TCGA-EL-A3GU 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3GV                     TCGA-EL-A3GW 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3GX                     TCGA-EL-A3GY 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3GZ                     TCGA-EL-A3H2 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3H3                     TCGA-EL-A3H4 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3H5                     TCGA-EL-A3H7 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3H8                     TCGA-EL-A3MW 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3MX                     TCGA-EL-A3MY 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3MZ                     TCGA-EL-A3N2 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3N3                     TCGA-EL-A3T1 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3T2                     TCGA-EL-A3T3 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3T6                     TCGA-EL-A3T7 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3T8                     TCGA-EL-A3T9 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3TA                     TCGA-EL-A3TB 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZG                     TCGA-EL-A3ZH 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZK                     TCGA-EL-A3ZL 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZM                     TCGA-EL-A3ZN 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZO                     TCGA-EL-A3ZP 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZQ                     TCGA-EL-A3ZR 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZS                     TCGA-EL-A3ZT 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4JV                     TCGA-EL-A4JW 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4JX                     TCGA-EL-A4JZ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4K0                     TCGA-EL-A4K1 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4K2                     TCGA-EL-A4K4 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4K6                     TCGA-EL-A4K7 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4K9                     TCGA-EL-A4KD 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4KG                     TCGA-EL-A4KH 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4KI                     TCGA-EM-A1CS 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A1CT                     TCGA-EM-A1CU 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A1CV                     TCGA-EM-A1CW 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A1YA                     TCGA-EM-A1YB 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A1YD                     TCGA-EM-A1YE 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A22I                     TCGA-EM-A22J 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A22K                     TCGA-EM-A22L 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A22O                     TCGA-EM-A22P 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A22Q                     TCGA-EM-A2CJ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2CK                     TCGA-EM-A2CL 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2CN                     TCGA-EM-A2CO 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2CP                     TCGA-EM-A2CQ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2CT                     TCGA-EM-A2CU 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2OW                     TCGA-EM-A2OX 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2OY                     TCGA-EM-A2P0 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2P1                     TCGA-EM-A2P2 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2P3                     TCGA-EM-A3AI 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3AJ                     TCGA-EM-A3AK 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3AL                     TCGA-EM-A3AN 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3AO                     TCGA-EM-A3AP 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3AQ                     TCGA-EM-A3AR 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3FJ                     TCGA-EM-A3FM 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3FN                     TCGA-EM-A3FO 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3FP                     TCGA-EM-A3FR 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3O3                     TCGA-EM-A3O6 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3O7                     TCGA-EM-A3O8 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3O9                     TCGA-EM-A3OA 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3OB                     TCGA-EM-A3ST 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3SU                     TCGA-EM-A3SX 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3SY                     TCGA-EM-A3SZ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A4FF                     TCGA-EM-A4FH 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A4FK                     TCGA-EM-A4FM 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A4FN                     TCGA-EM-A4FQ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A4FR                     TCGA-EM-A4FU 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A4FV                     TCGA-EM-A4G1 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25G                     TCGA-ET-A25I 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25J                     TCGA-ET-A25K 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25L                     TCGA-ET-A25M 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25N                     TCGA-ET-A25O 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25P                     TCGA-ET-A25R 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A2MY                     TCGA-ET-A2MZ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A2N0                     TCGA-ET-A2N5 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A39J                     TCGA-ET-A39M 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A39N                     TCGA-ET-A39O 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A39P                     TCGA-ET-A39T 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3BN                     TCGA-ET-A3BO 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3BP                     TCGA-ET-A3BQ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3BS                     TCGA-ET-A3BT 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3BU                     TCGA-ET-A3BV 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3BW                     TCGA-ET-A3BX 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3DO                     TCGA-ET-A3DS 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3DT                     TCGA-ET-A40P 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A40Q                     TCGA-ET-A40R 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A40S                     TCGA-ET-A4KN 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A4KQ                     TCGA-FE-A22Z 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A230                     TCGA-FE-A232 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A233                     TCGA-FE-A234 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A235                     TCGA-FE-A236 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A237                     TCGA-FE-A238 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A239                     TCGA-FE-A23A 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A3PA                     TCGA-FE-A3PB 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A3PC                     TCGA-FE-A3PD 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A2QD                     TCGA-FY-A3I4 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3I5                     TCGA-FY-A3ON 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3R8                     TCGA-FY-A3TY 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3W9                     TCGA-FY-A3YR 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A40K                     TCGA-FY-A40L 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A40M                     TCGA-FY-A40N 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A4B3                     TCGA-FY-A76V 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-GE-A2C6                     TCGA-H2-A421 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-IM-A3EB                     TCGA-IM-A3ED 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-IM-A3U2                     TCGA-IM-A3U3 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-IM-A41Y                     TCGA-IM-A41Z 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-IM-A420                     TCGA-IM-A4EB 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-J8-A3O0                     TCGA-J8-A3YD 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-J8-A3YG                     TCGA-KS-A41F 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A41I                     TCGA-KS-A41J 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A41L                     TCGA-KS-A4I3 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A4I5                     TCGA-KS-A4I7 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A4I9                     TCGA-KS-A4IB 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A4IC                     TCGA-KS-A4ID 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-L6-A4EP                     TCGA-L6-A4EQ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-L6-A4ET                     TCGA-L6-A4EU 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-MK-A4N6                     TCGA-MK-A4N7 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-MK-A4N9                     TCGA-MK-A84Z 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-QD-A8IV 
"AMP PEAK 34(10Q24.2) WILD-TYPE" 
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 34(10Q24.2) MUTATED                                  0     0
  AMP PEAK 34(10Q24.2) WILD-TYPE                                1    52
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 34(10Q24.2) MUTATED                           0     1
  AMP PEAK 34(10Q24.2) WILD-TYPE                        27   327
D33V16, multiclass
[1] "Remove cluster labels:"       "AMP PEAK 34(10Q24.2) MUTATED"
clus
  AMP PEAK 34(10Q24.2) MUTATED AMP PEAK 34(10Q24.2) WILD-TYPE 
                             1                            407 
                    TCGA-4C-A93U                     TCGA-BJ-A0YZ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A0Z2                     TCGA-BJ-A0Z3 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A0Z5                     TCGA-BJ-A0Z9 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A0ZA                     TCGA-BJ-A0ZB 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A0ZC                     TCGA-BJ-A0ZE 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A0ZG                     TCGA-BJ-A0ZH 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A0ZJ                     TCGA-BJ-A18Y 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A18Z                     TCGA-BJ-A190 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A191                     TCGA-BJ-A192 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A28R                     TCGA-BJ-A28S 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A28T                     TCGA-BJ-A28V 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A28W                     TCGA-BJ-A28X 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A28Z                     TCGA-BJ-A290 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A291                     TCGA-BJ-A2N7 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A2N8                     TCGA-BJ-A2N9 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A2NA                     TCGA-BJ-A2P4 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A3EZ                     TCGA-BJ-A3F0 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A3PR                     TCGA-BJ-A3PT 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A3PU                     TCGA-BJ-A45C 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A45D                     TCGA-BJ-A45E 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A45F                     TCGA-BJ-A45G 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A45H                     TCGA-BJ-A45I 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A45J                     TCGA-BJ-A45K 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A4O8                     TCGA-BJ-A4O9 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-CE-A13K                     TCGA-CE-A27D 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-CE-A3MD                     TCGA-CE-A3ME 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-CE-A481                     TCGA-CE-A482 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-CE-A483                     TCGA-CE-A484 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-CE-A485                     TCGA-DE-A0XZ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A0Y2                     TCGA-DE-A0Y3 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A2OL                     TCGA-DE-A3KN 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A4M8                     TCGA-DE-A4M9 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A4MA                     TCGA-DE-A4MB 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A4MC                     TCGA-DE-A4MD 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A69J                     TCGA-DE-A69K 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A7U5                     TCGA-DJ-A13L 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A13M                     TCGA-DJ-A13O 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A13P                     TCGA-DJ-A13R 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A13S                     TCGA-DJ-A13T 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A13U                     TCGA-DJ-A13W 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A1QD                     TCGA-DJ-A1QE 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A1QF                     TCGA-DJ-A1QG 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A1QH                     TCGA-DJ-A1QI 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A1QM                     TCGA-DJ-A1QO 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A1QQ                     TCGA-DJ-A2PN 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PO                     TCGA-DJ-A2PQ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PR                     TCGA-DJ-A2PS 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PT                     TCGA-DJ-A2PU 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PV                     TCGA-DJ-A2PW 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PX                     TCGA-DJ-A2PY 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PZ                     TCGA-DJ-A2Q0 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2Q1                     TCGA-DJ-A2Q2 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2Q3                     TCGA-DJ-A2Q4 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2Q5                     TCGA-DJ-A2Q6 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2Q7                     TCGA-DJ-A2Q9 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2QA                     TCGA-DJ-A2QB 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UK                     TCGA-DJ-A3UM 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UN                     TCGA-DJ-A3UO 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UQ                     TCGA-DJ-A3UR 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3US                     TCGA-DJ-A3UT 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UU                     TCGA-DJ-A3UW 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UX                     TCGA-DJ-A3UY 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UZ                     TCGA-DJ-A3V2 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3V3                     TCGA-DJ-A3V4 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3V5                     TCGA-DJ-A3V7 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3V8                     TCGA-DJ-A3V9 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3VD                     TCGA-DJ-A3VE 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3VF                     TCGA-DJ-A3VG 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3VI                     TCGA-DJ-A3VJ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3VK                     TCGA-DJ-A3VL 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3VM                     TCGA-DJ-A4UL 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A4UP                     TCGA-DJ-A4UQ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A4UR                     TCGA-DJ-A4UT 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A4UW                     TCGA-DJ-A4V0 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A4V4                     TCGA-DJ-A4V5 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DO-A1JZ                     TCGA-DO-A1K0 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-DO-A2HM                     TCGA-E3-A3DY 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-E3-A3DZ                     TCGA-E3-A3E0 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-E3-A3E1                     TCGA-E3-A3E2 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-E3-A3E3                     TCGA-E3-A3E5 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-E8-A242                     TCGA-E8-A2EA 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-E8-A3X7                     TCGA-E8-A413 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-E8-A414                     TCGA-E8-A415 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-E8-A416                     TCGA-E8-A417 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-E8-A418                     TCGA-E8-A419 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-E8-A432                     TCGA-E8-A433 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-E8-A434                     TCGA-E8-A436 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-E8-A437                     TCGA-E8-A438 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-E8-A44K                     TCGA-E8-A44M 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CL                     TCGA-EL-A3CM 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CN                     TCGA-EL-A3CO 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CP                     TCGA-EL-A3CR 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CS                     TCGA-EL-A3CT 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CU                     TCGA-EL-A3CV 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CW                     TCGA-EL-A3CX 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CY                     TCGA-EL-A3CZ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3D0                     TCGA-EL-A3D1 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3D4                     TCGA-EL-A3D5 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3D6                     TCGA-EL-A3GO 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3GP                     TCGA-EL-A3GQ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3GR                     TCGA-EL-A3GS 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3GU                     TCGA-EL-A3GV 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3GW                     TCGA-EL-A3GX 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3GY                     TCGA-EL-A3GZ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3H1                     TCGA-EL-A3H2 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3H3                     TCGA-EL-A3H4 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3H5                     TCGA-EL-A3H7 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3H8                     TCGA-EL-A3MW 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3MX                     TCGA-EL-A3MY 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3MZ                     TCGA-EL-A3N2 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3N3                     TCGA-EL-A3T0 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3T1                     TCGA-EL-A3T2 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3T3                     TCGA-EL-A3T6 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3T7                     TCGA-EL-A3T8 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3T9                     TCGA-EL-A3TA 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3TB                     TCGA-EL-A3ZG 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZH                     TCGA-EL-A3ZK 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZL                     TCGA-EL-A3ZN 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZO                     TCGA-EL-A3ZP 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZQ                     TCGA-EL-A3ZR 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZS                     TCGA-EL-A3ZT 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4JV                     TCGA-EL-A4JW 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4JX                     TCGA-EL-A4JZ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4K0                     TCGA-EL-A4K1 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4K2                     TCGA-EL-A4K4 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4K6                     TCGA-EL-A4K7 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4K9                     TCGA-EL-A4KD 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4KG                     TCGA-EL-A4KH 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4KI                     TCGA-EM-A22M 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A22O                     TCGA-EM-A2OV 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3AI                     TCGA-ET-A25G 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25I                     TCGA-ET-A25J 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25K                     TCGA-ET-A25L 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25M                     TCGA-ET-A25N 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25O                     TCGA-ET-A25P 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25R                     TCGA-ET-A2MX 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A2MY                     TCGA-ET-A2MZ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A2N0                     TCGA-ET-A2N1 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A2N3                     TCGA-ET-A2N4 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A2N5                     TCGA-ET-A39J 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A39K                     TCGA-ET-A39M 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A39N                     TCGA-ET-A39O 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A39P                     TCGA-ET-A39R 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A39S                     TCGA-ET-A39T 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3BN                     TCGA-ET-A3BO 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3BP                     TCGA-ET-A3BQ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3BS                     TCGA-ET-A3BT 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3BU                     TCGA-ET-A3BV 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3BW                     TCGA-ET-A3BX 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3DO                     TCGA-ET-A3DP 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3DQ                     TCGA-ET-A3DR 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3DS                     TCGA-ET-A3DT 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3DU                     TCGA-ET-A3DV 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3DW                     TCGA-ET-A40P 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A40Q                     TCGA-ET-A40R 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A40S                     TCGA-ET-A40T 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A4KN                     TCGA-ET-A4KQ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A22Z                     TCGA-FE-A230 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A231                     TCGA-FE-A232 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A233                     TCGA-FE-A234 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A235                     TCGA-FE-A236 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A237                     TCGA-FE-A238 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A239                     TCGA-FE-A23A 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A3PA                     TCGA-FE-A3PB 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A3PC                     TCGA-FE-A3PD 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FK-A3S3                     TCGA-FK-A3SB 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FK-A3SD                     TCGA-FK-A3SE 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FK-A3SG                     TCGA-FK-A3SH 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FK-A4UB                     TCGA-FY-A2QD 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3BL                     TCGA-FY-A3I4 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3I5                     TCGA-FY-A3NM 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3ON                     TCGA-FY-A3R6 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3R7                     TCGA-FY-A3R8 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3R9                     TCGA-FY-A3RA 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3W9                     TCGA-FY-A3WA 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3YR                     TCGA-FY-A40K 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A40L                     TCGA-FY-A40M 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A40N                     TCGA-FY-A4B0 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A4B3                     TCGA-FY-A4B4 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A76V                     TCGA-GE-A2C6 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-H2-A26U                     TCGA-H2-A2K9 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-H2-A3RH                     TCGA-H2-A3RI 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-H2-A421                     TCGA-H2-A422 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-IM-A3EB                     TCGA-IM-A3ED 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-IM-A3U2                     TCGA-IM-A3U3 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-IM-A41Y                     TCGA-IM-A41Z 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-IM-A420                     TCGA-IM-A4EB 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-J8-A3NZ                     TCGA-J8-A3O0 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-J8-A3O1                     TCGA-J8-A3O2 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-J8-A3YD                     TCGA-J8-A3YE 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-J8-A3YF                     TCGA-J8-A3YG 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-J8-A3YH                     TCGA-J8-A42S 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-J8-A4HW                     TCGA-J8-A4HY 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A41F                     TCGA-KS-A41I 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A41J                     TCGA-KS-A41L 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A4I1                     TCGA-KS-A4I3 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A4I5                     TCGA-KS-A4I7 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A4I9                     TCGA-KS-A4IB 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A4IC                     TCGA-KS-A4ID 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-L6-A4EP                     TCGA-L6-A4EQ 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-L6-A4ET                     TCGA-L6-A4EU 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-MK-A4N6                     TCGA-MK-A4N7 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-MK-A4N9                     TCGA-MK-A84Z 
"AMP PEAK 34(10Q24.2) WILD-TYPE" "AMP PEAK 34(10Q24.2) WILD-TYPE" 
                    TCGA-QD-A8IV 
"AMP PEAK 34(10Q24.2) WILD-TYPE" 
D33V17, binary
                                cls
clus                               0   1
  AMP PEAK 34(10Q24.2) MUTATED     0   1
  AMP PEAK 34(10Q24.2) WILD-TYPE  38 358
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 34(10Q24.2) MUTATED      0    1
  AMP PEAK 34(10Q24.2) WILD-TYPE   38  358
                        clus
vv                       AMP PEAK 34(10Q24.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            1
                        clus
vv                       AMP PEAK 34(10Q24.2) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            358
[1] 2 2
[1] FALSE

Clustering(34) Variable = AMP PEAK 35(10Q25.1) MUTATION ANALYSIS
D34V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 35(10Q25.1) MUTATED     4   0
  AMP PEAK 35(10Q25.1) WILD-TYPE 477  16
  AMP PEAK 35(10Q25.1) MUTATED AMP PEAK 35(10Q25.1) WILD-TYPE 
                             4                            493 
  AMP PEAK 35(10Q25.1) MUTATED AMP PEAK 35(10Q25.1) WILD-TYPE 
                             0                             16 
$`AMP PEAK 35(10Q25.1) MUTATED`
TCGA-DJ-A3UQ TCGA-EM-A1YC TCGA-EM-A22N TCGA-ET-A2MZ 
       19.56        78.61        10.65        37.25 

$`AMP PEAK 35(10Q25.1) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
       30.58        35.41        27.45        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74         6.77        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UR 
       36.92        31.04        32.42        31.46        16.41        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        30.61         0.16         0.23        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        33.50         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        69.57        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       49.51        50.24       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       150.48       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        89.56        78.97        51.78 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        47.38        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       60.16         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        47.84        43.59        24.30        27.06        23.90 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.46        57.01        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       10.45        14.53        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
       17.88        13.18        23.51         6.05         2.99        12.30 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       48.46        13.15        22.16        40.34        19.73        32.32 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       33.96        17.59        17.46        17.29        14.60        22.52 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.06         7.33         0.49         9.24        13.91        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.86        29.95        29.85        13.51        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        63.45        88.41        58.75        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       83.34         2.66        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      108.46        84.89       123.32       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        98.20        28.24        50.40        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.79        87.62        77.82        75.42        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       62.83       166.62        24.72        43.99        46.26        44.38 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       40.21        37.48        33.17        31.40        73.74        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
      112.80        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        13.28 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10       116.09         1.25        20.42        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        7.82         0.99        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08         0.30         0.76        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       15.16         6.58        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83        31.10         8.22        25.64        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        23.93 
TCGA-QD-A8IV 
       12.89 

  AMP PEAK 35(10Q25.1) MUTATED AMP PEAK 35(10Q25.1) WILD-TYPE 
                         10.65                           0.16 
  AMP PEAK 35(10Q25.1) MUTATED AMP PEAK 35(10Q25.1) WILD-TYPE 
                         78.61                         169.32 
  AMP PEAK 35(10Q25.1) MUTATED AMP PEAK 35(10Q25.1) WILD-TYPE 
                        28.405                         30.610 
[1] "10.7 - 78.6 (28.4)" "0.2 - 169.3 (30.6)"
[1] "hr="     "3300000"
D34V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 35(10Q25.1) MUTATED         2        0         2        0         0
  AMP PEAK 35(10Q25.1) WILD-TYPE     280       50       109        2        46
                                vv
clus                             STAGE IVC
  AMP PEAK 35(10Q25.1) MUTATED           0
  AMP PEAK 35(10Q25.1) WILD-TYPE         6
D34V3, multiclass
           clus
vv          AMP PEAK 35(10Q25.1) MUTATED AMP PEAK 35(10Q25.1) WILD-TYPE
  STAGE I                              2                            280
  STAGE II                             0                             50
  STAGE III                            2                            109
  STAGE IV                             0                              2
  STAGE IVA                            0                             46
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 35(10Q25.1) MUTATED     2   0   2   0
  AMP PEAK 35(10Q25.1) WILD-TYPE 140 165 165  23
D34V4, multiclass
    clus
vv   AMP PEAK 35(10Q25.1) MUTATED AMP PEAK 35(10Q25.1) WILD-TYPE
  T1                            2                            140
  T2                            0                            165
  T3                            2                            165
  T4                            0                             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"
D34V5, binary
                                cls
clus                               0   1
  AMP PEAK 35(10Q25.1) MUTATED     3   1
  AMP PEAK 35(10Q25.1) WILD-TYPE 222 223
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 35(10Q25.1) MUTATED      3    1
  AMP PEAK 35(10Q25.1) WILD-TYPE  222  223
   clus
vv  AMP PEAK 35(10Q25.1) MUTATED AMP PEAK 35(10Q25.1) WILD-TYPE
  0                            3                            222
  1                            1                            223
[1] 2 2
[1] FALSE
D34V6, binary
                                cls
clus                               0   1
  AMP PEAK 35(10Q25.1) MUTATED     1   0
  AMP PEAK 35(10Q25.1) WILD-TYPE 277   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 35(10Q25.1) MUTATED      1    0
  AMP PEAK 35(10Q25.1) WILD-TYPE  277    9
   clus
vv  AMP PEAK 35(10Q25.1) MUTATED AMP PEAK 35(10Q25.1) WILD-TYPE
  0                            1                            277
  1                            0                              9
[1] 2 2
[1] FALSE
D34V7, binary
                                cls
clus                               0   1
  AMP PEAK 35(10Q25.1) MUTATED     3   1
  AMP PEAK 35(10Q25.1) WILD-TYPE 362 133
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 35(10Q25.1) MUTATED      3    1
  AMP PEAK 35(10Q25.1) WILD-TYPE  362  133
        clus
vv       AMP PEAK 35(10Q25.1) MUTATED AMP PEAK 35(10Q25.1) WILD-TYPE
  FEMALE                            3                            362
  MALE                              1                            133
[1] 2 2
[1] FALSE
D34V8, binary
                                cls
clus                               0   1
  AMP PEAK 35(10Q25.1) MUTATED     1   3
  AMP PEAK 35(10Q25.1) WILD-TYPE 184 287
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 35(10Q25.1) MUTATED      1    3
  AMP PEAK 35(10Q25.1) WILD-TYPE  184  287
     clus
vv    AMP PEAK 35(10Q25.1) MUTATED AMP PEAK 35(10Q25.1) WILD-TYPE
  NO                             1                            184
  YES                            3                            287
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 35(10Q25.1) MUTATED                0
  AMP PEAK 35(10Q25.1) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 35(10Q25.1) MUTATED                                               1
  AMP PEAK 35(10Q25.1) WILD-TYPE                                           354
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 35(10Q25.1) MUTATED                                                                        2
  AMP PEAK 35(10Q25.1) WILD-TYPE                                                                     98
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 35(10Q25.1) MUTATED                                                                     1
  AMP PEAK 35(10Q25.1) WILD-TYPE                                                                  35
D34V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 35(10Q25.1) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     1
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               1
                                                                        clus
vv                                                                       AMP PEAK 35(10Q25.1) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     354
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V10, binary
                                cls
clus                               0   1
  AMP PEAK 35(10Q25.1) MUTATED     4   0
  AMP PEAK 35(10Q25.1) WILD-TYPE 416  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 35(10Q25.1) MUTATED      4    0
  AMP PEAK 35(10Q25.1) WILD-TYPE  416   17
     clus
vv    AMP PEAK 35(10Q25.1) MUTATED AMP PEAK 35(10Q25.1) WILD-TYPE
  NO                             4                            416
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 35(10Q25.1) MUTATED              1                       0    3
  AMP PEAK 35(10Q25.1) WILD-TYPE          131                      18  327
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 35(10Q25.1) MUTATED                     0
  AMP PEAK 35(10Q25.1) WILD-TYPE                   1
D34V11, multiclass
                         clus
vv                        AMP PEAK 35(10Q25.1) MUTATED
  MINIMAL (T3)                                       1
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               3
  VERY ADVANCED (T4B)                                0
                         clus
vv                        AMP PEAK 35(10Q25.1) WILD-TYPE
  MINIMAL (T3)                                       131
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               327
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 35(10Q25.1) MUTATED     2   0   0   2
  AMP PEAK 35(10Q25.1) WILD-TYPE 381  51   4  28
D34V12, multiclass
    clus
vv   AMP PEAK 35(10Q25.1) MUTATED AMP PEAK 35(10Q25.1) WILD-TYPE
  R0                            2                            381
  R1                            0                             51
  R2                            0                              4
  RX                            2                             28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V13, continuous
D34V14, binary
                                cls
clus                               0   1
  AMP PEAK 35(10Q25.1) MUTATED     2   2
  AMP PEAK 35(10Q25.1) WILD-TYPE 223 262
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 35(10Q25.1) MUTATED      2    2
  AMP PEAK 35(10Q25.1) WILD-TYPE  223  262
            clus
vv           AMP PEAK 35(10Q25.1) MUTATED AMP PEAK 35(10Q25.1) WILD-TYPE
  MULTIFOCAL                            2                            223
  UNIFOCAL                              2                            262
[1] 2 2
[1] FALSE
D34V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 35(10Q25.1) MUTATED                                  0     1
  AMP PEAK 35(10Q25.1) WILD-TYPE                                1    51
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 35(10Q25.1) MUTATED                           0     1
  AMP PEAK 35(10Q25.1) WILD-TYPE                        27   327
D34V16, multiclass
[1] "Remove cluster labels:"       "AMP PEAK 35(10Q25.1) MUTATED"
clus
  AMP PEAK 35(10Q25.1) MUTATED AMP PEAK 35(10Q25.1) WILD-TYPE 
                             2                            406 
                    TCGA-4C-A93U                     TCGA-BJ-A0YZ 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A0Z2                     TCGA-BJ-A0Z3 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A0Z5                     TCGA-BJ-A0Z9 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A0ZA                     TCGA-BJ-A0ZB 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A0ZC                     TCGA-BJ-A0ZE 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A0ZG                     TCGA-BJ-A0ZH 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A0ZJ                     TCGA-BJ-A18Y 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A18Z                     TCGA-BJ-A190 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A191                     TCGA-BJ-A192 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A28R                     TCGA-BJ-A28S 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A28T                     TCGA-BJ-A28V 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A28W                     TCGA-BJ-A28X 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A28Z                     TCGA-BJ-A290 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A291                     TCGA-BJ-A2N7 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A2N8                     TCGA-BJ-A2N9 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A2NA                     TCGA-BJ-A2P4 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A3EZ                     TCGA-BJ-A3F0 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A3PR                     TCGA-BJ-A3PT 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A3PU                     TCGA-BJ-A45C 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A45D                     TCGA-BJ-A45E 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A45F                     TCGA-BJ-A45G 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A45H                     TCGA-BJ-A45I 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A45J                     TCGA-BJ-A45K 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A4O8                     TCGA-BJ-A4O9 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-CE-A13K                     TCGA-CE-A27D 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-CE-A3MD                     TCGA-CE-A3ME 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-CE-A481                     TCGA-CE-A482 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-CE-A483                     TCGA-CE-A484 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-CE-A485                     TCGA-DE-A0XZ 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DE-A0Y2                     TCGA-DE-A0Y3 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DE-A2OL                     TCGA-DE-A3KN 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DE-A4M8                     TCGA-DE-A4M9 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DE-A4MA                     TCGA-DE-A4MB 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DE-A4MC                     TCGA-DE-A4MD 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DE-A69J                     TCGA-DE-A69K 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DE-A7U5                     TCGA-DJ-A13L 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A13M                     TCGA-DJ-A13O 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A13P                     TCGA-DJ-A13R 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A13S                     TCGA-DJ-A13T 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A13U                     TCGA-DJ-A13W 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A1QD                     TCGA-DJ-A1QE 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A1QF                     TCGA-DJ-A1QG 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A1QH                     TCGA-DJ-A1QI 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A1QM                     TCGA-DJ-A1QO 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A1QQ                     TCGA-DJ-A2PN 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A2PO                     TCGA-DJ-A2PQ 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A2PR                     TCGA-DJ-A2PS 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A2PT                     TCGA-DJ-A2PU 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A2PV                     TCGA-DJ-A2PW 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A2PX                     TCGA-DJ-A2PY 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A2PZ                     TCGA-DJ-A2Q0 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A2Q1                     TCGA-DJ-A2Q2 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A2Q3                     TCGA-DJ-A2Q4 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A2Q5                     TCGA-DJ-A2Q6 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A2Q7                     TCGA-DJ-A2Q9 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A2QA                     TCGA-DJ-A2QB 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A3UK                     TCGA-DJ-A3UM 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A3UN                     TCGA-DJ-A3UO 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A3UR                     TCGA-DJ-A3US 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A3UT                     TCGA-DJ-A3UU 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A3UW                     TCGA-DJ-A3UX 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A3UY                     TCGA-DJ-A3UZ 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A3V2                     TCGA-DJ-A3V3 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A3V4                     TCGA-DJ-A3V5 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A3V7                     TCGA-DJ-A3V8 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A3V9                     TCGA-DJ-A3VD 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A3VE                     TCGA-DJ-A3VF 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A3VG                     TCGA-DJ-A3VI 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A3VJ                     TCGA-DJ-A3VK 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A3VL                     TCGA-DJ-A3VM 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A4UL                     TCGA-DJ-A4UP 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A4UQ                     TCGA-DJ-A4UR 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A4UT                     TCGA-DJ-A4UW 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A4V0                     TCGA-DJ-A4V4 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A4V5                     TCGA-DO-A1JZ 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-DO-A1K0                     TCGA-DO-A2HM 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-E3-A3DY                     TCGA-E3-A3DZ 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-E3-A3E0                     TCGA-E3-A3E1 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-E3-A3E2                     TCGA-E3-A3E3 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-E3-A3E5                     TCGA-E8-A242 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-E8-A2EA                     TCGA-E8-A3X7 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-E8-A413                     TCGA-E8-A414 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-E8-A415                     TCGA-E8-A416 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-E8-A417                     TCGA-E8-A418 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-E8-A419                     TCGA-E8-A432 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-E8-A433                     TCGA-E8-A434 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-E8-A436                     TCGA-E8-A437 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-E8-A438                     TCGA-E8-A44K 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-E8-A44M                     TCGA-EL-A3CL 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3CM                     TCGA-EL-A3CN 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3CO                     TCGA-EL-A3CP 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3CR                     TCGA-EL-A3CS 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3CT                     TCGA-EL-A3CU 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3CV                     TCGA-EL-A3CW 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3CX                     TCGA-EL-A3CY 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3CZ                     TCGA-EL-A3D0 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3D1                     TCGA-EL-A3D4 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3D5                     TCGA-EL-A3D6 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3GO                     TCGA-EL-A3GP 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3GQ                     TCGA-EL-A3GR 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3GS                     TCGA-EL-A3GU 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3GV                     TCGA-EL-A3GW 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3GX                     TCGA-EL-A3GY 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3GZ                     TCGA-EL-A3H1 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3H2                     TCGA-EL-A3H3 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3H4                     TCGA-EL-A3H5 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3H7                     TCGA-EL-A3H8 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3MW                     TCGA-EL-A3MX 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3MY                     TCGA-EL-A3MZ 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3N2                     TCGA-EL-A3N3 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3T0                     TCGA-EL-A3T1 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3T2                     TCGA-EL-A3T3 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3T6                     TCGA-EL-A3T7 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3T8                     TCGA-EL-A3T9 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3TA                     TCGA-EL-A3TB 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3ZG                     TCGA-EL-A3ZH 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3ZK                     TCGA-EL-A3ZL 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3ZN                     TCGA-EL-A3ZO 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3ZP                     TCGA-EL-A3ZQ 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3ZR                     TCGA-EL-A3ZS 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3ZT                     TCGA-EL-A4JV 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A4JW                     TCGA-EL-A4JX 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A4JZ                     TCGA-EL-A4K0 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A4K1                     TCGA-EL-A4K2 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A4K4                     TCGA-EL-A4K6 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A4K7                     TCGA-EL-A4K9 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A4KD                     TCGA-EL-A4KG 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A4KH                     TCGA-EL-A4KI 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EM-A22M                     TCGA-EM-A22O 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-EM-A2OV                     TCGA-EM-A3AI 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A25G                     TCGA-ET-A25I 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A25J                     TCGA-ET-A25K 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A25L                     TCGA-ET-A25M 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A25N                     TCGA-ET-A25O 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A25P                     TCGA-ET-A25R 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A2MX                     TCGA-ET-A2MY 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A2N0                     TCGA-ET-A2N1 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A2N3                     TCGA-ET-A2N4 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A2N5                     TCGA-ET-A39I 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A39J                     TCGA-ET-A39K 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A39M                     TCGA-ET-A39N 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A39O                     TCGA-ET-A39P 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A39R                     TCGA-ET-A39S 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A39T                     TCGA-ET-A3BN 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A3BO                     TCGA-ET-A3BP 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A3BQ                     TCGA-ET-A3BS 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A3BT                     TCGA-ET-A3BU 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A3BV                     TCGA-ET-A3BW 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A3BX                     TCGA-ET-A3DO 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A3DP                     TCGA-ET-A3DQ 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A3DR                     TCGA-ET-A3DS 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A3DT                     TCGA-ET-A3DU 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A3DV                     TCGA-ET-A3DW 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A40P                     TCGA-ET-A40Q 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A40R                     TCGA-ET-A40S 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A40T                     TCGA-ET-A4KN 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A4KQ                     TCGA-FE-A22Z 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-FE-A230                     TCGA-FE-A231 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-FE-A232                     TCGA-FE-A233 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-FE-A234                     TCGA-FE-A235 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-FE-A236                     TCGA-FE-A237 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-FE-A238                     TCGA-FE-A239 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-FE-A23A                     TCGA-FE-A3PA 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-FE-A3PB                     TCGA-FE-A3PC 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-FE-A3PD                     TCGA-FK-A3S3 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-FK-A3SB                     TCGA-FK-A3SD 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-FK-A3SE                     TCGA-FK-A3SG 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-FK-A3SH                     TCGA-FK-A4UB 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-FY-A2QD                     TCGA-FY-A3BL 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-FY-A3I4                     TCGA-FY-A3I5 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-FY-A3NM                     TCGA-FY-A3ON 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-FY-A3R6                     TCGA-FY-A3R7 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-FY-A3R8                     TCGA-FY-A3R9 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-FY-A3RA                     TCGA-FY-A3W9 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-FY-A3WA                     TCGA-FY-A3YR 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-FY-A40K                     TCGA-FY-A40L 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-FY-A40M                     TCGA-FY-A40N 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-FY-A4B0                     TCGA-FY-A4B3 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-FY-A4B4                     TCGA-FY-A76V 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-GE-A2C6                     TCGA-H2-A26U 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-H2-A2K9                     TCGA-H2-A3RH 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-H2-A3RI                     TCGA-H2-A421 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-H2-A422                     TCGA-IM-A3EB 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-IM-A3ED                     TCGA-IM-A3U2 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-IM-A3U3                     TCGA-IM-A41Y 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-IM-A41Z                     TCGA-IM-A420 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-IM-A4EB                     TCGA-J8-A3NZ 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-J8-A3O0                     TCGA-J8-A3O1 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-J8-A3O2                     TCGA-J8-A3YD 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-J8-A3YE                     TCGA-J8-A3YF 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-J8-A3YG                     TCGA-J8-A3YH 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-J8-A42S                     TCGA-J8-A4HW 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-J8-A4HY                     TCGA-KS-A41F 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-KS-A41I                     TCGA-KS-A41J 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-KS-A41L                     TCGA-KS-A4I1 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-KS-A4I3                     TCGA-KS-A4I5 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-KS-A4I7                     TCGA-KS-A4I9 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-KS-A4IB                     TCGA-KS-A4IC 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-KS-A4ID                     TCGA-L6-A4EP 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-L6-A4EQ                     TCGA-L6-A4ET 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-L6-A4EU                     TCGA-MK-A4N6 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-MK-A4N7                     TCGA-MK-A4N9 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
                    TCGA-MK-A84Z                     TCGA-QD-A8IV 
"AMP PEAK 35(10Q25.1) WILD-TYPE" "AMP PEAK 35(10Q25.1) WILD-TYPE" 
D34V17, binary
                                cls
clus                               0   1
  AMP PEAK 35(10Q25.1) MUTATED     0   2
  AMP PEAK 35(10Q25.1) WILD-TYPE  38 357
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 35(10Q25.1) MUTATED      0    2
  AMP PEAK 35(10Q25.1) WILD-TYPE   38  357
                        clus
vv                       AMP PEAK 35(10Q25.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            2
                        clus
vv                       AMP PEAK 35(10Q25.1) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            357
[1] 2 2
[1] FALSE

Clustering(35) Variable = AMP PEAK 36(11P13) MUTATION ANALYSIS
D35V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 36(11P13) MUTATED     8   0
  AMP PEAK 36(11P13) WILD-TYPE 473  16
  AMP PEAK 36(11P13) MUTATED AMP PEAK 36(11P13) WILD-TYPE 
                           8                          489 
  AMP PEAK 36(11P13) MUTATED AMP PEAK 36(11P13) WILD-TYPE 
                           0                           16 
$`AMP PEAK 36(11P13) MUTATED`
TCGA-DJ-A2Q7 TCGA-E8-A414 TCGA-EL-A3ZR TCGA-EM-A1YC TCGA-EM-A2P2 TCGA-EM-A3SY 
       35.11        31.50        60.16        78.61        17.29        13.51 
TCGA-ET-A2MZ TCGA-ET-A39N 
       37.25       123.32 

$`AMP PEAK 36(11P13) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
       30.58        35.41        27.45        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74         6.77        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       31.27        29.98        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS 
       36.03        53.06        47.38        65.49        61.22         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       34.39        30.51        53.36        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       43.59        24.30        27.06        23.90        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YD 
       20.91        48.49        18.05        19.79        19.46        57.01 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       54.08        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.65        44.19        41.29        14.24        47.57        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       13.18        23.51         6.05         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        40.34        19.73        32.32        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.59        17.46        14.60        22.52        30.94        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR 
       14.14        33.07        13.38         8.35        29.72        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        47.38        21.01        12.07        17.49 
TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 
       17.39        16.18        15.02        14.50        15.06         7.33 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
        0.49         9.24        13.91        38.66        38.86        29.95 
TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       29.85        12.79        84.59        29.33        21.34         5.33 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
       26.37        26.37        22.45        21.53        60.49        24.46 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
       13.68        81.93        81.70        77.56        70.42        56.58 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       60.20        63.39        65.29        18.38        63.45        88.41 
TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       58.75        52.60        54.35        83.34         2.66        80.88 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O 
       33.24       106.09       107.41       108.46        84.89       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       95.34        94.13        55.10        98.20        28.24        50.40 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
       79.10        76.64         5.79        87.62        77.82        75.42 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
       46.65        52.47       116.78        94.59        84.85        80.58 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
       66.84        43.73        62.83       166.62        24.72        43.99 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
       46.26        44.38        40.21        37.48        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      117.40        66.77       112.80        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        1.05        13.28         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
       20.42        17.82         7.82         0.99        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08         0.30         0.76 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16         6.58        22.49        19.04 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35        21.60         1.68        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46         2.99        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       18.51        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       17.23        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY 
       24.69        22.29         5.75         2.47         2.60         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.40        40.37        21.83         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       30.21        23.93        12.89 

  AMP PEAK 36(11P13) MUTATED AMP PEAK 36(11P13) WILD-TYPE 
                       13.51                         0.16 
  AMP PEAK 36(11P13) MUTATED AMP PEAK 36(11P13) WILD-TYPE 
                      123.32                       169.32 
  AMP PEAK 36(11P13) MUTATED AMP PEAK 36(11P13) WILD-TYPE 
                       36.18                        30.58 
[1] "13.5 - 123.3 (36.2)" "0.2 - 169.3 (30.6)" 
[1] "hr="     "9200000"
D35V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 36(11P13) MUTATED         3        1         4        0         0
  AMP PEAK 36(11P13) WILD-TYPE     279       49       107        2        46
                              vv
clus                           STAGE IVC
  AMP PEAK 36(11P13) MUTATED           0
  AMP PEAK 36(11P13) WILD-TYPE         6
D35V3, multiclass
           clus
vv          AMP PEAK 36(11P13) MUTATED AMP PEAK 36(11P13) WILD-TYPE
  STAGE I                            3                          279
  STAGE II                           1                           49
  STAGE III                          4                          107
  STAGE IV                           0                            2
  STAGE IVA                          0                           46
  STAGE IVC                          0                            6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 36(11P13) MUTATED     2   2   4   0
  AMP PEAK 36(11P13) WILD-TYPE 140 163 163  23
D35V4, multiclass
    clus
vv   AMP PEAK 36(11P13) MUTATED AMP PEAK 36(11P13) WILD-TYPE
  T1                          2                          140
  T2                          2                          163
  T3                          4                          163
  T4                          0                           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"
D35V5, binary
                              cls
clus                             0   1
  AMP PEAK 36(11P13) MUTATED     5   1
  AMP PEAK 36(11P13) WILD-TYPE 220 223
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 36(11P13) MUTATED      5    1
  AMP PEAK 36(11P13) WILD-TYPE  220  223
   clus
vv  AMP PEAK 36(11P13) MUTATED AMP PEAK 36(11P13) WILD-TYPE
  0                          5                          220
  1                          1                          223
[1] 2 2
[1] FALSE
D35V6, binary
                              cls
clus                             0   1
  AMP PEAK 36(11P13) MUTATED     3   0
  AMP PEAK 36(11P13) WILD-TYPE 275   9
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 36(11P13) MUTATED      3    0
  AMP PEAK 36(11P13) WILD-TYPE  275    9
   clus
vv  AMP PEAK 36(11P13) MUTATED AMP PEAK 36(11P13) WILD-TYPE
  0                          3                          275
  1                          0                            9
[1] 2 2
[1] FALSE
D35V7, binary
                              cls
clus                             0   1
  AMP PEAK 36(11P13) MUTATED     5   3
  AMP PEAK 36(11P13) WILD-TYPE 360 131
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 36(11P13) MUTATED      5    3
  AMP PEAK 36(11P13) WILD-TYPE  360  131
        clus
vv       AMP PEAK 36(11P13) MUTATED AMP PEAK 36(11P13) WILD-TYPE
  FEMALE                          5                          360
  MALE                            3                          131
[1] 2 2
[1] FALSE
D35V8, binary
                              cls
clus                             0   1
  AMP PEAK 36(11P13) MUTATED     4   4
  AMP PEAK 36(11P13) WILD-TYPE 181 286
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 36(11P13) MUTATED      4    4
  AMP PEAK 36(11P13) WILD-TYPE  181  286
     clus
vv    AMP PEAK 36(11P13) MUTATED AMP PEAK 36(11P13) WILD-TYPE
  NO                           4                          181
  YES                          4                          286
[1] 2 2
[1] FALSE
                              vv
clus                           OTHER  SPECIFY
  AMP PEAK 36(11P13) MUTATED                0
  AMP PEAK 36(11P13) WILD-TYPE              8
                              vv
clus                           THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 36(11P13) MUTATED                                               5
  AMP PEAK 36(11P13) WILD-TYPE                                           350
                              vv
clus                           THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 36(11P13) MUTATED                                                                        3
  AMP PEAK 36(11P13) WILD-TYPE                                                                     97
                              vv
clus                           THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 36(11P13) MUTATED                                                                     0
  AMP PEAK 36(11P13) WILD-TYPE                                                                  36
D35V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 36(11P13) MUTATED
  OTHER  SPECIFY                                                                                  0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   5
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                             0
                                                                        clus
vv                                                                       AMP PEAK 36(11P13) WILD-TYPE
  OTHER  SPECIFY                                                                                    8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           97
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V10, binary
                              cls
clus                             0   1
  AMP PEAK 36(11P13) MUTATED     8   0
  AMP PEAK 36(11P13) WILD-TYPE 412  17
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 36(11P13) MUTATED      8    0
  AMP PEAK 36(11P13) WILD-TYPE  412   17
     clus
vv    AMP PEAK 36(11P13) MUTATED AMP PEAK 36(11P13) WILD-TYPE
  NO                           8                          412
  YES                          0                           17
[1] 2 2
[1] FALSE
                              vv
clus                           MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 36(11P13) MUTATED              1                       0    7
  AMP PEAK 36(11P13) WILD-TYPE          131                      18  323
                              vv
clus                           VERY ADVANCED (T4B)
  AMP PEAK 36(11P13) MUTATED                     0
  AMP PEAK 36(11P13) WILD-TYPE                   1
D35V11, multiclass
                         clus
vv                        AMP PEAK 36(11P13) MUTATED
  MINIMAL (T3)                                     1
  MODERATE/ADVANCED (T4A)                          0
  NONE                                             7
  VERY ADVANCED (T4B)                              0
                         clus
vv                        AMP PEAK 36(11P13) WILD-TYPE
  MINIMAL (T3)                                     131
  MODERATE/ADVANCED (T4A)                           18
  NONE                                             323
  VERY ADVANCED (T4B)                                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 36(11P13) MUTATED     7   0   0   1
  AMP PEAK 36(11P13) WILD-TYPE 376  51   4  29
D35V12, multiclass
    clus
vv   AMP PEAK 36(11P13) MUTATED AMP PEAK 36(11P13) WILD-TYPE
  R0                          7                          376
  R1                          0                           51
  R2                          0                            4
  RX                          1                           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"
D35V13, continuous
D35V14, binary
                              cls
clus                             0   1
  AMP PEAK 36(11P13) MUTATED     2   6
  AMP PEAK 36(11P13) WILD-TYPE 223 258
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 36(11P13) MUTATED      2    6
  AMP PEAK 36(11P13) WILD-TYPE  223  258
            clus
vv           AMP PEAK 36(11P13) MUTATED AMP PEAK 36(11P13) WILD-TYPE
  MULTIFOCAL                          2                          223
  UNIFOCAL                            6                          258
[1] 2 2
[1] FALSE
D35V15, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 36(11P13) MUTATED                                  0     2
  AMP PEAK 36(11P13) WILD-TYPE                                1    50
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 36(11P13) MUTATED                           0     3
  AMP PEAK 36(11P13) WILD-TYPE                        27   325
D35V16, multiclass
                                  clus
vv                                 AMP PEAK 36(11P13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                 0
  WHITE                                                     3
                                  clus
vv                                 AMP PEAK 36(11P13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      50
  BLACK OR AFRICAN AMERICAN                                  27
  WHITE                                                     325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V17, binary
                              cls
clus                             0   1
  AMP PEAK 36(11P13) MUTATED     0   5
  AMP PEAK 36(11P13) WILD-TYPE  38 354
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 36(11P13) MUTATED      0    5
  AMP PEAK 36(11P13) WILD-TYPE   38  354
                        clus
vv                       AMP PEAK 36(11P13) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                          5
                        clus
vv                       AMP PEAK 36(11P13) WILD-TYPE
  HISPANIC OR LATINO                               38
  NOT HISPANIC OR LATINO                          354
[1] 2 2
[1] FALSE

Clustering(36) Variable = AMP PEAK 37(12P11.1) MUTATION ANALYSIS
D36V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 37(12P11.1) MUTATED    16   0
  AMP PEAK 37(12P11.1) WILD-TYPE 465  16
  AMP PEAK 37(12P11.1) MUTATED AMP PEAK 37(12P11.1) WILD-TYPE 
                            16                            481 
  AMP PEAK 37(12P11.1) MUTATED AMP PEAK 37(12P11.1) WILD-TYPE 
                             0                             16 
$`AMP PEAK 37(12P11.1) MUTATED`
TCGA-BJ-A190 TCGA-BJ-A2N9 TCGA-DJ-A1QE TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N 
       20.58        20.48       135.91        78.61        57.01        10.65 
TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A2N3 
        6.05        32.32        22.52        13.51        37.25        83.34 
TCGA-ET-A39N TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3WA 
      123.32         7.82         0.99        17.06 

$`AMP PEAK 37(12P11.1) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        42.08        51.39        41.52         4.83        44.35 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
       42.15        21.04        35.54        32.45        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
       11.08        30.21        22.88        18.38        16.57        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        7.99        10.88        21.01         3.45        23.84        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
       15.45        21.63        23.18        19.43        23.47        12.66 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
       12.43        12.66        35.84        21.63        50.17        37.64 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M 
       25.12        14.70        14.27         2.76         9.96        48.79 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       38.17       169.32        18.58         8.71        56.19        23.38 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QF TCGA-DJ-A1QG 
       43.17        52.37         8.32        11.01        30.61        44.98 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
       42.51        14.96        17.59         6.02        42.58        47.41 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
       17.56        10.09         7.82        30.58        35.41        27.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
       26.20        38.83        33.96        31.99        34.85        28.96 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42        34.36        37.74         6.77        40.24 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
       33.93        37.48        36.46        35.11        39.09        35.90 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       33.53        35.18        15.88        36.92        31.04        32.42 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        36.33 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        59.57        11.34        35.87        40.96        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        42.54        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM 
       35.67         3.12        36.43        24.76        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       30.87        21.34        33.04        34.78        27.06        26.93 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       35.54         3.12        15.81        35.38        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        92.55        47.21        66.38        80.52        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 
       52.44        39.95        31.23        35.67        31.27        29.98 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 
       31.50        31.04         0.72         0.26         3.02        25.45 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       30.61         0.16         0.23        14.96         7.69        33.50 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
        0.39         0.39        31.66        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      158.83         7.66        45.53        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 
       57.01       106.62         4.18        79.50       139.86        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       69.57        57.11       108.36        64.87        49.51        50.24 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
      115.10        65.39       136.01        50.37        50.20       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       83.57       139.00       150.48       108.66        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       52.50        29.65       147.42       142.52       129.57        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      132.07        98.24        41.29       107.47         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM 
       82.82        89.56        78.97        51.78        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        65.49        61.22        60.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       34.39        30.51        53.36        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       43.59        24.30        27.06        23.90        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE 
       20.91        48.49        18.05        19.79        19.46        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O 
       14.73        14.50        15.75        10.45        14.53        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       19.73        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.06         7.33         0.49         9.24        13.91        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       38.86        29.95        29.85        12.79        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
       21.34         5.33        26.37        26.37        22.45        21.53 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       60.49        24.46        13.68        81.93        81.70        77.56 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       70.42        56.58        60.20        63.39        65.29        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N4 
       63.45        88.41        58.75        52.60        54.35         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       80.88        33.24       106.09       107.41       108.46        84.89 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
      100.57        95.34        94.13        55.10        98.20        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
       50.40        79.10        76.64         5.79        87.62        77.82 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       75.42        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       117.40        66.77       112.80        39.95        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.11         1.05        13.28         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        1.25        20.42        17.82        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3YR 
       15.68        16.57        18.08         0.30         0.76        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       15.16         6.58        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83        31.10         8.22        25.64        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        23.93 
TCGA-QD-A8IV 
       12.89 

  AMP PEAK 37(12P11.1) MUTATED AMP PEAK 37(12P11.1) WILD-TYPE 
                          0.99                           0.16 
  AMP PEAK 37(12P11.1) MUTATED AMP PEAK 37(12P11.1) WILD-TYPE 
                        135.91                         169.32 
  AMP PEAK 37(12P11.1) MUTATED AMP PEAK 37(12P11.1) WILD-TYPE 
                         21.55                          30.61 
[1] "1.0 - 135.9 (21.5)" "0.2 - 169.3 (30.6)"
[1] "hr="     "2.6e+07"
D36V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 37(12P11.1) MUTATED         7        5         4        0         0
  AMP PEAK 37(12P11.1) WILD-TYPE     275       45       107        2        46
                                vv
clus                             STAGE IVC
  AMP PEAK 37(12P11.1) MUTATED           0
  AMP PEAK 37(12P11.1) WILD-TYPE         6
D36V3, multiclass
           clus
vv          AMP PEAK 37(12P11.1) MUTATED AMP PEAK 37(12P11.1) WILD-TYPE
  STAGE I                              7                            275
  STAGE II                             5                             45
  STAGE III                            4                            107
  STAGE IV                             0                              2
  STAGE IVA                            0                             46
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 37(12P11.1) MUTATED     4   7   5   0
  AMP PEAK 37(12P11.1) WILD-TYPE 138 158 162  23
D36V4, multiclass
    clus
vv   AMP PEAK 37(12P11.1) MUTATED AMP PEAK 37(12P11.1) WILD-TYPE
  T1                            4                            138
  T2                            7                            158
  T3                            5                            162
  T4                            0                             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"
D36V5, binary
                                cls
clus                               0   1
  AMP PEAK 37(12P11.1) MUTATED    10   0
  AMP PEAK 37(12P11.1) WILD-TYPE 215 224
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 37(12P11.1) MUTATED     10    0
  AMP PEAK 37(12P11.1) WILD-TYPE  215  224
   clus
vv  AMP PEAK 37(12P11.1) MUTATED AMP PEAK 37(12P11.1) WILD-TYPE
  0                           10                            215
  1                            0                            224
[1] 2 2
[1] FALSE
D36V6, binary
                                cls
clus                               0   1
  AMP PEAK 37(12P11.1) MUTATED     2   0
  AMP PEAK 37(12P11.1) WILD-TYPE 276   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 37(12P11.1) MUTATED      2    0
  AMP PEAK 37(12P11.1) WILD-TYPE  276    9
   clus
vv  AMP PEAK 37(12P11.1) MUTATED AMP PEAK 37(12P11.1) WILD-TYPE
  0                            2                            276
  1                            0                              9
[1] 2 2
[1] FALSE
D36V7, binary
                                cls
clus                               0   1
  AMP PEAK 37(12P11.1) MUTATED    13   3
  AMP PEAK 37(12P11.1) WILD-TYPE 352 131
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 37(12P11.1) MUTATED     13    3
  AMP PEAK 37(12P11.1) WILD-TYPE  352  131
        clus
vv       AMP PEAK 37(12P11.1) MUTATED AMP PEAK 37(12P11.1) WILD-TYPE
  FEMALE                           13                            352
  MALE                              3                            131
[1] 2 2
[1] FALSE
D36V8, binary
                                cls
clus                               0   1
  AMP PEAK 37(12P11.1) MUTATED     6   8
  AMP PEAK 37(12P11.1) WILD-TYPE 179 282
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 37(12P11.1) MUTATED      6    8
  AMP PEAK 37(12P11.1) WILD-TYPE  179  282
     clus
vv    AMP PEAK 37(12P11.1) MUTATED AMP PEAK 37(12P11.1) WILD-TYPE
  NO                             6                            179
  YES                            8                            282
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 37(12P11.1) MUTATED                0
  AMP PEAK 37(12P11.1) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 37(12P11.1) MUTATED                                               6
  AMP PEAK 37(12P11.1) WILD-TYPE                                           349
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 37(12P11.1) MUTATED                                                                       10
  AMP PEAK 37(12P11.1) WILD-TYPE                                                                     90
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 37(12P11.1) MUTATED                                                                     0
  AMP PEAK 37(12P11.1) WILD-TYPE                                                                  36
D36V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 37(12P11.1) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     6
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           10
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       AMP PEAK 37(12P11.1) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     349
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             90
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V10, binary
                                cls
clus                               0   1
  AMP PEAK 37(12P11.1) MUTATED    15   0
  AMP PEAK 37(12P11.1) WILD-TYPE 405  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 37(12P11.1) MUTATED     15    0
  AMP PEAK 37(12P11.1) WILD-TYPE  405   17
     clus
vv    AMP PEAK 37(12P11.1) MUTATED AMP PEAK 37(12P11.1) WILD-TYPE
  NO                            15                            405
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 37(12P11.1) MUTATED              2                       0   14
  AMP PEAK 37(12P11.1) WILD-TYPE          130                      18  316
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 37(12P11.1) MUTATED                     0
  AMP PEAK 37(12P11.1) WILD-TYPE                   1
D36V11, multiclass
                         clus
vv                        AMP PEAK 37(12P11.1) MUTATED
  MINIMAL (T3)                                       2
  MODERATE/ADVANCED (T4A)                            0
  NONE                                              14
  VERY ADVANCED (T4B)                                0
                         clus
vv                        AMP PEAK 37(12P11.1) WILD-TYPE
  MINIMAL (T3)                                       130
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               316
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 37(12P11.1) MUTATED    12   1   0   3
  AMP PEAK 37(12P11.1) WILD-TYPE 371  50   4  27
D36V12, multiclass
    clus
vv   AMP PEAK 37(12P11.1) MUTATED AMP PEAK 37(12P11.1) WILD-TYPE
  R0                           12                            371
  R1                            1                             50
  R2                            0                              4
  RX                            3                             27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V13, continuous
D36V14, binary
                                cls
clus                               0   1
  AMP PEAK 37(12P11.1) MUTATED     7   9
  AMP PEAK 37(12P11.1) WILD-TYPE 218 255
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 37(12P11.1) MUTATED      7    9
  AMP PEAK 37(12P11.1) WILD-TYPE  218  255
            clus
vv           AMP PEAK 37(12P11.1) MUTATED AMP PEAK 37(12P11.1) WILD-TYPE
  MULTIFOCAL                            7                            218
  UNIFOCAL                              9                            255
[1] 2 2
[1] FALSE
D36V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 37(12P11.1) MUTATED                                  0     0
  AMP PEAK 37(12P11.1) WILD-TYPE                                1    52
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 37(12P11.1) MUTATED                           0    10
  AMP PEAK 37(12P11.1) WILD-TYPE                        27   318
D36V16, multiclass
                                  clus
vv                                 AMP PEAK 37(12P11.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                      10
                                  clus
vv                                 AMP PEAK 37(12P11.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        52
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       318
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V17, binary
                                cls
clus                               0   1
  AMP PEAK 37(12P11.1) MUTATED     0   9
  AMP PEAK 37(12P11.1) WILD-TYPE  38 350
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 37(12P11.1) MUTATED      0    9
  AMP PEAK 37(12P11.1) WILD-TYPE   38  350
                        clus
vv                       AMP PEAK 37(12P11.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            9
                        clus
vv                       AMP PEAK 37(12P11.1) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            350
[1] 2 2
[1] FALSE

Clustering(37) Variable = AMP PEAK 38(12Q21.31) MUTATION ANALYSIS
D37V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 38(12Q21.31) MUTATED    17   0
  AMP PEAK 38(12Q21.31) WILD-TYPE 464  16
  AMP PEAK 38(12Q21.31) MUTATED AMP PEAK 38(12Q21.31) WILD-TYPE 
                             17                             480 
  AMP PEAK 38(12Q21.31) MUTATED AMP PEAK 38(12Q21.31) WILD-TYPE 
                              0                              16 
$`AMP PEAK 38(12Q21.31) MUTATED`
TCGA-BJ-A190 TCGA-BJ-A2N9 TCGA-EL-A3GO TCGA-EL-A3ZQ TCGA-EM-A1YC TCGA-EM-A1YD 
       20.58        20.48        64.87        61.22        78.61        57.01 
TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3SY TCGA-ET-A2MZ 
       10.65         6.05        32.32        22.52        13.51        37.25 
TCGA-ET-A39N TCGA-ET-A3DS TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3WA 
      123.32        66.84         7.82         0.99        17.06 

$`AMP PEAK 38(12Q21.31) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        42.08        51.39        41.52         4.83        44.35 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
       42.15        21.04        35.54        32.45        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
       11.08        30.21        22.88        18.38        16.57        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        7.99        10.88        21.01         3.45        23.84        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
       15.45        21.63        23.18        19.43        23.47        12.66 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
       12.43        12.66        35.84        21.63        50.17        37.64 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M 
       25.12        14.70        14.27         2.76         9.96        48.79 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       38.17       169.32        18.58         8.71        56.19        23.38 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       43.17        52.37         8.32        11.01       135.91        30.61 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       44.98        42.51        14.96        17.59         6.02        42.58 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
       47.41        17.56        10.09         7.82        30.58        35.41 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       27.45        26.20        38.83        33.96        31.99        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       28.96         8.78         8.42        34.36        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24        33.93        37.48        36.46        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        33.53        35.18        15.88        36.92        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       32.42        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        17.69        59.57        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        42.54        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL 
        7.76        35.67         3.12        36.43        24.76        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        21.34        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        52.44        39.95        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GP TCGA-EL-A3GQ 
       98.53        69.57        57.11       108.36        49.51        50.24 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
      115.10        65.39       136.01        50.37        50.20       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       83.57       139.00       150.48       108.66        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       52.50        29.65       147.42       142.52       129.57        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      132.07        98.24        41.29       107.47         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM 
       82.82        89.56        78.97        51.78        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       53.06        47.38        65.49        60.16         7.07        59.44 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       57.47        34.72        45.96        37.94        31.04        34.39 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        53.36        44.15        41.13        47.84        43.59 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       24.30        27.06        23.90        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I 
       48.49        18.05        19.79        19.46        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P 
       14.50        15.75        10.45        14.53        44.19        41.29 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP 
       14.24        47.57        17.88        13.18        23.51         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ 
       33.96        17.59        17.46        17.29        14.60        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        33.07        13.38         8.35        29.72 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        47.38        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 
       17.49        17.39        16.18        15.02        14.50        15.06 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33         0.49         9.24        13.91        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       29.95        29.85        12.79        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        5.33        26.37        26.37        22.45        21.53        60.49 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       24.46        13.68        81.93        81.70        77.56        70.42 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       56.58        60.20        63.39        65.29        18.38        63.45 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       88.41        58.75        52.60        54.35        83.34         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       80.88        33.24       106.09       107.41       108.46        84.89 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
      100.57        95.34        94.13        55.10        98.20        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
       50.40        79.10        76.64         5.79        87.62        77.82 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       75.42        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
       80.58        43.73        62.83       166.62        24.72        43.99 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
       46.26        44.38        40.21        37.48        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      117.40        66.77       112.80        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        1.05        13.28         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       20.42        17.82        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3YR TCGA-FY-A40K 
       16.57        18.08         0.30         0.76        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58        22.49        19.04         1.35        21.60         1.68 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46         2.99        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        18.51        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
       31.10         8.22        25.64        17.23        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
      113.85        26.70        43.69        18.64        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       84.72        35.28        33.24        33.40        40.37        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        9.50        36.10        32.45        30.21        23.93        12.89 

  AMP PEAK 38(12Q21.31) MUTATED AMP PEAK 38(12Q21.31) WILD-TYPE 
                           0.99                            0.16 
  AMP PEAK 38(12Q21.31) MUTATED AMP PEAK 38(12Q21.31) WILD-TYPE 
                         123.32                          169.32 
  AMP PEAK 38(12Q21.31) MUTATED AMP PEAK 38(12Q21.31) WILD-TYPE 
                          22.52                           30.61 
[1] "1.0 - 123.3 (22.5)" "0.2 - 169.3 (30.6)"
[1] "hr="     "2.6e+07"
D37V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 38(12Q21.31) MUTATED         8        6         3        0         0
  AMP PEAK 38(12Q21.31) WILD-TYPE     274       44       108        2        46
                                 vv
clus                              STAGE IVC
  AMP PEAK 38(12Q21.31) MUTATED           0
  AMP PEAK 38(12Q21.31) WILD-TYPE         6
D37V3, multiclass
           clus
vv          AMP PEAK 38(12Q21.31) MUTATED AMP PEAK 38(12Q21.31) WILD-TYPE
  STAGE I                               8                             274
  STAGE II                              6                              44
  STAGE III                             3                             108
  STAGE IV                              0                               2
  STAGE IVA                             0                              46
  STAGE IVC                             0                               6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 38(12Q21.31) MUTATED     5   8   4   0
  AMP PEAK 38(12Q21.31) WILD-TYPE 137 157 163  23
D37V4, multiclass
    clus
vv   AMP PEAK 38(12Q21.31) MUTATED AMP PEAK 38(12Q21.31) WILD-TYPE
  T1                             5                             137
  T2                             8                             157
  T3                             4                             163
  T4                             0                              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"
D37V5, binary
                                 cls
clus                                0   1
  AMP PEAK 38(12Q21.31) MUTATED    12   0
  AMP PEAK 38(12Q21.31) WILD-TYPE 213 224
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 38(12Q21.31) MUTATED     12    0
  AMP PEAK 38(12Q21.31) WILD-TYPE  213  224
   clus
vv  AMP PEAK 38(12Q21.31) MUTATED AMP PEAK 38(12Q21.31) WILD-TYPE
  0                            12                             213
  1                             0                             224
[1] 2 2
[1] FALSE
D37V6, binary
                                 cls
clus                                0   1
  AMP PEAK 38(12Q21.31) MUTATED     3   0
  AMP PEAK 38(12Q21.31) WILD-TYPE 275   9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 38(12Q21.31) MUTATED      3    0
  AMP PEAK 38(12Q21.31) WILD-TYPE  275    9
   clus
vv  AMP PEAK 38(12Q21.31) MUTATED AMP PEAK 38(12Q21.31) WILD-TYPE
  0                             3                             275
  1                             0                               9
[1] 2 2
[1] FALSE
D37V7, binary
                                 cls
clus                                0   1
  AMP PEAK 38(12Q21.31) MUTATED    14   3
  AMP PEAK 38(12Q21.31) WILD-TYPE 351 131
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 38(12Q21.31) MUTATED     14    3
  AMP PEAK 38(12Q21.31) WILD-TYPE  351  131
        clus
vv       AMP PEAK 38(12Q21.31) MUTATED AMP PEAK 38(12Q21.31) WILD-TYPE
  FEMALE                            14                             351
  MALE                               3                             131
[1] 2 2
[1] FALSE
D37V8, binary
                                 cls
clus                                0   1
  AMP PEAK 38(12Q21.31) MUTATED     7   8
  AMP PEAK 38(12Q21.31) WILD-TYPE 178 282
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 38(12Q21.31) MUTATED      7    8
  AMP PEAK 38(12Q21.31) WILD-TYPE  178  282
     clus
vv    AMP PEAK 38(12Q21.31) MUTATED AMP PEAK 38(12Q21.31) WILD-TYPE
  NO                              7                             178
  YES                             8                             282
[1] 2 2
[1] FALSE
                                 vv
clus                              OTHER  SPECIFY
  AMP PEAK 38(12Q21.31) MUTATED                0
  AMP PEAK 38(12Q21.31) WILD-TYPE              8
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 38(12Q21.31) MUTATED                                               8
  AMP PEAK 38(12Q21.31) WILD-TYPE                                           347
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 38(12Q21.31) MUTATED                                                                        9
  AMP PEAK 38(12Q21.31) WILD-TYPE                                                                     91
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 38(12Q21.31) MUTATED                                                                     0
  AMP PEAK 38(12Q21.31) WILD-TYPE                                                                  36
D37V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 38(12Q21.31) MUTATED
  OTHER  SPECIFY                                                                                     0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      8
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             9
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                0
                                                                        clus
vv                                                                       AMP PEAK 38(12Q21.31) WILD-TYPE
  OTHER  SPECIFY                                                                                       8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      347
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                              91
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V10, binary
                                 cls
clus                                0   1
  AMP PEAK 38(12Q21.31) MUTATED    16   0
  AMP PEAK 38(12Q21.31) WILD-TYPE 404  17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 38(12Q21.31) MUTATED     16    0
  AMP PEAK 38(12Q21.31) WILD-TYPE  404   17
     clus
vv    AMP PEAK 38(12Q21.31) MUTATED AMP PEAK 38(12Q21.31) WILD-TYPE
  NO                             16                             404
  YES                             0                              17
[1] 2 2
[1] FALSE
                                 vv
clus                              MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 38(12Q21.31) MUTATED              1                       0   16
  AMP PEAK 38(12Q21.31) WILD-TYPE          131                      18  314
                                 vv
clus                              VERY ADVANCED (T4B)
  AMP PEAK 38(12Q21.31) MUTATED                     0
  AMP PEAK 38(12Q21.31) WILD-TYPE                   1
D37V11, multiclass
                         clus
vv                        AMP PEAK 38(12Q21.31) MUTATED
  MINIMAL (T3)                                        1
  MODERATE/ADVANCED (T4A)                             0
  NONE                                               16
  VERY ADVANCED (T4B)                                 0
                         clus
vv                        AMP PEAK 38(12Q21.31) WILD-TYPE
  MINIMAL (T3)                                        131
  MODERATE/ADVANCED (T4A)                              18
  NONE                                                314
  VERY ADVANCED (T4B)                                   1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 38(12Q21.31) MUTATED    14   1   0   2
  AMP PEAK 38(12Q21.31) WILD-TYPE 369  50   4  28
D37V12, multiclass
    clus
vv   AMP PEAK 38(12Q21.31) MUTATED AMP PEAK 38(12Q21.31) WILD-TYPE
  R0                            14                             369
  R1                             1                              50
  R2                             0                               4
  RX                             2                              28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V13, continuous
D37V14, binary
                                 cls
clus                                0   1
  AMP PEAK 38(12Q21.31) MUTATED     7  10
  AMP PEAK 38(12Q21.31) WILD-TYPE 218 254
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 38(12Q21.31) MUTATED      7   10
  AMP PEAK 38(12Q21.31) WILD-TYPE  218  254
            clus
vv           AMP PEAK 38(12Q21.31) MUTATED AMP PEAK 38(12Q21.31) WILD-TYPE
  MULTIFOCAL                             7                             218
  UNIFOCAL                              10                             254
[1] 2 2
[1] FALSE
D37V15, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 38(12Q21.31) MUTATED                                  0     0
  AMP PEAK 38(12Q21.31) WILD-TYPE                                1    52
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 38(12Q21.31) MUTATED                           0    11
  AMP PEAK 38(12Q21.31) WILD-TYPE                        27   317
D37V16, multiclass
                                  clus
vv                                 AMP PEAK 38(12Q21.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                    0
  WHITE                                                       11
                                  clus
vv                                 AMP PEAK 38(12Q21.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         52
  BLACK OR AFRICAN AMERICAN                                     27
  WHITE                                                        317
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V17, binary
                                 cls
clus                                0   1
  AMP PEAK 38(12Q21.31) MUTATED     1  10
  AMP PEAK 38(12Q21.31) WILD-TYPE  37 349
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 38(12Q21.31) MUTATED      1   10
  AMP PEAK 38(12Q21.31) WILD-TYPE   37  349
                        clus
vv                       AMP PEAK 38(12Q21.31) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            10
                        clus
vv                       AMP PEAK 38(12Q21.31) WILD-TYPE
  HISPANIC OR LATINO                                  37
  NOT HISPANIC OR LATINO                             349
[1] 2 2
[1] FALSE

Clustering(38) Variable = AMP PEAK 39(12Q23.1) MUTATION ANALYSIS
D38V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 39(12Q23.1) MUTATED    17   0
  AMP PEAK 39(12Q23.1) WILD-TYPE 464  16
  AMP PEAK 39(12Q23.1) MUTATED AMP PEAK 39(12Q23.1) WILD-TYPE 
                            17                            480 
  AMP PEAK 39(12Q23.1) MUTATED AMP PEAK 39(12Q23.1) WILD-TYPE 
                             0                             16 
$`AMP PEAK 39(12Q23.1) MUTATED`
TCGA-BJ-A190 TCGA-BJ-A2N9 TCGA-DJ-A1QF TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N 
       20.58        20.48        30.61        78.61        57.01        10.65 
TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N 
        6.05        32.32        22.52        13.51        37.25       123.32 
TCGA-ET-A3DS TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3WA TCGA-J8-A4HW 
       66.84         7.82         0.99        17.06         2.60 

$`AMP PEAK 39(12Q23.1) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        42.08        51.39        41.52         4.83        44.35 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
       42.15        21.04        35.54        32.45        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
       11.08        30.21        22.88        18.38        16.57        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        7.99        10.88        21.01         3.45        23.84        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
       15.45        21.63        23.18        19.43        23.47        12.66 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
       12.43        12.66        35.84        21.63        50.17        37.64 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M 
       25.12        14.70        14.27         2.76         9.96        48.79 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       38.17       169.32        18.58         8.71        56.19        23.38 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QG 
       43.17        52.37         8.32        11.01       135.91        44.98 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
       42.51        14.96        17.59         6.02        42.58        47.41 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
       17.56        10.09         7.82        30.58        35.41        27.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
       26.20        38.83        33.96        31.99        34.85        28.96 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42        34.36        37.74         6.77        40.24 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
       33.93        37.48        36.46        35.11        39.09        35.90 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       33.53        35.18        15.88        36.92        31.04        32.42 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        36.33 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        59.57        11.34        35.87        40.96        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        42.54        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM 
       35.67         3.12        36.43        24.76        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       30.87        21.34        33.04        34.78        27.06        26.93 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       35.54         3.12        15.81        35.38        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        92.55        47.21        66.38        80.52        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 
       52.44        39.95        31.23        35.67        31.27        29.98 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 
       31.50        31.04         0.72         0.26         3.02        25.45 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       30.61         0.16         0.23        14.96         7.69        33.50 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
        0.39         0.39        31.66        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      158.83         7.66        45.53        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 
       57.01       106.62         4.18        79.50       139.86        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       69.57        57.11       108.36        64.87        49.51        50.24 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
      115.10        65.39       136.01        50.37        50.20       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       83.57       139.00       150.48       108.66        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       52.50        29.65       147.42       142.52       129.57        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      132.07        98.24        41.29       107.47         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM 
       82.82        89.56        78.97        51.78        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        65.49        61.22        60.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       34.39        30.51        53.36        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       43.59        24.30        27.06        23.90        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE 
       20.91        48.49        18.05        19.79        19.46        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O 
       14.73        14.50        15.75        10.45        14.53        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       19.73        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.06         7.33         0.49         9.24        13.91        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       38.86        29.95        29.85        12.79        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
       21.34         5.33        26.37        26.37        22.45        21.53 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       60.49        24.46        13.68        81.93        81.70        77.56 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       70.42        56.58        60.20        63.39        65.29        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       63.45        88.41        58.75        52.60        54.35        83.34 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89       100.57        95.34        94.13        55.10        98.20 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24        50.40        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       77.82        75.42        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       84.85        80.58        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       117.40        66.77       112.80        39.95        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.11         1.05        13.28         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        1.25        20.42        17.82        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3YR 
       15.68        16.57        18.08         0.30         0.76        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       15.16         6.58        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83        31.10         8.22        25.64        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        5.75         2.47         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
      113.85        26.70        43.69        18.64        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       84.72        35.28        33.24        33.40        40.37        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        9.50        36.10        32.45        30.21        23.93        12.89 

  AMP PEAK 39(12Q23.1) MUTATED AMP PEAK 39(12Q23.1) WILD-TYPE 
                          0.99                           0.16 
  AMP PEAK 39(12Q23.1) MUTATED AMP PEAK 39(12Q23.1) WILD-TYPE 
                        123.32                         169.32 
  AMP PEAK 39(12Q23.1) MUTATED AMP PEAK 39(12Q23.1) WILD-TYPE 
                        20.580                         30.905 
[1] "1.0 - 123.3 (20.6)" "0.2 - 169.3 (30.9)"
[1] "hr="     "2.5e+07"
D38V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 39(12Q23.1) MUTATED         7        6         4        0         0
  AMP PEAK 39(12Q23.1) WILD-TYPE     275       44       107        2        46
                                vv
clus                             STAGE IVC
  AMP PEAK 39(12Q23.1) MUTATED           0
  AMP PEAK 39(12Q23.1) WILD-TYPE         6
D38V3, multiclass
           clus
vv          AMP PEAK 39(12Q23.1) MUTATED AMP PEAK 39(12Q23.1) WILD-TYPE
  STAGE I                              7                            275
  STAGE II                             6                             44
  STAGE III                            4                            107
  STAGE IV                             0                              2
  STAGE IVA                            0                             46
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 39(12Q23.1) MUTATED     5   8   4   0
  AMP PEAK 39(12Q23.1) WILD-TYPE 137 157 163  23
D38V4, multiclass
    clus
vv   AMP PEAK 39(12Q23.1) MUTATED AMP PEAK 39(12Q23.1) WILD-TYPE
  T1                            5                            137
  T2                            8                            157
  T3                            4                            163
  T4                            0                             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"
D38V5, binary
                                cls
clus                               0   1
  AMP PEAK 39(12Q23.1) MUTATED    11   1
  AMP PEAK 39(12Q23.1) WILD-TYPE 214 223
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 39(12Q23.1) MUTATED     11    1
  AMP PEAK 39(12Q23.1) WILD-TYPE  214  223
   clus
vv  AMP PEAK 39(12Q23.1) MUTATED AMP PEAK 39(12Q23.1) WILD-TYPE
  0                           11                            214
  1                            1                            223
[1] 2 2
[1] FALSE
D38V6, binary
                                cls
clus                               0   1
  AMP PEAK 39(12Q23.1) MUTATED     3   0
  AMP PEAK 39(12Q23.1) WILD-TYPE 275   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 39(12Q23.1) MUTATED      3    0
  AMP PEAK 39(12Q23.1) WILD-TYPE  275    9
   clus
vv  AMP PEAK 39(12Q23.1) MUTATED AMP PEAK 39(12Q23.1) WILD-TYPE
  0                            3                            275
  1                            0                              9
[1] 2 2
[1] FALSE
D38V7, binary
                                cls
clus                               0   1
  AMP PEAK 39(12Q23.1) MUTATED    14   3
  AMP PEAK 39(12Q23.1) WILD-TYPE 351 131
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 39(12Q23.1) MUTATED     14    3
  AMP PEAK 39(12Q23.1) WILD-TYPE  351  131
        clus
vv       AMP PEAK 39(12Q23.1) MUTATED AMP PEAK 39(12Q23.1) WILD-TYPE
  FEMALE                           14                            351
  MALE                              3                            131
[1] 2 2
[1] FALSE
D38V8, binary
                                cls
clus                               0   1
  AMP PEAK 39(12Q23.1) MUTATED     7   8
  AMP PEAK 39(12Q23.1) WILD-TYPE 178 282
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 39(12Q23.1) MUTATED      7    8
  AMP PEAK 39(12Q23.1) WILD-TYPE  178  282
     clus
vv    AMP PEAK 39(12Q23.1) MUTATED AMP PEAK 39(12Q23.1) WILD-TYPE
  NO                             7                            178
  YES                            8                            282
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 39(12Q23.1) MUTATED                0
  AMP PEAK 39(12Q23.1) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 39(12Q23.1) MUTATED                                               8
  AMP PEAK 39(12Q23.1) WILD-TYPE                                           347
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 39(12Q23.1) MUTATED                                                                        9
  AMP PEAK 39(12Q23.1) WILD-TYPE                                                                     91
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 39(12Q23.1) MUTATED                                                                     0
  AMP PEAK 39(12Q23.1) WILD-TYPE                                                                  36
D38V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 39(12Q23.1) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     8
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            9
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       AMP PEAK 39(12Q23.1) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     347
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             91
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V10, binary
                                cls
clus                               0   1
  AMP PEAK 39(12Q23.1) MUTATED    16   0
  AMP PEAK 39(12Q23.1) WILD-TYPE 404  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 39(12Q23.1) MUTATED     16    0
  AMP PEAK 39(12Q23.1) WILD-TYPE  404   17
     clus
vv    AMP PEAK 39(12Q23.1) MUTATED AMP PEAK 39(12Q23.1) WILD-TYPE
  NO                            16                            404
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 39(12Q23.1) MUTATED              1                       0   16
  AMP PEAK 39(12Q23.1) WILD-TYPE          131                      18  314
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 39(12Q23.1) MUTATED                     0
  AMP PEAK 39(12Q23.1) WILD-TYPE                   1
D38V11, multiclass
                         clus
vv                        AMP PEAK 39(12Q23.1) MUTATED
  MINIMAL (T3)                                       1
  MODERATE/ADVANCED (T4A)                            0
  NONE                                              16
  VERY ADVANCED (T4B)                                0
                         clus
vv                        AMP PEAK 39(12Q23.1) WILD-TYPE
  MINIMAL (T3)                                       131
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               314
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 39(12Q23.1) MUTATED    14   1   0   2
  AMP PEAK 39(12Q23.1) WILD-TYPE 369  50   4  28
D38V12, multiclass
    clus
vv   AMP PEAK 39(12Q23.1) MUTATED AMP PEAK 39(12Q23.1) WILD-TYPE
  R0                           14                            369
  R1                            1                             50
  R2                            0                              4
  RX                            2                             28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V13, continuous
D38V14, binary
                                cls
clus                               0   1
  AMP PEAK 39(12Q23.1) MUTATED     9   8
  AMP PEAK 39(12Q23.1) WILD-TYPE 216 256
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 39(12Q23.1) MUTATED      9    8
  AMP PEAK 39(12Q23.1) WILD-TYPE  216  256
            clus
vv           AMP PEAK 39(12Q23.1) MUTATED AMP PEAK 39(12Q23.1) WILD-TYPE
  MULTIFOCAL                            9                            216
  UNIFOCAL                              8                            256
[1] 2 2
[1] FALSE
D38V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 39(12Q23.1) MUTATED                                  0     0
  AMP PEAK 39(12Q23.1) WILD-TYPE                                1    52
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 39(12Q23.1) MUTATED                           0    11
  AMP PEAK 39(12Q23.1) WILD-TYPE                        27   317
D38V16, multiclass
                                  clus
vv                                 AMP PEAK 39(12Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                      11
                                  clus
vv                                 AMP PEAK 39(12Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        52
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       317
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V17, binary
                                cls
clus                               0   1
  AMP PEAK 39(12Q23.1) MUTATED     0   9
  AMP PEAK 39(12Q23.1) WILD-TYPE  38 350
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 39(12Q23.1) MUTATED      0    9
  AMP PEAK 39(12Q23.1) WILD-TYPE   38  350
                        clus
vv                       AMP PEAK 39(12Q23.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            9
                        clus
vv                       AMP PEAK 39(12Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            350
[1] 2 2
[1] FALSE

Clustering(39) Variable = AMP PEAK 40(13Q14.2) MUTATION ANALYSIS
D39V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 40(13Q14.2) MUTATED     6   0
  AMP PEAK 40(13Q14.2) WILD-TYPE 475  16
  AMP PEAK 40(13Q14.2) MUTATED AMP PEAK 40(13Q14.2) WILD-TYPE 
                             6                            491 
  AMP PEAK 40(13Q14.2) MUTATED AMP PEAK 40(13Q14.2) WILD-TYPE 
                             0                             16 
$`AMP PEAK 40(13Q14.2) MUTATED`
TCGA-BJ-A45E TCGA-CE-A482 TCGA-EL-A4KI TCGA-EM-A1YD TCGA-EM-A2CO TCGA-EM-A2OY 
       21.01        10.68        23.90        57.01         6.05        32.32 

$`AMP PEAK 40(13Q14.2) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G 
       23.31        18.64         7.99        10.88         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A483 
       12.66        12.30        12.79        12.46        11.38        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
       12.43        12.66        35.84        21.63        50.17        37.64 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M 
       25.12        14.70        14.27         2.76         9.96        48.79 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       38.17       169.32        18.58         8.71        56.19        23.38 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       43.17        52.37         8.32        11.01       135.91        30.61 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       44.98        42.51        14.96        17.59         6.02        42.58 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
       47.41        17.56        10.09         7.82        30.58        35.41 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       27.45        26.20        38.83        33.96        31.99        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       28.96         8.78         8.42        34.36        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24        33.93        37.48        36.46        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        33.53        35.18        15.88        36.92        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       32.42        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        17.69        59.57        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        42.54        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL 
        7.76        35.67         3.12        36.43        24.76        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        21.34        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        52.44        39.95        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT 
       47.84        43.59        24.30        27.06        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        48.49        18.05        19.79        19.46        78.61 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       54.08        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.65        44.19        41.29        14.24        47.57        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU 
       13.18        23.51         2.99        12.30        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        40.34        19.73        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       33.07        13.38         8.35        29.72        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        47.38        21.01        12.07        17.49        17.39 
TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 
       16.18        15.02        14.50        15.06         7.33         0.49 
TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
        9.24        13.91        38.66        38.86        29.95        29.85 
TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       13.51        12.79        84.59        29.33        21.34         5.33 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
       26.37        26.37        22.45        21.53        60.49        24.46 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
       13.68        81.93        81.70        77.56        70.42        56.58 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       60.20        63.39        65.29        18.38        63.45        88.41 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       58.75        37.25        52.60        54.35        83.34         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       80.88        33.24       106.09       107.41       108.46        84.89 
TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
      123.32       100.57        95.34        94.13        55.10        98.20 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24        50.40        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       77.82        75.42        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       71.08         4.11         1.05        13.28         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
      116.09         1.25        20.42        17.82         7.82         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
        0.30         0.76        17.06        17.36        15.16         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
       22.49        19.04         1.35        21.60         1.68        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46         2.99        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        8.22        25.64        17.23        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
       26.70        43.69        18.64        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       36.10        32.45        30.21        23.93        12.89 

  AMP PEAK 40(13Q14.2) MUTATED AMP PEAK 40(13Q14.2) WILD-TYPE 
                          6.05                           0.16 
  AMP PEAK 40(13Q14.2) MUTATED AMP PEAK 40(13Q14.2) WILD-TYPE 
                         57.01                         169.32 
  AMP PEAK 40(13Q14.2) MUTATED AMP PEAK 40(13Q14.2) WILD-TYPE 
                        22.455                         30.610 
[1] "6.0 - 57.0 (22.5)"  "0.2 - 169.3 (30.6)"
[1] "hr="     "3300000"
D39V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 40(13Q14.2) MUTATED         2        3         1        0         0
  AMP PEAK 40(13Q14.2) WILD-TYPE     280       47       110        2        46
                                vv
clus                             STAGE IVC
  AMP PEAK 40(13Q14.2) MUTATED           0
  AMP PEAK 40(13Q14.2) WILD-TYPE         6
D39V3, multiclass
           clus
vv          AMP PEAK 40(13Q14.2) MUTATED AMP PEAK 40(13Q14.2) WILD-TYPE
  STAGE I                              2                            280
  STAGE II                             3                             47
  STAGE III                            1                            110
  STAGE IV                             0                              2
  STAGE IVA                            0                             46
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 40(13Q14.2) MUTATED     2   3   1   0
  AMP PEAK 40(13Q14.2) WILD-TYPE 140 162 166  23
D39V4, multiclass
    clus
vv   AMP PEAK 40(13Q14.2) MUTATED AMP PEAK 40(13Q14.2) WILD-TYPE
  T1                            2                            140
  T2                            3                            162
  T3                            1                            166
  T4                            0                             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"
D39V5, binary
                                cls
clus                               0   1
  AMP PEAK 40(13Q14.2) MUTATED     4   1
  AMP PEAK 40(13Q14.2) WILD-TYPE 221 223
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 40(13Q14.2) MUTATED      4    1
  AMP PEAK 40(13Q14.2) WILD-TYPE  221  223
   clus
vv  AMP PEAK 40(13Q14.2) MUTATED AMP PEAK 40(13Q14.2) WILD-TYPE
  0                            4                            221
  1                            1                            223
[1] 2 2
[1] FALSE
D39V6, binary
                                cls
clus                               0   1
  AMP PEAK 40(13Q14.2) MUTATED     2   0
  AMP PEAK 40(13Q14.2) WILD-TYPE 276   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 40(13Q14.2) MUTATED      2    0
  AMP PEAK 40(13Q14.2) WILD-TYPE  276    9
   clus
vv  AMP PEAK 40(13Q14.2) MUTATED AMP PEAK 40(13Q14.2) WILD-TYPE
  0                            2                            276
  1                            0                              9
[1] 2 2
[1] FALSE
D39V7, binary
                                cls
clus                               0   1
  AMP PEAK 40(13Q14.2) MUTATED     5   1
  AMP PEAK 40(13Q14.2) WILD-TYPE 360 133
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 40(13Q14.2) MUTATED      5    1
  AMP PEAK 40(13Q14.2) WILD-TYPE  360  133
        clus
vv       AMP PEAK 40(13Q14.2) MUTATED AMP PEAK 40(13Q14.2) WILD-TYPE
  FEMALE                            5                            360
  MALE                              1                            133
[1] 2 2
[1] FALSE
D39V8, binary
                                cls
clus                               0   1
  AMP PEAK 40(13Q14.2) MUTATED     3   3
  AMP PEAK 40(13Q14.2) WILD-TYPE 182 287
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 40(13Q14.2) MUTATED      3    3
  AMP PEAK 40(13Q14.2) WILD-TYPE  182  287
     clus
vv    AMP PEAK 40(13Q14.2) MUTATED AMP PEAK 40(13Q14.2) WILD-TYPE
  NO                             3                            182
  YES                            3                            287
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 40(13Q14.2) MUTATED                0
  AMP PEAK 40(13Q14.2) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 40(13Q14.2) MUTATED                                               3
  AMP PEAK 40(13Q14.2) WILD-TYPE                                           352
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 40(13Q14.2) MUTATED                                                                        3
  AMP PEAK 40(13Q14.2) WILD-TYPE                                                                     97
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 40(13Q14.2) MUTATED                                                                     0
  AMP PEAK 40(13Q14.2) WILD-TYPE                                                                  36
D39V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 40(13Q14.2) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       AMP PEAK 40(13Q14.2) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             97
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V10, binary
                                cls
clus                               0   1
  AMP PEAK 40(13Q14.2) MUTATED     5   0
  AMP PEAK 40(13Q14.2) WILD-TYPE 415  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 40(13Q14.2) MUTATED      5    0
  AMP PEAK 40(13Q14.2) WILD-TYPE  415   17
     clus
vv    AMP PEAK 40(13Q14.2) MUTATED AMP PEAK 40(13Q14.2) WILD-TYPE
  NO                             5                            415
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 40(13Q14.2) MUTATED              1                       0    4
  AMP PEAK 40(13Q14.2) WILD-TYPE          131                      18  326
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 40(13Q14.2) MUTATED                     0
  AMP PEAK 40(13Q14.2) WILD-TYPE                   1
D39V11, multiclass
                         clus
vv                        AMP PEAK 40(13Q14.2) MUTATED
  MINIMAL (T3)                                       1
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               4
  VERY ADVANCED (T4B)                                0
                         clus
vv                        AMP PEAK 40(13Q14.2) WILD-TYPE
  MINIMAL (T3)                                       131
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               326
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 40(13Q14.2) MUTATED     5   0   0   0
  AMP PEAK 40(13Q14.2) WILD-TYPE 378  51   4  30
D39V12, multiclass
    clus
vv   AMP PEAK 40(13Q14.2) MUTATED AMP PEAK 40(13Q14.2) WILD-TYPE
  R0                            5                            378
  R1                            0                             51
  R2                            0                              4
  RX                            0                             30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V13, continuous
D39V14, binary
                                cls
clus                               0   1
  AMP PEAK 40(13Q14.2) MUTATED     3   3
  AMP PEAK 40(13Q14.2) WILD-TYPE 222 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 40(13Q14.2) MUTATED      3    3
  AMP PEAK 40(13Q14.2) WILD-TYPE  222  261
            clus
vv           AMP PEAK 40(13Q14.2) MUTATED AMP PEAK 40(13Q14.2) WILD-TYPE
  MULTIFOCAL                            3                            222
  UNIFOCAL                              3                            261
[1] 2 2
[1] FALSE
D39V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 40(13Q14.2) MUTATED                                  0     1
  AMP PEAK 40(13Q14.2) WILD-TYPE                                1    51
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 40(13Q14.2) MUTATED                           0     2
  AMP PEAK 40(13Q14.2) WILD-TYPE                        27   326
D39V16, multiclass
                                  clus
vv                                 AMP PEAK 40(13Q14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       2
                                  clus
vv                                 AMP PEAK 40(13Q14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        51
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V17, binary
                                cls
clus                               0   1
  AMP PEAK 40(13Q14.2) MUTATED     0   3
  AMP PEAK 40(13Q14.2) WILD-TYPE  38 356
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 40(13Q14.2) MUTATED      0    3
  AMP PEAK 40(13Q14.2) WILD-TYPE   38  356
                        clus
vv                       AMP PEAK 40(13Q14.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            3
                        clus
vv                       AMP PEAK 40(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            356
[1] 2 2
[1] FALSE

Clustering(40) Variable = AMP PEAK 41(13Q34) MUTATION ANALYSIS
D40V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 41(13Q34) MUTATED     7   0
  AMP PEAK 41(13Q34) WILD-TYPE 474  16
  AMP PEAK 41(13Q34) MUTATED AMP PEAK 41(13Q34) WILD-TYPE 
                           7                          490 
  AMP PEAK 41(13Q34) MUTATED AMP PEAK 41(13Q34) WILD-TYPE 
                           0                           16 
$`AMP PEAK 41(13Q34) MUTATED`
TCGA-BJ-A45E TCGA-E3-A3DY TCGA-EL-A4KI TCGA-EM-A1YD TCGA-EM-A2CO TCGA-EM-A2OY 
       21.01        92.55        23.90        57.01         6.05        32.32 
TCGA-KS-A4ID 
       33.24 

$`AMP PEAK 41(13Q34) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G 
       23.31        18.64         7.99        10.88         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       54.90        21.53         2.33        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        52.44        39.95        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT 
       47.84        43.59        24.30        27.06        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        48.49        18.05        19.79        19.46        78.61 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       54.08        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.65        44.19        41.29        14.24        47.57        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU 
       13.18        23.51         2.99        12.30        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        40.34        19.73        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       33.07        13.38         8.35        29.72        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        47.38        21.01        12.07        17.49        17.39 
TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 
       16.18        15.02        14.50        15.06         7.33         0.49 
TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
        9.24        13.91        38.66        38.86        29.95        29.85 
TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       13.51        12.79        84.59        29.33        21.34         5.33 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
       26.37        26.37        22.45        21.53        60.49        24.46 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
       13.68        81.93        81.70        77.56        70.42        56.58 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       60.20        63.39        65.29        18.38        63.45        88.41 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       58.75        37.25        52.60        54.35        83.34         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       80.88        33.24       106.09       107.41       108.46        84.89 
TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
      123.32       100.57        95.34        94.13        55.10        98.20 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24        50.40        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       77.82        75.42        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       71.08         4.11         1.05        13.28         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
      116.09         1.25        20.42        17.82         7.82         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
        0.30         0.76        17.06        17.36        15.16         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
       22.49        19.04         1.35        21.60         1.68        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46         2.99        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        8.22        25.64        17.23        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
       26.70        43.69        18.64        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       35.28        33.40        40.37        21.83         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45        30.21        23.93        12.89 

  AMP PEAK 41(13Q34) MUTATED AMP PEAK 41(13Q34) WILD-TYPE 
                        6.05                         0.16 
  AMP PEAK 41(13Q34) MUTATED AMP PEAK 41(13Q34) WILD-TYPE 
                       92.55                       169.32 
  AMP PEAK 41(13Q34) MUTATED AMP PEAK 41(13Q34) WILD-TYPE 
                       32.32                        30.61 
[1] "6.0 - 92.5 (32.3)"  "0.2 - 169.3 (30.6)"
[1] "hr="     "9100000"
D40V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 41(13Q34) MUTATED         3        3         1        0         0
  AMP PEAK 41(13Q34) WILD-TYPE     279       47       110        2        46
                              vv
clus                           STAGE IVC
  AMP PEAK 41(13Q34) MUTATED           0
  AMP PEAK 41(13Q34) WILD-TYPE         6
D40V3, multiclass
           clus
vv          AMP PEAK 41(13Q34) MUTATED AMP PEAK 41(13Q34) WILD-TYPE
  STAGE I                            3                          279
  STAGE II                           3                           47
  STAGE III                          1                          110
  STAGE IV                           0                            2
  STAGE IVA                          0                           46
  STAGE IVC                          0                            6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 41(13Q34) MUTATED     2   3   2   0
  AMP PEAK 41(13Q34) WILD-TYPE 140 162 165  23
D40V4, multiclass
    clus
vv   AMP PEAK 41(13Q34) MUTATED AMP PEAK 41(13Q34) WILD-TYPE
  T1                          2                          140
  T2                          3                          162
  T3                          2                          165
  T4                          0                           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"
D40V5, binary
                              cls
clus                             0   1
  AMP PEAK 41(13Q34) MUTATED     5   1
  AMP PEAK 41(13Q34) WILD-TYPE 220 223
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 41(13Q34) MUTATED      5    1
  AMP PEAK 41(13Q34) WILD-TYPE  220  223
   clus
vv  AMP PEAK 41(13Q34) MUTATED AMP PEAK 41(13Q34) WILD-TYPE
  0                          5                          220
  1                          1                          223
[1] 2 2
[1] FALSE
D40V6, binary
                              cls
clus                             0   1
  AMP PEAK 41(13Q34) MUTATED     3   0
  AMP PEAK 41(13Q34) WILD-TYPE 275   9
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 41(13Q34) MUTATED      3    0
  AMP PEAK 41(13Q34) WILD-TYPE  275    9
   clus
vv  AMP PEAK 41(13Q34) MUTATED AMP PEAK 41(13Q34) WILD-TYPE
  0                          3                          275
  1                          0                            9
[1] 2 2
[1] FALSE
D40V7, binary
                              cls
clus                             0   1
  AMP PEAK 41(13Q34) MUTATED     5   2
  AMP PEAK 41(13Q34) WILD-TYPE 360 132
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 41(13Q34) MUTATED      5    2
  AMP PEAK 41(13Q34) WILD-TYPE  360  132
        clus
vv       AMP PEAK 41(13Q34) MUTATED AMP PEAK 41(13Q34) WILD-TYPE
  FEMALE                          5                          360
  MALE                            2                          132
[1] 2 2
[1] FALSE
D40V8, binary
                              cls
clus                             0   1
  AMP PEAK 41(13Q34) MUTATED     3   4
  AMP PEAK 41(13Q34) WILD-TYPE 182 286
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 41(13Q34) MUTATED      3    4
  AMP PEAK 41(13Q34) WILD-TYPE  182  286
     clus
vv    AMP PEAK 41(13Q34) MUTATED AMP PEAK 41(13Q34) WILD-TYPE
  NO                           3                          182
  YES                          4                          286
[1] 2 2
[1] FALSE
                              vv
clus                           OTHER  SPECIFY
  AMP PEAK 41(13Q34) MUTATED                1
  AMP PEAK 41(13Q34) WILD-TYPE              7
                              vv
clus                           THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 41(13Q34) MUTATED                                               2
  AMP PEAK 41(13Q34) WILD-TYPE                                           353
                              vv
clus                           THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 41(13Q34) MUTATED                                                                        4
  AMP PEAK 41(13Q34) WILD-TYPE                                                                     96
                              vv
clus                           THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 41(13Q34) MUTATED                                                                     0
  AMP PEAK 41(13Q34) WILD-TYPE                                                                  36
D40V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 41(13Q34) MUTATED
  OTHER  SPECIFY                                                                                  1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          4
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                             0
                                                                        clus
vv                                                                       AMP PEAK 41(13Q34) WILD-TYPE
  OTHER  SPECIFY                                                                                    7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V10, binary
                              cls
clus                             0   1
  AMP PEAK 41(13Q34) MUTATED     6   0
  AMP PEAK 41(13Q34) WILD-TYPE 414  17
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 41(13Q34) MUTATED      6    0
  AMP PEAK 41(13Q34) WILD-TYPE  414   17
     clus
vv    AMP PEAK 41(13Q34) MUTATED AMP PEAK 41(13Q34) WILD-TYPE
  NO                           6                          414
  YES                          0                           17
[1] 2 2
[1] FALSE
                              vv
clus                           MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 41(13Q34) MUTATED              1                       0    5
  AMP PEAK 41(13Q34) WILD-TYPE          131                      18  325
                              vv
clus                           VERY ADVANCED (T4B)
  AMP PEAK 41(13Q34) MUTATED                     0
  AMP PEAK 41(13Q34) WILD-TYPE                   1
D40V11, multiclass
                         clus
vv                        AMP PEAK 41(13Q34) MUTATED
  MINIMAL (T3)                                     1
  MODERATE/ADVANCED (T4A)                          0
  NONE                                             5
  VERY ADVANCED (T4B)                              0
                         clus
vv                        AMP PEAK 41(13Q34) WILD-TYPE
  MINIMAL (T3)                                     131
  MODERATE/ADVANCED (T4A)                           18
  NONE                                             325
  VERY ADVANCED (T4B)                                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 41(13Q34) MUTATED     6   0   0   0
  AMP PEAK 41(13Q34) WILD-TYPE 377  51   4  30
D40V12, multiclass
    clus
vv   AMP PEAK 41(13Q34) MUTATED AMP PEAK 41(13Q34) WILD-TYPE
  R0                          6                          377
  R1                          0                           51
  R2                          0                            4
  RX                          0                           30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V13, continuous
D40V14, binary
                              cls
clus                             0   1
  AMP PEAK 41(13Q34) MUTATED     4   3
  AMP PEAK 41(13Q34) WILD-TYPE 221 261
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 41(13Q34) MUTATED      4    3
  AMP PEAK 41(13Q34) WILD-TYPE  221  261
            clus
vv           AMP PEAK 41(13Q34) MUTATED AMP PEAK 41(13Q34) WILD-TYPE
  MULTIFOCAL                          4                          221
  UNIFOCAL                            3                          261
[1] 2 2
[1] FALSE
D40V15, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 41(13Q34) MUTATED                                  0     0
  AMP PEAK 41(13Q34) WILD-TYPE                                1    52
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 41(13Q34) MUTATED                           0     4
  AMP PEAK 41(13Q34) WILD-TYPE                        27   324
D40V16, multiclass
                                  clus
vv                                 AMP PEAK 41(13Q34) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     0
  BLACK OR AFRICAN AMERICAN                                 0
  WHITE                                                     4
                                  clus
vv                                 AMP PEAK 41(13Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      52
  BLACK OR AFRICAN AMERICAN                                  27
  WHITE                                                     324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V17, binary
                              cls
clus                             0   1
  AMP PEAK 41(13Q34) MUTATED     0   3
  AMP PEAK 41(13Q34) WILD-TYPE  38 356
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 41(13Q34) MUTATED      0    3
  AMP PEAK 41(13Q34) WILD-TYPE   38  356
                        clus
vv                       AMP PEAK 41(13Q34) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                          3
                        clus
vv                       AMP PEAK 41(13Q34) WILD-TYPE
  HISPANIC OR LATINO                               38
  NOT HISPANIC OR LATINO                          356
[1] 2 2
[1] FALSE

Clustering(41) Variable = AMP PEAK 42(14Q12) MUTATION ANALYSIS
D41V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 42(14Q12) MUTATED    13   0
  AMP PEAK 42(14Q12) WILD-TYPE 468  16
  AMP PEAK 42(14Q12) MUTATED AMP PEAK 42(14Q12) WILD-TYPE 
                          13                          484 
  AMP PEAK 42(14Q12) MUTATED AMP PEAK 42(14Q12) WILD-TYPE 
                           0                           16 
$`AMP PEAK 42(14Q12) MUTATED`
TCGA-DJ-A4V5 TCGA-EL-A3ZR TCGA-EL-A4KI TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO 
       35.38        60.16        23.90        57.01        10.65         6.05 
TCGA-EM-A2OY TCGA-EM-A3AI TCGA-ET-A39N TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-J8-A3YG 
       32.32        22.52       123.32         7.82         0.99        22.29 
TCGA-KS-A4I9 
       87.39 

$`AMP PEAK 42(14Q12) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
       30.58        35.41        27.45        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74         6.77        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        36.33        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       35.87        40.96        36.99        20.22        30.61        42.54 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20        23.21        21.27        20.48        24.82        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ 
       21.01        18.97         7.76        35.67         3.12        36.43 
TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       24.76        17.23        27.62        30.87        21.34        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        30.61         0.16         0.23        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        33.50         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        69.57        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       49.51        50.24       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       150.48       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        89.56        78.97        51.78 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        47.38        65.49        61.22 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT 
       47.84        43.59        24.30        27.06        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        48.49        18.05        19.79        19.46        78.61 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       54.08        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       44.19        41.29        14.24        47.57        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
       23.51         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       40.34        19.73        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       14.60        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33         0.49         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
      106.09       107.41       108.46        84.89       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       94.13        55.10        98.20        28.24        50.40        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
       76.64         5.79        87.62        77.82        75.42        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
       52.47       116.78        94.59        84.85        80.58        66.84 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       43.73        62.83       166.62        24.72        43.99        46.26 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
       44.38        40.21        37.48        33.17        31.40        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       71.44        31.59        79.69        24.69        68.22       117.40 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77       112.80        39.95        33.63        81.83       106.36 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD 
       85.15        85.68        78.77        71.08         4.11         1.05 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       13.28         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
       17.82        19.56        13.91        16.27        15.68        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08         0.30         0.76        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58        22.49        19.04         1.35        21.60         1.68 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46         2.99        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        18.51        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
       31.10         8.22        25.64        17.23        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YH TCGA-J8-A42S 
       11.24        31.82        27.85        24.69         5.75         2.47 
TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4IB TCGA-KS-A4IC 
       26.70        43.69        18.64        32.45        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       33.24        33.40        40.37        21.83         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45        30.21        23.93        12.89 

  AMP PEAK 42(14Q12) MUTATED AMP PEAK 42(14Q12) WILD-TYPE 
                        0.99                         0.16 
  AMP PEAK 42(14Q12) MUTATED AMP PEAK 42(14Q12) WILD-TYPE 
                      123.32                       169.32 
  AMP PEAK 42(14Q12) MUTATED AMP PEAK 42(14Q12) WILD-TYPE 
                       23.90                        30.61 
[1] "1.0 - 123.3 (23.9)" "0.2 - 169.3 (30.6)"
[1] "hr="     "9300000"
D41V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 42(14Q12) MUTATED         3        5         4        0         1
  AMP PEAK 42(14Q12) WILD-TYPE     279       45       107        2        45
                              vv
clus                           STAGE IVC
  AMP PEAK 42(14Q12) MUTATED           0
  AMP PEAK 42(14Q12) WILD-TYPE         6
D41V3, multiclass
           clus
vv          AMP PEAK 42(14Q12) MUTATED AMP PEAK 42(14Q12) WILD-TYPE
  STAGE I                            3                          279
  STAGE II                           5                           45
  STAGE III                          4                          107
  STAGE IV                           0                            2
  STAGE IVA                          1                           45
  STAGE IVC                          0                            6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 42(14Q12) MUTATED     2   6   5   0
  AMP PEAK 42(14Q12) WILD-TYPE 140 159 162  23
D41V4, multiclass
    clus
vv   AMP PEAK 42(14Q12) MUTATED AMP PEAK 42(14Q12) WILD-TYPE
  T1                          2                          140
  T2                          6                          159
  T3                          5                          162
  T4                          0                           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"
D41V5, binary
                              cls
clus                             0   1
  AMP PEAK 42(14Q12) MUTATED     8   2
  AMP PEAK 42(14Q12) WILD-TYPE 217 222
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 42(14Q12) MUTATED      8    2
  AMP PEAK 42(14Q12) WILD-TYPE  217  222
   clus
vv  AMP PEAK 42(14Q12) MUTATED AMP PEAK 42(14Q12) WILD-TYPE
  0                          8                          217
  1                          2                          222
[1] 2 2
[1] FALSE
D41V6, binary
                              cls
clus                             0   1
  AMP PEAK 42(14Q12) MUTATED     4   0
  AMP PEAK 42(14Q12) WILD-TYPE 274   9
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 42(14Q12) MUTATED      4    0
  AMP PEAK 42(14Q12) WILD-TYPE  274    9
   clus
vv  AMP PEAK 42(14Q12) MUTATED AMP PEAK 42(14Q12) WILD-TYPE
  0                          4                          274
  1                          0                            9
[1] 2 2
[1] FALSE
D41V7, binary
                              cls
clus                             0   1
  AMP PEAK 42(14Q12) MUTATED    11   2
  AMP PEAK 42(14Q12) WILD-TYPE 354 132
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 42(14Q12) MUTATED     11    2
  AMP PEAK 42(14Q12) WILD-TYPE  354  132
        clus
vv       AMP PEAK 42(14Q12) MUTATED AMP PEAK 42(14Q12) WILD-TYPE
  FEMALE                         11                          354
  MALE                            2                          132
[1] 2 2
[1] FALSE
D41V8, binary
                              cls
clus                             0   1
  AMP PEAK 42(14Q12) MUTATED     1  10
  AMP PEAK 42(14Q12) WILD-TYPE 184 280
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 42(14Q12) MUTATED      1   10
  AMP PEAK 42(14Q12) WILD-TYPE  184  280
     clus
vv    AMP PEAK 42(14Q12) MUTATED AMP PEAK 42(14Q12) WILD-TYPE
  NO                           1                          184
  YES                         10                          280
[1] 2 2
[1] FALSE
                              vv
clus                           OTHER  SPECIFY
  AMP PEAK 42(14Q12) MUTATED                0
  AMP PEAK 42(14Q12) WILD-TYPE              8
                              vv
clus                           THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 42(14Q12) MUTATED                                               7
  AMP PEAK 42(14Q12) WILD-TYPE                                           348
                              vv
clus                           THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 42(14Q12) MUTATED                                                                        6
  AMP PEAK 42(14Q12) WILD-TYPE                                                                     94
                              vv
clus                           THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 42(14Q12) MUTATED                                                                     0
  AMP PEAK 42(14Q12) WILD-TYPE                                                                  36
D41V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 42(14Q12) MUTATED
  OTHER  SPECIFY                                                                                  0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   7
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          6
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                             0
                                                                        clus
vv                                                                       AMP PEAK 42(14Q12) WILD-TYPE
  OTHER  SPECIFY                                                                                    8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   348
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           94
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V10, binary
                              cls
clus                             0   1
  AMP PEAK 42(14Q12) MUTATED    11   0
  AMP PEAK 42(14Q12) WILD-TYPE 409  17
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 42(14Q12) MUTATED     11    0
  AMP PEAK 42(14Q12) WILD-TYPE  409   17
     clus
vv    AMP PEAK 42(14Q12) MUTATED AMP PEAK 42(14Q12) WILD-TYPE
  NO                          11                          409
  YES                          0                           17
[1] 2 2
[1] FALSE
                              vv
clus                           MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 42(14Q12) MUTATED              3                       0   10
  AMP PEAK 42(14Q12) WILD-TYPE          129                      18  320
                              vv
clus                           VERY ADVANCED (T4B)
  AMP PEAK 42(14Q12) MUTATED                     0
  AMP PEAK 42(14Q12) WILD-TYPE                   1
D41V11, multiclass
                         clus
vv                        AMP PEAK 42(14Q12) MUTATED
  MINIMAL (T3)                                     3
  MODERATE/ADVANCED (T4A)                          0
  NONE                                            10
  VERY ADVANCED (T4B)                              0
                         clus
vv                        AMP PEAK 42(14Q12) WILD-TYPE
  MINIMAL (T3)                                     129
  MODERATE/ADVANCED (T4A)                           18
  NONE                                             320
  VERY ADVANCED (T4B)                                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 42(14Q12) MUTATED    12   0   0   1
  AMP PEAK 42(14Q12) WILD-TYPE 371  51   4  29
D41V12, multiclass
    clus
vv   AMP PEAK 42(14Q12) MUTATED AMP PEAK 42(14Q12) WILD-TYPE
  R0                         12                          371
  R1                          0                           51
  R2                          0                            4
  RX                          1                           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"
D41V13, continuous
D41V14, binary
                              cls
clus                             0   1
  AMP PEAK 42(14Q12) MUTATED     8   5
  AMP PEAK 42(14Q12) WILD-TYPE 217 259
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 42(14Q12) MUTATED      8    5
  AMP PEAK 42(14Q12) WILD-TYPE  217  259
            clus
vv           AMP PEAK 42(14Q12) MUTATED AMP PEAK 42(14Q12) WILD-TYPE
  MULTIFOCAL                          8                          217
  UNIFOCAL                            5                          259
[1] 2 2
[1] FALSE
D41V15, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 42(14Q12) MUTATED                                  0     0
  AMP PEAK 42(14Q12) WILD-TYPE                                1    52
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 42(14Q12) MUTATED                           1     8
  AMP PEAK 42(14Q12) WILD-TYPE                        26   320
D41V16, multiclass
                                  clus
vv                                 AMP PEAK 42(14Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     0
  BLACK OR AFRICAN AMERICAN                                 1
  WHITE                                                     8
                                  clus
vv                                 AMP PEAK 42(14Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      52
  BLACK OR AFRICAN AMERICAN                                  26
  WHITE                                                     320
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V17, binary
                              cls
clus                             0   1
  AMP PEAK 42(14Q12) MUTATED     0   7
  AMP PEAK 42(14Q12) WILD-TYPE  38 352
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 42(14Q12) MUTATED      0    7
  AMP PEAK 42(14Q12) WILD-TYPE   38  352
                        clus
vv                       AMP PEAK 42(14Q12) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                          7
                        clus
vv                       AMP PEAK 42(14Q12) WILD-TYPE
  HISPANIC OR LATINO                               38
  NOT HISPANIC OR LATINO                          352
[1] 2 2
[1] FALSE

Clustering(42) Variable = AMP PEAK 43(14Q32.31) MUTATION ANALYSIS
D42V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 43(14Q32.31) MUTATED    13   0
  AMP PEAK 43(14Q32.31) WILD-TYPE 468  16
  AMP PEAK 43(14Q32.31) MUTATED AMP PEAK 43(14Q32.31) WILD-TYPE 
                             13                             484 
  AMP PEAK 43(14Q32.31) MUTATED AMP PEAK 43(14Q32.31) WILD-TYPE 
                              0                              16 
$`AMP PEAK 43(14Q32.31) MUTATED`
TCGA-EL-A3ZR TCGA-EL-A4KI TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY 
       60.16        23.90        57.01        10.65         6.05        32.32 
TCGA-EM-A2P2 TCGA-EM-A3AI TCGA-ET-A39N TCGA-ET-A4KN TCGA-FY-A3I5 TCGA-FY-A3NM 
       17.29        22.52       123.32        33.17         7.82         0.99 
TCGA-J8-A3YG 
       22.29 

$`AMP PEAK 43(14Q32.31) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
       30.58        35.41        27.45        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74         6.77        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        36.33        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       35.87        40.96        36.99        20.22        30.61        42.54 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20        23.21        21.27        20.48        24.82        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ 
       21.01        18.97         7.76        35.67         3.12        36.43 
TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       24.76        17.23        27.62        30.87        21.34        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        80.52        63.19        52.44        39.95        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04         0.72 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
        0.26         3.02        25.45        30.61         0.16         0.23 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        33.50         0.39         0.39        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS 
       26.73       155.54        97.74       158.83         7.66        45.53 
TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY 
       60.95       157.15        37.94        57.01       106.62         4.18 
TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 
       79.50       139.86        98.53        69.57        57.11       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
       64.87        49.51        50.24       115.10        65.39       136.01 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        50.20       147.75       101.13       139.99        49.32 
TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 
       33.50        43.36        49.71        83.57       139.00       150.48 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 
      108.66        57.63        17.52        52.50        29.65       147.42 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        47.38        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       61.22         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS 
       41.13        47.84        43.59        24.30        27.06        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       78.61        54.08        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       14.53        44.19        41.29        14.24        47.57        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU 
       13.18        23.51         2.99        12.30        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        40.34        19.73        33.96        17.59        17.46 
TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       14.60        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33         0.49         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
      106.09       107.41       108.46        84.89       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       94.13        55.10        98.20        28.24        50.40        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
       76.64         5.79        87.62        77.82        75.42        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
       52.47       116.78        94.59        84.85        80.58        66.84 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       43.73        62.83       166.62        24.72        43.99        46.26 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       44.38        40.21        37.48        31.40        73.74        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
      112.80        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        13.28 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10       116.09         1.25        20.42        17.82 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
        0.30         0.76        17.06        17.36        15.16         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
       22.49        19.04         1.35        21.60         1.68        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46         2.99        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        8.22        25.64        17.23        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW 
       31.82        27.85        24.69         5.75         2.47         2.60 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       43.69        18.64        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       33.24        33.40        40.37        21.83         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45        30.21        23.93        12.89 

  AMP PEAK 43(14Q32.31) MUTATED AMP PEAK 43(14Q32.31) WILD-TYPE 
                           0.99                            0.16 
  AMP PEAK 43(14Q32.31) MUTATED AMP PEAK 43(14Q32.31) WILD-TYPE 
                         123.32                          169.32 
  AMP PEAK 43(14Q32.31) MUTATED AMP PEAK 43(14Q32.31) WILD-TYPE 
                          22.52                           30.74 
[1] "1.0 - 123.3 (22.5)" "0.2 - 169.3 (30.7)"
[1] "hr="     "9200000"
D42V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 43(14Q32.31) MUTATED         2        5         6        0         0
  AMP PEAK 43(14Q32.31) WILD-TYPE     280       45       105        2        46
                                 vv
clus                              STAGE IVC
  AMP PEAK 43(14Q32.31) MUTATED           0
  AMP PEAK 43(14Q32.31) WILD-TYPE         6
D42V3, multiclass
           clus
vv          AMP PEAK 43(14Q32.31) MUTATED AMP PEAK 43(14Q32.31) WILD-TYPE
  STAGE I                               2                             280
  STAGE II                              5                              45
  STAGE III                             6                             105
  STAGE IV                              0                               2
  STAGE IVA                             0                              46
  STAGE IVC                             0                               6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 43(14Q32.31) MUTATED     1   6   6   0
  AMP PEAK 43(14Q32.31) WILD-TYPE 141 159 161  23
D42V4, multiclass
    clus
vv   AMP PEAK 43(14Q32.31) MUTATED AMP PEAK 43(14Q32.31) WILD-TYPE
  T1                             1                             141
  T2                             6                             159
  T3                             6                             161
  T4                             0                              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"
D42V5, binary
                                 cls
clus                                0   1
  AMP PEAK 43(14Q32.31) MUTATED     9   1
  AMP PEAK 43(14Q32.31) WILD-TYPE 216 223
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 43(14Q32.31) MUTATED      9    1
  AMP PEAK 43(14Q32.31) WILD-TYPE  216  223
   clus
vv  AMP PEAK 43(14Q32.31) MUTATED AMP PEAK 43(14Q32.31) WILD-TYPE
  0                             9                             216
  1                             1                             223
[1] 2 2
[1] FALSE
D42V6, binary
                                 cls
clus                                0   1
  AMP PEAK 43(14Q32.31) MUTATED     2   0
  AMP PEAK 43(14Q32.31) WILD-TYPE 276   9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 43(14Q32.31) MUTATED      2    0
  AMP PEAK 43(14Q32.31) WILD-TYPE  276    9
   clus
vv  AMP PEAK 43(14Q32.31) MUTATED AMP PEAK 43(14Q32.31) WILD-TYPE
  0                             2                             276
  1                             0                               9
[1] 2 2
[1] FALSE
D42V7, binary
                                 cls
clus                                0   1
  AMP PEAK 43(14Q32.31) MUTATED    11   2
  AMP PEAK 43(14Q32.31) WILD-TYPE 354 132
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 43(14Q32.31) MUTATED     11    2
  AMP PEAK 43(14Q32.31) WILD-TYPE  354  132
        clus
vv       AMP PEAK 43(14Q32.31) MUTATED AMP PEAK 43(14Q32.31) WILD-TYPE
  FEMALE                            11                             354
  MALE                               2                             132
[1] 2 2
[1] FALSE
D42V8, binary
                                 cls
clus                                0   1
  AMP PEAK 43(14Q32.31) MUTATED     1  10
  AMP PEAK 43(14Q32.31) WILD-TYPE 184 280
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 43(14Q32.31) MUTATED      1   10
  AMP PEAK 43(14Q32.31) WILD-TYPE  184  280
     clus
vv    AMP PEAK 43(14Q32.31) MUTATED AMP PEAK 43(14Q32.31) WILD-TYPE
  NO                              1                             184
  YES                            10                             280
[1] 2 2
[1] FALSE
                                 vv
clus                              OTHER  SPECIFY
  AMP PEAK 43(14Q32.31) MUTATED                0
  AMP PEAK 43(14Q32.31) WILD-TYPE              8
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 43(14Q32.31) MUTATED                                               5
  AMP PEAK 43(14Q32.31) WILD-TYPE                                           350
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 43(14Q32.31) MUTATED                                                                        7
  AMP PEAK 43(14Q32.31) WILD-TYPE                                                                     93
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 43(14Q32.31) MUTATED                                                                     1
  AMP PEAK 43(14Q32.31) WILD-TYPE                                                                  35
D42V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 43(14Q32.31) MUTATED
  OTHER  SPECIFY                                                                                     0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      5
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             7
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                1
                                                                        clus
vv                                                                       AMP PEAK 43(14Q32.31) WILD-TYPE
  OTHER  SPECIFY                                                                                       8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                              93
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                 35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V10, binary
                                 cls
clus                                0   1
  AMP PEAK 43(14Q32.31) MUTATED    12   0
  AMP PEAK 43(14Q32.31) WILD-TYPE 408  17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 43(14Q32.31) MUTATED     12    0
  AMP PEAK 43(14Q32.31) WILD-TYPE  408   17
     clus
vv    AMP PEAK 43(14Q32.31) MUTATED AMP PEAK 43(14Q32.31) WILD-TYPE
  NO                             12                             408
  YES                             0                              17
[1] 2 2
[1] FALSE
                                 vv
clus                              MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 43(14Q32.31) MUTATED              3                       0   10
  AMP PEAK 43(14Q32.31) WILD-TYPE          129                      18  320
                                 vv
clus                              VERY ADVANCED (T4B)
  AMP PEAK 43(14Q32.31) MUTATED                     0
  AMP PEAK 43(14Q32.31) WILD-TYPE                   1
D42V11, multiclass
                         clus
vv                        AMP PEAK 43(14Q32.31) MUTATED
  MINIMAL (T3)                                        3
  MODERATE/ADVANCED (T4A)                             0
  NONE                                               10
  VERY ADVANCED (T4B)                                 0
                         clus
vv                        AMP PEAK 43(14Q32.31) WILD-TYPE
  MINIMAL (T3)                                        129
  MODERATE/ADVANCED (T4A)                              18
  NONE                                                320
  VERY ADVANCED (T4B)                                   1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 43(14Q32.31) MUTATED    12   0   0   1
  AMP PEAK 43(14Q32.31) WILD-TYPE 371  51   4  29
D42V12, multiclass
    clus
vv   AMP PEAK 43(14Q32.31) MUTATED AMP PEAK 43(14Q32.31) WILD-TYPE
  R0                            12                             371
  R1                             0                              51
  R2                             0                               4
  RX                             1                              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"
D42V13, continuous
D42V14, binary
                                 cls
clus                                0   1
  AMP PEAK 43(14Q32.31) MUTATED     9   4
  AMP PEAK 43(14Q32.31) WILD-TYPE 216 260
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 43(14Q32.31) MUTATED      9    4
  AMP PEAK 43(14Q32.31) WILD-TYPE  216  260
            clus
vv           AMP PEAK 43(14Q32.31) MUTATED AMP PEAK 43(14Q32.31) WILD-TYPE
  MULTIFOCAL                             9                             216
  UNIFOCAL                               4                             260
[1] 2 2
[1] FALSE
D42V15, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 43(14Q32.31) MUTATED                                  0     0
  AMP PEAK 43(14Q32.31) WILD-TYPE                                1    52
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 43(14Q32.31) MUTATED                           0     8
  AMP PEAK 43(14Q32.31) WILD-TYPE                        27   320
D42V16, multiclass
                                  clus
vv                                 AMP PEAK 43(14Q32.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                    0
  WHITE                                                        8
                                  clus
vv                                 AMP PEAK 43(14Q32.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         52
  BLACK OR AFRICAN AMERICAN                                     27
  WHITE                                                        320
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V17, binary
                                 cls
clus                                0   1
  AMP PEAK 43(14Q32.31) MUTATED     0   6
  AMP PEAK 43(14Q32.31) WILD-TYPE  38 353
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 43(14Q32.31) MUTATED      0    6
  AMP PEAK 43(14Q32.31) WILD-TYPE   38  353
                        clus
vv                       AMP PEAK 43(14Q32.31) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                             6
                        clus
vv                       AMP PEAK 43(14Q32.31) WILD-TYPE
  HISPANIC OR LATINO                                  38
  NOT HISPANIC OR LATINO                             353
[1] 2 2
[1] FALSE

Clustering(43) Variable = AMP PEAK 46(18Q12.1) MUTATION ANALYSIS
D43V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 46(18Q12.1) MUTATED     7   0
  AMP PEAK 46(18Q12.1) WILD-TYPE 474  16
  AMP PEAK 46(18Q12.1) MUTATED AMP PEAK 46(18Q12.1) WILD-TYPE 
                             7                            490 
  AMP PEAK 46(18Q12.1) MUTATED AMP PEAK 46(18Q12.1) WILD-TYPE 
                             0                             16 
$`AMP PEAK 46(18Q12.1) MUTATED`
TCGA-BJ-A45E TCGA-CE-A484 TCGA-EL-A3ZR TCGA-EL-A4KI TCGA-ET-A2MZ TCGA-ET-A39N 
       21.01        12.43        60.16        23.90        37.25       123.32 
TCGA-FY-A3I5 
        7.82 

$`AMP PEAK 46(18Q12.1) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G 
       23.31        18.64         7.99        10.88         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
       15.02        12.66        35.84        21.63        50.17        37.64 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M 
       25.12        14.70        14.27         2.76         9.96        48.79 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       38.17       169.32        18.58         8.71        56.19        23.38 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       43.17        52.37         8.32        11.01       135.91        30.61 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       44.98        42.51        14.96        17.59         6.02        42.58 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
       47.41        17.56        10.09         7.82        30.58        35.41 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       27.45        26.20        38.83        33.96        31.99        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       28.96         8.78         8.42        34.36        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24        33.93        37.48        36.46        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        33.53        35.18        15.88        36.92        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       32.42        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        17.69        59.57        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        42.54        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL 
        7.76        35.67         3.12        36.43        24.76        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        21.34        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        52.44        39.95        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS 
       36.03        53.06        47.38        65.49        61.22         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       34.39        30.51        53.36        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       43.59        24.30        27.06        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
       48.49        18.05        19.79        19.46        78.61        57.01 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       54.08        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.65        44.19        41.29        14.24        47.57        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       13.18        23.51         6.05         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        40.34        19.73        32.32        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ 
       17.59        17.46        17.29        14.60        22.52        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        33.07        13.38         8.35        29.72 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        47.38        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 
       17.49        17.39        16.18        15.02        14.50        15.06 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33         0.49         9.24        13.91        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       29.95        29.85        13.51        12.79        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
       21.34         5.33        26.37        26.37        22.45        21.53 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       60.49        24.46        13.68        81.93        81.70        77.56 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       70.42        56.58        60.20        63.39        65.29        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       63.45        88.41        58.75        52.60        54.35        83.34 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89       100.57        95.34        94.13        55.10        98.20 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24        50.40        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       77.82        75.42        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       71.08         4.11         1.05        13.28         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON 
      116.09         1.25        20.42        17.82         0.99        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
       13.91        16.27        15.68        16.57        18.08         0.30 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
        0.76        17.06        17.36        15.16         6.58        22.49 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04         1.35        21.60         1.68        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46         2.99        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        18.51        16.90        21.83        31.10         8.22 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
       25.64        17.23        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW 
       27.85        24.69        22.29         5.75         2.47         2.60 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       43.69        18.64        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       33.24        33.40        40.37        21.83         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45        30.21        23.93        12.89 

  AMP PEAK 46(18Q12.1) MUTATED AMP PEAK 46(18Q12.1) WILD-TYPE 
                          7.82                           0.16 
  AMP PEAK 46(18Q12.1) MUTATED AMP PEAK 46(18Q12.1) WILD-TYPE 
                        123.32                         169.32 
  AMP PEAK 46(18Q12.1) MUTATED AMP PEAK 46(18Q12.1) WILD-TYPE 
                         23.90                          30.61 
[1] "7.8 - 123.3 (23.9)" "0.2 - 169.3 (30.6)"
[1] "hr="     "9100000"
D43V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 46(18Q12.1) MUTATED         4        1         2        0         0
  AMP PEAK 46(18Q12.1) WILD-TYPE     278       49       109        2        46
                                vv
clus                             STAGE IVC
  AMP PEAK 46(18Q12.1) MUTATED           0
  AMP PEAK 46(18Q12.1) WILD-TYPE         6
D43V3, multiclass
           clus
vv          AMP PEAK 46(18Q12.1) MUTATED AMP PEAK 46(18Q12.1) WILD-TYPE
  STAGE I                              4                            278
  STAGE II                             1                             49
  STAGE III                            2                            109
  STAGE IV                             0                              2
  STAGE IVA                            0                             46
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 46(18Q12.1) MUTATED     2   2   3   0
  AMP PEAK 46(18Q12.1) WILD-TYPE 140 163 164  23
D43V4, multiclass
    clus
vv   AMP PEAK 46(18Q12.1) MUTATED AMP PEAK 46(18Q12.1) WILD-TYPE
  T1                            2                            140
  T2                            2                            163
  T3                            3                            164
  T4                            0                             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"
D43V5, binary
                                cls
clus                               0   1
  AMP PEAK 46(18Q12.1) MUTATED     5   1
  AMP PEAK 46(18Q12.1) WILD-TYPE 220 223
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 46(18Q12.1) MUTATED      5    1
  AMP PEAK 46(18Q12.1) WILD-TYPE  220  223
   clus
vv  AMP PEAK 46(18Q12.1) MUTATED AMP PEAK 46(18Q12.1) WILD-TYPE
  0                            5                            220
  1                            1                            223
[1] 2 2
[1] FALSE
D43V6, binary
                                cls
clus                               0   1
  AMP PEAK 46(18Q12.1) MUTATED     3   0
  AMP PEAK 46(18Q12.1) WILD-TYPE 275   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 46(18Q12.1) MUTATED      3    0
  AMP PEAK 46(18Q12.1) WILD-TYPE  275    9
   clus
vv  AMP PEAK 46(18Q12.1) MUTATED AMP PEAK 46(18Q12.1) WILD-TYPE
  0                            3                            275
  1                            0                              9
[1] 2 2
[1] FALSE
D43V7, binary
                                cls
clus                               0   1
  AMP PEAK 46(18Q12.1) MUTATED     5   2
  AMP PEAK 46(18Q12.1) WILD-TYPE 360 132
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 46(18Q12.1) MUTATED      5    2
  AMP PEAK 46(18Q12.1) WILD-TYPE  360  132
        clus
vv       AMP PEAK 46(18Q12.1) MUTATED AMP PEAK 46(18Q12.1) WILD-TYPE
  FEMALE                            5                            360
  MALE                              2                            132
[1] 2 2
[1] FALSE
D43V8, binary
                                cls
clus                               0   1
  AMP PEAK 46(18Q12.1) MUTATED     3   3
  AMP PEAK 46(18Q12.1) WILD-TYPE 182 287
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 46(18Q12.1) MUTATED      3    3
  AMP PEAK 46(18Q12.1) WILD-TYPE  182  287
     clus
vv    AMP PEAK 46(18Q12.1) MUTATED AMP PEAK 46(18Q12.1) WILD-TYPE
  NO                             3                            182
  YES                            3                            287
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 46(18Q12.1) MUTATED                0
  AMP PEAK 46(18Q12.1) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 46(18Q12.1) MUTATED                                               6
  AMP PEAK 46(18Q12.1) WILD-TYPE                                           349
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 46(18Q12.1) MUTATED                                                                        1
  AMP PEAK 46(18Q12.1) WILD-TYPE                                                                     99
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 46(18Q12.1) MUTATED                                                                     0
  AMP PEAK 46(18Q12.1) WILD-TYPE                                                                  36
D43V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 46(18Q12.1) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     6
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       AMP PEAK 46(18Q12.1) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     349
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             99
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V10, binary
                                cls
clus                               0   1
  AMP PEAK 46(18Q12.1) MUTATED     5   0
  AMP PEAK 46(18Q12.1) WILD-TYPE 415  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 46(18Q12.1) MUTATED      5    0
  AMP PEAK 46(18Q12.1) WILD-TYPE  415   17
     clus
vv    AMP PEAK 46(18Q12.1) MUTATED AMP PEAK 46(18Q12.1) WILD-TYPE
  NO                             5                            415
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 46(18Q12.1) MUTATED              1                       0    5
  AMP PEAK 46(18Q12.1) WILD-TYPE          131                      18  325
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 46(18Q12.1) MUTATED                     0
  AMP PEAK 46(18Q12.1) WILD-TYPE                   1
D43V11, multiclass
                         clus
vv                        AMP PEAK 46(18Q12.1) MUTATED
  MINIMAL (T3)                                       1
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               5
  VERY ADVANCED (T4B)                                0
                         clus
vv                        AMP PEAK 46(18Q12.1) WILD-TYPE
  MINIMAL (T3)                                       131
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               325
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 46(18Q12.1) MUTATED     5   0   0   1
  AMP PEAK 46(18Q12.1) WILD-TYPE 378  51   4  29
D43V12, multiclass
    clus
vv   AMP PEAK 46(18Q12.1) MUTATED AMP PEAK 46(18Q12.1) WILD-TYPE
  R0                            5                            378
  R1                            0                             51
  R2                            0                              4
  RX                            1                             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"
D43V13, continuous
D43V14, binary
                                cls
clus                               0   1
  AMP PEAK 46(18Q12.1) MUTATED     2   5
  AMP PEAK 46(18Q12.1) WILD-TYPE 223 259
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 46(18Q12.1) MUTATED      2    5
  AMP PEAK 46(18Q12.1) WILD-TYPE  223  259
            clus
vv           AMP PEAK 46(18Q12.1) MUTATED AMP PEAK 46(18Q12.1) WILD-TYPE
  MULTIFOCAL                            2                            223
  UNIFOCAL                              5                            259
[1] 2 2
[1] FALSE
D43V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 46(18Q12.1) MUTATED                                  0     1
  AMP PEAK 46(18Q12.1) WILD-TYPE                                1    51
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 46(18Q12.1) MUTATED                           0     6
  AMP PEAK 46(18Q12.1) WILD-TYPE                        27   322
D43V16, multiclass
                                  clus
vv                                 AMP PEAK 46(18Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       6
                                  clus
vv                                 AMP PEAK 46(18Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        51
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       322
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V17, binary
                                cls
clus                               0   1
  AMP PEAK 46(18Q12.1) MUTATED     0   7
  AMP PEAK 46(18Q12.1) WILD-TYPE  38 352
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 46(18Q12.1) MUTATED      0    7
  AMP PEAK 46(18Q12.1) WILD-TYPE   38  352
                        clus
vv                       AMP PEAK 46(18Q12.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            7
                        clus
vv                       AMP PEAK 46(18Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            352
[1] 2 2
[1] FALSE

Clustering(44) Variable = AMP PEAK 47(18Q22.1) MUTATION ANALYSIS
D44V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 47(18Q22.1) MUTATED     7   0
  AMP PEAK 47(18Q22.1) WILD-TYPE 474  16
  AMP PEAK 47(18Q22.1) MUTATED AMP PEAK 47(18Q22.1) WILD-TYPE 
                             7                            490 
  AMP PEAK 47(18Q22.1) MUTATED AMP PEAK 47(18Q22.1) WILD-TYPE 
                             0                             16 
$`AMP PEAK 47(18Q22.1) MUTATED`
TCGA-BJ-A45E TCGA-EL-A3ZR TCGA-EL-A4KI TCGA-EM-A3AN TCGA-ET-A2MZ TCGA-ET-A39N 
       21.01        60.16        23.90        33.07        37.25       123.32 
TCGA-FY-A3I5 
        7.82 

$`AMP PEAK 47(18Q22.1) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G 
       23.31        18.64         7.99        10.88         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        30.61         0.16         0.23        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        33.50         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        69.57        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       49.51        50.24       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       150.48       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        89.56        78.97        51.78 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        47.38        65.49        61.22 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT 
       47.84        43.59        24.30        27.06        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        48.49        18.05        19.79        19.46        78.61 
TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       57.01        54.08        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       14.53        10.65        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
       17.88        13.18        23.51         6.05         2.99        12.30 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       48.46        13.15        22.16        40.34        19.73        32.32 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       33.96        17.59        17.46        17.29        14.60        22.52 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       30.94        15.68        14.14        13.38         8.35        29.72 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        47.38        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 
       17.49        17.39        16.18        15.02        14.50        15.06 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33         0.49         9.24        13.91        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       29.95        29.85        13.51        12.79        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
       21.34         5.33        26.37        26.37        22.45        21.53 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       60.49        24.46        13.68        81.93        81.70        77.56 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       70.42        56.58        60.20        63.39        65.29        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       63.45        88.41        58.75        52.60        54.35        83.34 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89       100.57        95.34        94.13        55.10        98.20 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24        50.40        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       77.82        75.42        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       71.08         4.11         1.05        13.28         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON 
      116.09         1.25        20.42        17.82         0.99        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
       13.91        16.27        15.68        16.57        18.08         0.30 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
        0.76        17.06        17.36        15.16         6.58        22.49 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04         1.35        21.60         1.68        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46         2.99        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        18.51        16.90        21.83        31.10         8.22 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
       25.64        17.23        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW 
       27.85        24.69        22.29         5.75         2.47         2.60 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       43.69        18.64        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       33.24        33.40        40.37        21.83         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45        30.21        23.93        12.89 

  AMP PEAK 47(18Q22.1) MUTATED AMP PEAK 47(18Q22.1) WILD-TYPE 
                          7.82                           0.16 
  AMP PEAK 47(18Q22.1) MUTATED AMP PEAK 47(18Q22.1) WILD-TYPE 
                        123.32                         169.32 
  AMP PEAK 47(18Q22.1) MUTATED AMP PEAK 47(18Q22.1) WILD-TYPE 
                         33.07                          30.61 
[1] "7.8 - 123.3 (33.1)" "0.2 - 169.3 (30.6)"
[1] "hr="     "9100000"
D44V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 47(18Q22.1) MUTATED         4        1         2        0         0
  AMP PEAK 47(18Q22.1) WILD-TYPE     278       49       109        2        46
                                vv
clus                             STAGE IVC
  AMP PEAK 47(18Q22.1) MUTATED           0
  AMP PEAK 47(18Q22.1) WILD-TYPE         6
D44V3, multiclass
           clus
vv          AMP PEAK 47(18Q22.1) MUTATED AMP PEAK 47(18Q22.1) WILD-TYPE
  STAGE I                              4                            278
  STAGE II                             1                             49
  STAGE III                            2                            109
  STAGE IV                             0                              2
  STAGE IVA                            0                             46
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 47(18Q22.1) MUTATED     3   1   3   0
  AMP PEAK 47(18Q22.1) WILD-TYPE 139 164 164  23
D44V4, multiclass
    clus
vv   AMP PEAK 47(18Q22.1) MUTATED AMP PEAK 47(18Q22.1) WILD-TYPE
  T1                            3                            139
  T2                            1                            164
  T3                            3                            164
  T4                            0                             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"
D44V5, binary
                                cls
clus                               0   1
  AMP PEAK 47(18Q22.1) MUTATED     5   1
  AMP PEAK 47(18Q22.1) WILD-TYPE 220 223
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 47(18Q22.1) MUTATED      5    1
  AMP PEAK 47(18Q22.1) WILD-TYPE  220  223
   clus
vv  AMP PEAK 47(18Q22.1) MUTATED AMP PEAK 47(18Q22.1) WILD-TYPE
  0                            5                            220
  1                            1                            223
[1] 2 2
[1] FALSE
D44V6, binary
                                cls
clus                               0   1
  AMP PEAK 47(18Q22.1) MUTATED     2   0
  AMP PEAK 47(18Q22.1) WILD-TYPE 276   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 47(18Q22.1) MUTATED      2    0
  AMP PEAK 47(18Q22.1) WILD-TYPE  276    9
   clus
vv  AMP PEAK 47(18Q22.1) MUTATED AMP PEAK 47(18Q22.1) WILD-TYPE
  0                            2                            276
  1                            0                              9
[1] 2 2
[1] FALSE
D44V7, binary
                                cls
clus                               0   1
  AMP PEAK 47(18Q22.1) MUTATED     5   2
  AMP PEAK 47(18Q22.1) WILD-TYPE 360 132
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 47(18Q22.1) MUTATED      5    2
  AMP PEAK 47(18Q22.1) WILD-TYPE  360  132
        clus
vv       AMP PEAK 47(18Q22.1) MUTATED AMP PEAK 47(18Q22.1) WILD-TYPE
  FEMALE                            5                            360
  MALE                              2                            132
[1] 2 2
[1] FALSE
D44V8, binary
                                cls
clus                               0   1
  AMP PEAK 47(18Q22.1) MUTATED     2   4
  AMP PEAK 47(18Q22.1) WILD-TYPE 183 286
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 47(18Q22.1) MUTATED      2    4
  AMP PEAK 47(18Q22.1) WILD-TYPE  183  286
     clus
vv    AMP PEAK 47(18Q22.1) MUTATED AMP PEAK 47(18Q22.1) WILD-TYPE
  NO                             2                            183
  YES                            4                            286
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 47(18Q22.1) MUTATED                0
  AMP PEAK 47(18Q22.1) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 47(18Q22.1) MUTATED                                               6
  AMP PEAK 47(18Q22.1) WILD-TYPE                                           349
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 47(18Q22.1) MUTATED                                                                        1
  AMP PEAK 47(18Q22.1) WILD-TYPE                                                                     99
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 47(18Q22.1) MUTATED                                                                     0
  AMP PEAK 47(18Q22.1) WILD-TYPE                                                                  36
D44V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 47(18Q22.1) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     6
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       AMP PEAK 47(18Q22.1) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     349
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             99
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V10, binary
                                cls
clus                               0   1
  AMP PEAK 47(18Q22.1) MUTATED     5   0
  AMP PEAK 47(18Q22.1) WILD-TYPE 415  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 47(18Q22.1) MUTATED      5    0
  AMP PEAK 47(18Q22.1) WILD-TYPE  415   17
     clus
vv    AMP PEAK 47(18Q22.1) MUTATED AMP PEAK 47(18Q22.1) WILD-TYPE
  NO                             5                            415
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 47(18Q22.1) MUTATED              1                       0    5
  AMP PEAK 47(18Q22.1) WILD-TYPE          131                      18  325
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 47(18Q22.1) MUTATED                     0
  AMP PEAK 47(18Q22.1) WILD-TYPE                   1
D44V11, multiclass
                         clus
vv                        AMP PEAK 47(18Q22.1) MUTATED
  MINIMAL (T3)                                       1
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               5
  VERY ADVANCED (T4B)                                0
                         clus
vv                        AMP PEAK 47(18Q22.1) WILD-TYPE
  MINIMAL (T3)                                       131
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               325
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 47(18Q22.1) MUTATED     4   1   0   1
  AMP PEAK 47(18Q22.1) WILD-TYPE 379  50   4  29
D44V12, multiclass
    clus
vv   AMP PEAK 47(18Q22.1) MUTATED AMP PEAK 47(18Q22.1) WILD-TYPE
  R0                            4                            379
  R1                            1                             50
  R2                            0                              4
  RX                            1                             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"
D44V13, continuous
D44V14, binary
                                cls
clus                               0   1
  AMP PEAK 47(18Q22.1) MUTATED     3   4
  AMP PEAK 47(18Q22.1) WILD-TYPE 222 260
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 47(18Q22.1) MUTATED      3    4
  AMP PEAK 47(18Q22.1) WILD-TYPE  222  260
            clus
vv           AMP PEAK 47(18Q22.1) MUTATED AMP PEAK 47(18Q22.1) WILD-TYPE
  MULTIFOCAL                            3                            222
  UNIFOCAL                              4                            260
[1] 2 2
[1] FALSE
D44V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 47(18Q22.1) MUTATED                                  0     0
  AMP PEAK 47(18Q22.1) WILD-TYPE                                1    52
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 47(18Q22.1) MUTATED                           0     6
  AMP PEAK 47(18Q22.1) WILD-TYPE                        27   322
D44V16, multiclass
                                  clus
vv                                 AMP PEAK 47(18Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       6
                                  clus
vv                                 AMP PEAK 47(18Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        52
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       322
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V17, binary
                                cls
clus                               0   1
  AMP PEAK 47(18Q22.1) MUTATED     0   6
  AMP PEAK 47(18Q22.1) WILD-TYPE  38 353
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 47(18Q22.1) MUTATED      0    6
  AMP PEAK 47(18Q22.1) WILD-TYPE   38  353
                        clus
vv                       AMP PEAK 47(18Q22.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            6
                        clus
vv                       AMP PEAK 47(18Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            353
[1] 2 2
[1] FALSE

Clustering(45) Variable = AMP PEAK 48(18Q22.3) MUTATION ANALYSIS
D45V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 48(18Q22.3) MUTATED     8   0
  AMP PEAK 48(18Q22.3) WILD-TYPE 473  16
  AMP PEAK 48(18Q22.3) MUTATED AMP PEAK 48(18Q22.3) WILD-TYPE 
                             8                            489 
  AMP PEAK 48(18Q22.3) MUTATED AMP PEAK 48(18Q22.3) WILD-TYPE 
                             0                             16 
$`AMP PEAK 48(18Q22.3) MUTATED`
TCGA-BJ-A45E TCGA-EL-A3ZR TCGA-EL-A4KI TCGA-EM-A2CT TCGA-ET-A2MZ TCGA-ET-A39N 
       21.01        60.16        23.90        48.46        37.25       123.32 
TCGA-FY-A3I5 TCGA-KS-A4ID 
        7.82        33.24 

$`AMP PEAK 48(18Q22.3) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G 
       23.31        18.64         7.99        10.88         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        30.61         0.16         0.23        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        33.50         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        69.57        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       49.51        50.24       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       150.48       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        89.56        78.97        51.78 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        47.38        65.49        61.22 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT 
       47.84        43.59        24.30        27.06        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        48.49        18.05        19.79        19.46        78.61 
TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       57.01        54.08        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       14.53        10.65        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
       17.88        13.18        23.51         6.05         2.99        12.30 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        40.34        19.73        32.32        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ 
       17.59        17.46        17.29        14.60        22.52        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        33.07        13.38         8.35        29.72 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        47.38        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 
       17.49        17.39        16.18        15.02        14.50        15.06 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33         0.49         9.24        13.91        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       29.95        29.85        13.51        12.79        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
       21.34         5.33        26.37        26.37        22.45        21.53 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       60.49        24.46        13.68        81.93        81.70        77.56 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       70.42        56.58        60.20        63.39        65.29        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       63.45        88.41        58.75        52.60        54.35        83.34 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89       100.57        95.34        94.13        55.10        98.20 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24        50.40        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       77.82        75.42        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       71.08         4.11         1.05        13.28         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON 
      116.09         1.25        20.42        17.82         0.99        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
       13.91        16.27        15.68        16.57        18.08         0.30 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
        0.76        17.06        17.36        15.16         6.58        22.49 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04         1.35        21.60         1.68        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46         2.99        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        18.51        16.90        21.83        31.10         8.22 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
       25.64        17.23        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW 
       27.85        24.69        22.29         5.75         2.47         2.60 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       43.69        18.64        32.45        87.39        84.72        35.28 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.40        40.37        21.83         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       30.21        23.93        12.89 

  AMP PEAK 48(18Q22.3) MUTATED AMP PEAK 48(18Q22.3) WILD-TYPE 
                          7.82                           0.16 
  AMP PEAK 48(18Q22.3) MUTATED AMP PEAK 48(18Q22.3) WILD-TYPE 
                        123.32                         169.32 
  AMP PEAK 48(18Q22.3) MUTATED AMP PEAK 48(18Q22.3) WILD-TYPE 
                        35.245                         30.610 
[1] "7.8 - 123.3 (35.2)" "0.2 - 169.3 (30.6)"
[1] "hr="     "9200000"
D45V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 48(18Q22.3) MUTATED         5        1         2        0         0
  AMP PEAK 48(18Q22.3) WILD-TYPE     277       49       109        2        46
                                vv
clus                             STAGE IVC
  AMP PEAK 48(18Q22.3) MUTATED           0
  AMP PEAK 48(18Q22.3) WILD-TYPE         6
D45V3, multiclass
           clus
vv          AMP PEAK 48(18Q22.3) MUTATED AMP PEAK 48(18Q22.3) WILD-TYPE
  STAGE I                              5                            277
  STAGE II                             1                             49
  STAGE III                            2                            109
  STAGE IV                             0                              2
  STAGE IVA                            0                             46
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 48(18Q22.3) MUTATED     4   1   3   0
  AMP PEAK 48(18Q22.3) WILD-TYPE 138 164 164  23
D45V4, multiclass
    clus
vv   AMP PEAK 48(18Q22.3) MUTATED AMP PEAK 48(18Q22.3) WILD-TYPE
  T1                            4                            138
  T2                            1                            164
  T3                            3                            164
  T4                            0                             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"
D45V5, binary
                                cls
clus                               0   1
  AMP PEAK 48(18Q22.3) MUTATED     7   0
  AMP PEAK 48(18Q22.3) WILD-TYPE 218 224
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 48(18Q22.3) MUTATED      7    0
  AMP PEAK 48(18Q22.3) WILD-TYPE  218  224
   clus
vv  AMP PEAK 48(18Q22.3) MUTATED AMP PEAK 48(18Q22.3) WILD-TYPE
  0                            7                            218
  1                            0                            224
[1] 2 2
[1] FALSE
D45V6, binary
                                cls
clus                               0   1
  AMP PEAK 48(18Q22.3) MUTATED     3   0
  AMP PEAK 48(18Q22.3) WILD-TYPE 275   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 48(18Q22.3) MUTATED      3    0
  AMP PEAK 48(18Q22.3) WILD-TYPE  275    9
   clus
vv  AMP PEAK 48(18Q22.3) MUTATED AMP PEAK 48(18Q22.3) WILD-TYPE
  0                            3                            275
  1                            0                              9
[1] 2 2
[1] FALSE
D45V7, binary
                                cls
clus                               0   1
  AMP PEAK 48(18Q22.3) MUTATED     6   2
  AMP PEAK 48(18Q22.3) WILD-TYPE 359 132
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 48(18Q22.3) MUTATED      6    2
  AMP PEAK 48(18Q22.3) WILD-TYPE  359  132
        clus
vv       AMP PEAK 48(18Q22.3) MUTATED AMP PEAK 48(18Q22.3) WILD-TYPE
  FEMALE                            6                            359
  MALE                              2                            132
[1] 2 2
[1] FALSE
D45V8, binary
                                cls
clus                               0   1
  AMP PEAK 48(18Q22.3) MUTATED     4   3
  AMP PEAK 48(18Q22.3) WILD-TYPE 181 287
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 48(18Q22.3) MUTATED      4    3
  AMP PEAK 48(18Q22.3) WILD-TYPE  181  287
     clus
vv    AMP PEAK 48(18Q22.3) MUTATED AMP PEAK 48(18Q22.3) WILD-TYPE
  NO                             4                            181
  YES                            3                            287
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 48(18Q22.3) MUTATED                0
  AMP PEAK 48(18Q22.3) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 48(18Q22.3) MUTATED                                               5
  AMP PEAK 48(18Q22.3) WILD-TYPE                                           350
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 48(18Q22.3) MUTATED                                                                        3
  AMP PEAK 48(18Q22.3) WILD-TYPE                                                                     97
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 48(18Q22.3) MUTATED                                                                     0
  AMP PEAK 48(18Q22.3) WILD-TYPE                                                                  36
D45V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 48(18Q22.3) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     5
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       AMP PEAK 48(18Q22.3) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             97
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V10, binary
                                cls
clus                               0   1
  AMP PEAK 48(18Q22.3) MUTATED     6   0
  AMP PEAK 48(18Q22.3) WILD-TYPE 414  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 48(18Q22.3) MUTATED      6    0
  AMP PEAK 48(18Q22.3) WILD-TYPE  414   17
     clus
vv    AMP PEAK 48(18Q22.3) MUTATED AMP PEAK 48(18Q22.3) WILD-TYPE
  NO                             6                            414
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 48(18Q22.3) MUTATED              1                       0    6
  AMP PEAK 48(18Q22.3) WILD-TYPE          131                      18  324
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 48(18Q22.3) MUTATED                     0
  AMP PEAK 48(18Q22.3) WILD-TYPE                   1
D45V11, multiclass
                         clus
vv                        AMP PEAK 48(18Q22.3) MUTATED
  MINIMAL (T3)                                       1
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               6
  VERY ADVANCED (T4B)                                0
                         clus
vv                        AMP PEAK 48(18Q22.3) WILD-TYPE
  MINIMAL (T3)                                       131
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               324
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 48(18Q22.3) MUTATED     6   0   0   1
  AMP PEAK 48(18Q22.3) WILD-TYPE 377  51   4  29
D45V12, multiclass
    clus
vv   AMP PEAK 48(18Q22.3) MUTATED AMP PEAK 48(18Q22.3) WILD-TYPE
  R0                            6                            377
  R1                            0                             51
  R2                            0                              4
  RX                            1                             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"
D45V13, continuous
D45V14, binary
                                cls
clus                               0   1
  AMP PEAK 48(18Q22.3) MUTATED     2   6
  AMP PEAK 48(18Q22.3) WILD-TYPE 223 258
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 48(18Q22.3) MUTATED      2    6
  AMP PEAK 48(18Q22.3) WILD-TYPE  223  258
            clus
vv           AMP PEAK 48(18Q22.3) MUTATED AMP PEAK 48(18Q22.3) WILD-TYPE
  MULTIFOCAL                            2                            223
  UNIFOCAL                              6                            258
[1] 2 2
[1] FALSE
D45V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 48(18Q22.3) MUTATED                                  0     0
  AMP PEAK 48(18Q22.3) WILD-TYPE                                1    52
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 48(18Q22.3) MUTATED                           0     7
  AMP PEAK 48(18Q22.3) WILD-TYPE                        27   321
D45V16, multiclass
                                  clus
vv                                 AMP PEAK 48(18Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       7
                                  clus
vv                                 AMP PEAK 48(18Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        52
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       321
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V17, binary
                                cls
clus                               0   1
  AMP PEAK 48(18Q22.3) MUTATED     0   6
  AMP PEAK 48(18Q22.3) WILD-TYPE  38 353
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 48(18Q22.3) MUTATED      0    6
  AMP PEAK 48(18Q22.3) WILD-TYPE   38  353
                        clus
vv                       AMP PEAK 48(18Q22.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            6
                        clus
vv                       AMP PEAK 48(18Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            353
[1] 2 2
[1] FALSE

Clustering(46) Variable = AMP PEAK 49(19P13.3) MUTATION ANALYSIS
D46V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 49(19P13.3) MUTATED     8   0
  AMP PEAK 49(19P13.3) WILD-TYPE 473  16
  AMP PEAK 49(19P13.3) MUTATED AMP PEAK 49(19P13.3) WILD-TYPE 
                             8                            489 
  AMP PEAK 49(19P13.3) MUTATED AMP PEAK 49(19P13.3) WILD-TYPE 
                             0                             16 
$`AMP PEAK 49(19P13.3) MUTATED`
TCGA-DE-A4MA TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A22N TCGA-EM-A2OY TCGA-EM-A3O9 
       30.12        23.90        78.61        10.65        32.32         9.24 
TCGA-EM-A3SY TCGA-FY-A3I5 
       13.51         7.82 

$`AMP PEAK 49(19P13.3) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MB 
       50.17        37.64        15.85        18.54        18.84        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        30.61         0.16         0.23        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        33.50         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        69.57        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       49.51        50.24       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       150.48       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        89.56        78.97        51.78 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        47.38        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       60.16         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS 
       41.13        47.84        43.59        24.30        27.06        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       57.01        54.08        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       14.53        44.19        41.29        14.24        47.57        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       13.18        23.51         6.05         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 
       13.15        22.16        40.34        19.73        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.46        17.29        14.60        22.52        30.94        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR 
       14.14        33.07        13.38         8.35        29.72        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        47.38        21.01        12.07        17.49 
TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 
       17.39        16.18        15.02        14.50        15.06         7.33 
TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
        0.49        13.91        38.66        38.86        29.95        29.85 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        84.59        29.33        21.34         5.33        26.37 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
       26.37        22.45        21.53        60.49        24.46        13.68 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       81.93        81.70        77.56        70.42        56.58        60.20 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       63.39        65.29        18.38        63.45        88.41        58.75 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       37.25        52.60        54.35        83.34         2.66        80.88 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
       33.24       106.09       107.41       108.46        84.89       123.32 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
      100.57        95.34        94.13        55.10        98.20        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
       50.40        79.10        76.64         5.79        87.62        77.82 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       75.42        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       117.40        66.77       112.80        39.95        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.11         1.05        13.28         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25        20.42        17.82         0.99        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08         0.30         0.76 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16         6.58        22.49        19.04 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35        21.60         1.68        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46         2.99        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       18.51        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       17.23        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY 
       24.69        22.29         5.75         2.47         2.60         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.40        40.37        21.83         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       30.21        23.93        12.89 

  AMP PEAK 49(19P13.3) MUTATED AMP PEAK 49(19P13.3) WILD-TYPE 
                          7.82                           0.16 
  AMP PEAK 49(19P13.3) MUTATED AMP PEAK 49(19P13.3) WILD-TYPE 
                         78.61                         169.32 
  AMP PEAK 49(19P13.3) MUTATED AMP PEAK 49(19P13.3) WILD-TYPE 
                        18.705                         30.870 
[1] "7.8 - 78.6 (18.7)"  "0.2 - 169.3 (30.9)"
[1] "hr="     "3300000"
D46V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 49(19P13.3) MUTATED         3        1         4        0         0
  AMP PEAK 49(19P13.3) WILD-TYPE     279       49       107        2        46
                                vv
clus                             STAGE IVC
  AMP PEAK 49(19P13.3) MUTATED           0
  AMP PEAK 49(19P13.3) WILD-TYPE         6
D46V3, multiclass
           clus
vv          AMP PEAK 49(19P13.3) MUTATED AMP PEAK 49(19P13.3) WILD-TYPE
  STAGE I                              3                            279
  STAGE II                             1                             49
  STAGE III                            4                            107
  STAGE IV                             0                              2
  STAGE IVA                            0                             46
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 49(19P13.3) MUTATED     2   1   5   0
  AMP PEAK 49(19P13.3) WILD-TYPE 140 164 162  23
D46V4, multiclass
    clus
vv   AMP PEAK 49(19P13.3) MUTATED AMP PEAK 49(19P13.3) WILD-TYPE
  T1                            2                            140
  T2                            1                            164
  T3                            5                            162
  T4                            0                             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"
D46V5, binary
                                cls
clus                               0   1
  AMP PEAK 49(19P13.3) MUTATED     6   1
  AMP PEAK 49(19P13.3) WILD-TYPE 219 223
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 49(19P13.3) MUTATED      6    1
  AMP PEAK 49(19P13.3) WILD-TYPE  219  223
   clus
vv  AMP PEAK 49(19P13.3) MUTATED AMP PEAK 49(19P13.3) WILD-TYPE
  0                            6                            219
  1                            1                            223
[1] 2 2
[1] FALSE
D46V6, binary
                                cls
clus                               0   1
  AMP PEAK 49(19P13.3) MUTATED     1   0
  AMP PEAK 49(19P13.3) WILD-TYPE 277   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 49(19P13.3) MUTATED      1    0
  AMP PEAK 49(19P13.3) WILD-TYPE  277    9
   clus
vv  AMP PEAK 49(19P13.3) MUTATED AMP PEAK 49(19P13.3) WILD-TYPE
  0                            1                            277
  1                            0                              9
[1] 2 2
[1] FALSE
D46V7, binary
                                cls
clus                               0   1
  AMP PEAK 49(19P13.3) MUTATED     5   3
  AMP PEAK 49(19P13.3) WILD-TYPE 360 131
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 49(19P13.3) MUTATED      5    3
  AMP PEAK 49(19P13.3) WILD-TYPE  360  131
        clus
vv       AMP PEAK 49(19P13.3) MUTATED AMP PEAK 49(19P13.3) WILD-TYPE
  FEMALE                            5                            360
  MALE                              3                            131
[1] 2 2
[1] FALSE
D46V8, binary
                                cls
clus                               0   1
  AMP PEAK 49(19P13.3) MUTATED     1   6
  AMP PEAK 49(19P13.3) WILD-TYPE 184 284
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 49(19P13.3) MUTATED      1    6
  AMP PEAK 49(19P13.3) WILD-TYPE  184  284
     clus
vv    AMP PEAK 49(19P13.3) MUTATED AMP PEAK 49(19P13.3) WILD-TYPE
  NO                             1                            184
  YES                            6                            284
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 49(19P13.3) MUTATED                0
  AMP PEAK 49(19P13.3) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 49(19P13.3) MUTATED                                               2
  AMP PEAK 49(19P13.3) WILD-TYPE                                           353
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 49(19P13.3) MUTATED                                                                        6
  AMP PEAK 49(19P13.3) WILD-TYPE                                                                     94
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 49(19P13.3) MUTATED                                                                     0
  AMP PEAK 49(19P13.3) WILD-TYPE                                                                  36
D46V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 49(19P13.3) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            6
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       AMP PEAK 49(19P13.3) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             94
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V10, binary
                                cls
clus                               0   1
  AMP PEAK 49(19P13.3) MUTATED     7   0
  AMP PEAK 49(19P13.3) WILD-TYPE 413  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 49(19P13.3) MUTATED      7    0
  AMP PEAK 49(19P13.3) WILD-TYPE  413   17
     clus
vv    AMP PEAK 49(19P13.3) MUTATED AMP PEAK 49(19P13.3) WILD-TYPE
  NO                             7                            413
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 49(19P13.3) MUTATED              2                       0    6
  AMP PEAK 49(19P13.3) WILD-TYPE          130                      18  324
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 49(19P13.3) MUTATED                     0
  AMP PEAK 49(19P13.3) WILD-TYPE                   1
D46V11, multiclass
                         clus
vv                        AMP PEAK 49(19P13.3) MUTATED
  MINIMAL (T3)                                       2
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               6
  VERY ADVANCED (T4B)                                0
                         clus
vv                        AMP PEAK 49(19P13.3) WILD-TYPE
  MINIMAL (T3)                                       130
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               324
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 49(19P13.3) MUTATED     7   0   0   1
  AMP PEAK 49(19P13.3) WILD-TYPE 376  51   4  29
D46V12, multiclass
    clus
vv   AMP PEAK 49(19P13.3) MUTATED AMP PEAK 49(19P13.3) WILD-TYPE
  R0                            7                            376
  R1                            0                             51
  R2                            0                              4
  RX                            1                             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"
D46V13, continuous
D46V14, binary
                                cls
clus                               0   1
  AMP PEAK 49(19P13.3) MUTATED     5   3
  AMP PEAK 49(19P13.3) WILD-TYPE 220 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 49(19P13.3) MUTATED      5    3
  AMP PEAK 49(19P13.3) WILD-TYPE  220  261
            clus
vv           AMP PEAK 49(19P13.3) MUTATED AMP PEAK 49(19P13.3) WILD-TYPE
  MULTIFOCAL                            5                            220
  UNIFOCAL                              3                            261
[1] 2 2
[1] FALSE
D46V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 49(19P13.3) MUTATED                                  0     0
  AMP PEAK 49(19P13.3) WILD-TYPE                                1    52
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 49(19P13.3) MUTATED                           1     2
  AMP PEAK 49(19P13.3) WILD-TYPE                        26   326
D46V16, multiclass
                                  clus
vv                                 AMP PEAK 49(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                       2
                                  clus
vv                                 AMP PEAK 49(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        52
  BLACK OR AFRICAN AMERICAN                                    26
  WHITE                                                       326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V17, binary
                                cls
clus                               0   1
  AMP PEAK 49(19P13.3) MUTATED     0   3
  AMP PEAK 49(19P13.3) WILD-TYPE  38 356
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 49(19P13.3) MUTATED      0    3
  AMP PEAK 49(19P13.3) WILD-TYPE   38  356
                        clus
vv                       AMP PEAK 49(19P13.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            3
                        clus
vv                       AMP PEAK 49(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            356
[1] 2 2
[1] FALSE

Clustering(47) Variable = AMP PEAK 50(20P13) MUTATION ANALYSIS
D47V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 50(20P13) MUTATED    13   1
  AMP PEAK 50(20P13) WILD-TYPE 468  15
  AMP PEAK 50(20P13) MUTATED AMP PEAK 50(20P13) WILD-TYPE 
                          14                          483 
  AMP PEAK 50(20P13) MUTATED AMP PEAK 50(20P13) WILD-TYPE 
                           1                           15 
$`AMP PEAK 50(20P13) MUTATED`
TCGA-BJ-A192 TCGA-EL-A3GO TCGA-EL-A3T9 TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A1YD 
       44.35        64.87         5.72        23.90        78.61        57.01 
TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A2MZ 
        6.05        32.32        22.52         9.24        13.51        37.25 
TCGA-ET-A39N TCGA-FY-A3I5 
      123.32         7.82 

$`AMP PEAK 50(20P13) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
       42.15        21.04        35.54        32.45        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.08        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        30.61         0.16         0.23        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        33.50         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GP 
      139.86        98.53        69.57        57.11       108.36        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA 
       32.48       132.07        98.24        41.29       107.47        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM 
       82.82        89.56        78.97        51.78        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        65.49        61.22        60.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       34.39        30.51        53.36        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       43.59        24.30        27.06        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I 
       48.49        18.05        19.79        19.46        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O 
       14.50        15.75        10.45        14.53        10.65        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       19.73        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
       15.06         7.33         0.49        13.91        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       29.95        29.85        12.79        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        5.33        26.37        26.37        22.45        21.53        60.49 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       24.46        13.68        81.93        81.70        77.56        70.42 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       56.58        60.20        63.39        65.29        18.38        63.45 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       88.41        58.75        52.60        54.35        83.34         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       80.88        33.24       106.09       107.41       108.46        84.89 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
      100.57        95.34        94.13        55.10        98.20        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
       50.40        79.10        76.64         5.79        87.62        77.82 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       75.42        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       117.40        66.77       112.80        39.95        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.11         1.05        13.28         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25        20.42        17.82         0.99        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08         0.30         0.76 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16         6.58        22.49        19.04 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35        21.60         1.68        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46         2.99        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       18.51        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       17.23        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY 
       24.69        22.29         5.75         2.47         2.60         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.40        40.37        21.83         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       30.21        23.93        12.89 

  AMP PEAK 50(20P13) MUTATED AMP PEAK 50(20P13) WILD-TYPE 
                        5.72                         0.16 
  AMP PEAK 50(20P13) MUTATED AMP PEAK 50(20P13) WILD-TYPE 
                      123.32                       169.32 
  AMP PEAK 50(20P13) MUTATED AMP PEAK 50(20P13) WILD-TYPE 
                       28.11                        30.61 
[1] "5.7 - 123.3 (28.1)" "0.2 - 169.3 (30.6)"
[1] "hr=" "2.2"
D47V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 50(20P13) MUTATED         5        4         4        1         0
  AMP PEAK 50(20P13) WILD-TYPE     277       46       107        1        46
                              vv
clus                           STAGE IVC
  AMP PEAK 50(20P13) MUTATED           0
  AMP PEAK 50(20P13) WILD-TYPE         6
D47V3, multiclass
           clus
vv          AMP PEAK 50(20P13) MUTATED AMP PEAK 50(20P13) WILD-TYPE
  STAGE I                            5                          277
  STAGE II                           4                           46
  STAGE III                          4                          107
  STAGE IV                           1                            1
  STAGE IVA                          0                           46
  STAGE IVC                          0                            6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 50(20P13) MUTATED     2   5   6   1
  AMP PEAK 50(20P13) WILD-TYPE 140 160 161  22
D47V4, multiclass
    clus
vv   AMP PEAK 50(20P13) MUTATED AMP PEAK 50(20P13) WILD-TYPE
  T1                          2                          140
  T2                          5                          160
  T3                          6                          161
  T4                          1                           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"
D47V5, binary
                              cls
clus                             0   1
  AMP PEAK 50(20P13) MUTATED     8   1
  AMP PEAK 50(20P13) WILD-TYPE 217 223
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 50(20P13) MUTATED      8    1
  AMP PEAK 50(20P13) WILD-TYPE  217  223
   clus
vv  AMP PEAK 50(20P13) MUTATED AMP PEAK 50(20P13) WILD-TYPE
  0                          8                          217
  1                          1                          223
[1] 2 2
[1] FALSE
D47V6, binary
                              cls
clus                             0   1
  AMP PEAK 50(20P13) MUTATED     2   0
  AMP PEAK 50(20P13) WILD-TYPE 276   9
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 50(20P13) MUTATED      2    0
  AMP PEAK 50(20P13) WILD-TYPE  276    9
   clus
vv  AMP PEAK 50(20P13) MUTATED AMP PEAK 50(20P13) WILD-TYPE
  0                          2                          276
  1                          0                            9
[1] 2 2
[1] FALSE
D47V7, binary
                              cls
clus                             0   1
  AMP PEAK 50(20P13) MUTATED    10   4
  AMP PEAK 50(20P13) WILD-TYPE 355 130
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 50(20P13) MUTATED     10    4
  AMP PEAK 50(20P13) WILD-TYPE  355  130
        clus
vv       AMP PEAK 50(20P13) MUTATED AMP PEAK 50(20P13) WILD-TYPE
  FEMALE                         10                          355
  MALE                            4                          130
[1] 2 2
[1] FALSE
D47V8, binary
                              cls
clus                             0   1
  AMP PEAK 50(20P13) MUTATED     5   7
  AMP PEAK 50(20P13) WILD-TYPE 180 283
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 50(20P13) MUTATED      5    7
  AMP PEAK 50(20P13) WILD-TYPE  180  283
     clus
vv    AMP PEAK 50(20P13) MUTATED AMP PEAK 50(20P13) WILD-TYPE
  NO                           5                          180
  YES                          7                          283
[1] 2 2
[1] FALSE
                              vv
clus                           OTHER  SPECIFY
  AMP PEAK 50(20P13) MUTATED                0
  AMP PEAK 50(20P13) WILD-TYPE              8
                              vv
clus                           THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 50(20P13) MUTATED                                               6
  AMP PEAK 50(20P13) WILD-TYPE                                           349
                              vv
clus                           THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 50(20P13) MUTATED                                                                        8
  AMP PEAK 50(20P13) WILD-TYPE                                                                     92
                              vv
clus                           THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 50(20P13) MUTATED                                                                     0
  AMP PEAK 50(20P13) WILD-TYPE                                                                  36
D47V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 50(20P13) MUTATED
  OTHER  SPECIFY                                                                                  0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   6
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          8
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                             0
                                                                        clus
vv                                                                       AMP PEAK 50(20P13) WILD-TYPE
  OTHER  SPECIFY                                                                                    8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   349
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           92
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V10, binary
                              cls
clus                             0   1
  AMP PEAK 50(20P13) MUTATED    13   0
  AMP PEAK 50(20P13) WILD-TYPE 407  17
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 50(20P13) MUTATED     13    0
  AMP PEAK 50(20P13) WILD-TYPE  407   17
     clus
vv    AMP PEAK 50(20P13) MUTATED AMP PEAK 50(20P13) WILD-TYPE
  NO                          13                          407
  YES                          0                           17
[1] 2 2
[1] FALSE
                              vv
clus                           MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 50(20P13) MUTATED              2                       0   11
  AMP PEAK 50(20P13) WILD-TYPE          130                      18  319
                              vv
clus                           VERY ADVANCED (T4B)
  AMP PEAK 50(20P13) MUTATED                     1
  AMP PEAK 50(20P13) WILD-TYPE                   0
D47V11, multiclass
                         clus
vv                        AMP PEAK 50(20P13) MUTATED
  MINIMAL (T3)                                     2
  MODERATE/ADVANCED (T4A)                          0
  NONE                                            11
  VERY ADVANCED (T4B)                              1
                         clus
vv                        AMP PEAK 50(20P13) WILD-TYPE
  MINIMAL (T3)                                     130
  MODERATE/ADVANCED (T4A)                           18
  NONE                                             319
  VERY ADVANCED (T4B)                                0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 50(20P13) MUTATED    11   1   0   2
  AMP PEAK 50(20P13) WILD-TYPE 372  50   4  28
D47V12, multiclass
    clus
vv   AMP PEAK 50(20P13) MUTATED AMP PEAK 50(20P13) WILD-TYPE
  R0                         11                          372
  R1                          1                           50
  R2                          0                            4
  RX                          2                           28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V13, continuous
D47V14, binary
                              cls
clus                             0   1
  AMP PEAK 50(20P13) MUTATED     6   8
  AMP PEAK 50(20P13) WILD-TYPE 219 256
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 50(20P13) MUTATED      6    8
  AMP PEAK 50(20P13) WILD-TYPE  219  256
            clus
vv           AMP PEAK 50(20P13) MUTATED AMP PEAK 50(20P13) WILD-TYPE
  MULTIFOCAL                          6                          219
  UNIFOCAL                            8                          256
[1] 2 2
[1] FALSE
D47V15, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 50(20P13) MUTATED                                  0     0
  AMP PEAK 50(20P13) WILD-TYPE                                1    52
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 50(20P13) MUTATED                           0     8
  AMP PEAK 50(20P13) WILD-TYPE                        27   320
D47V16, multiclass
                                  clus
vv                                 AMP PEAK 50(20P13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     0
  BLACK OR AFRICAN AMERICAN                                 0
  WHITE                                                     8
                                  clus
vv                                 AMP PEAK 50(20P13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      52
  BLACK OR AFRICAN AMERICAN                                  27
  WHITE                                                     320
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V17, binary
                              cls
clus                             0   1
  AMP PEAK 50(20P13) MUTATED     1   6
  AMP PEAK 50(20P13) WILD-TYPE  37 353
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 50(20P13) MUTATED      1    6
  AMP PEAK 50(20P13) WILD-TYPE   37  353
                        clus
vv                       AMP PEAK 50(20P13) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                          6
                        clus
vv                       AMP PEAK 50(20P13) WILD-TYPE
  HISPANIC OR LATINO                               37
  NOT HISPANIC OR LATINO                          353
[1] 2 2
[1] FALSE

Clustering(48) Variable = AMP PEAK 51(20Q13.11) MUTATION ANALYSIS
D48V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 51(20Q13.11) MUTATED    13   1
  AMP PEAK 51(20Q13.11) WILD-TYPE 468  15
  AMP PEAK 51(20Q13.11) MUTATED AMP PEAK 51(20Q13.11) WILD-TYPE 
                             14                             483 
  AMP PEAK 51(20Q13.11) MUTATED AMP PEAK 51(20Q13.11) WILD-TYPE 
                              1                              15 
$`AMP PEAK 51(20Q13.11) MUTATED`
TCGA-DJ-A3UP TCGA-EL-A3GO TCGA-EL-A3T9 TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A1YD 
       16.41        64.87         5.72        23.90        78.61        57.01 
TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A2MZ 
        6.05        32.32        22.52         9.24        13.51        37.25 
TCGA-ET-A39N TCGA-FY-A3I5 
      123.32         7.82 

$`AMP PEAK 51(20Q13.11) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
       30.58        35.41        27.45        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74         6.77        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       36.92        31.04        32.42        31.46        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        30.61         0.16         0.23        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        33.50         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GP 
      139.86        98.53        69.57        57.11       108.36        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA 
       32.48       132.07        98.24        41.29       107.47        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM 
       82.82        89.56        78.97        51.78        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        65.49        61.22        60.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       34.39        30.51        53.36        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       43.59        24.30        27.06        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I 
       48.49        18.05        19.79        19.46        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O 
       14.50        15.75        10.45        14.53        10.65        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       19.73        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
       15.06         7.33         0.49        13.91        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       29.95        29.85        12.79        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        5.33        26.37        26.37        22.45        21.53        60.49 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       24.46        13.68        81.93        81.70        77.56        70.42 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       56.58        60.20        63.39        65.29        18.38        63.45 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       88.41        58.75        52.60        54.35        83.34         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       80.88        33.24       106.09       107.41       108.46        84.89 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
      100.57        95.34        94.13        55.10        98.20        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
       50.40        79.10        76.64         5.79        87.62        77.82 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       75.42        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       117.40        66.77       112.80        39.95        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.11         1.05        13.28         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25        20.42        17.82         0.99        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08         0.30         0.76 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16         6.58        22.49        19.04 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35        21.60         1.68        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46         2.99        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       18.51        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       17.23        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY 
       24.69        22.29         5.75         2.47         2.60         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.40        40.37        21.83         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       30.21        23.93        12.89 

  AMP PEAK 51(20Q13.11) MUTATED AMP PEAK 51(20Q13.11) WILD-TYPE 
                           5.72                            0.16 
  AMP PEAK 51(20Q13.11) MUTATED AMP PEAK 51(20Q13.11) WILD-TYPE 
                         123.32                          169.32 
  AMP PEAK 51(20Q13.11) MUTATED AMP PEAK 51(20Q13.11) WILD-TYPE 
                          23.21                           30.61 
[1] "5.7 - 123.3 (23.2)" "0.2 - 169.3 (30.6)"
[1] "hr=" "2.3"
D48V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 51(20Q13.11) MUTATED         6        4         3        1         0
  AMP PEAK 51(20Q13.11) WILD-TYPE     276       46       108        1        46
                                 vv
clus                              STAGE IVC
  AMP PEAK 51(20Q13.11) MUTATED           0
  AMP PEAK 51(20Q13.11) WILD-TYPE         6
D48V3, multiclass
           clus
vv          AMP PEAK 51(20Q13.11) MUTATED AMP PEAK 51(20Q13.11) WILD-TYPE
  STAGE I                               6                             276
  STAGE II                              4                              46
  STAGE III                             3                             108
  STAGE IV                              1                               1
  STAGE IVA                             0                              46
  STAGE IVC                             0                               6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 51(20Q13.11) MUTATED     2   6   5   1
  AMP PEAK 51(20Q13.11) WILD-TYPE 140 159 162  22
D48V4, multiclass
    clus
vv   AMP PEAK 51(20Q13.11) MUTATED AMP PEAK 51(20Q13.11) WILD-TYPE
  T1                             2                             140
  T2                             6                             159
  T3                             5                             162
  T4                             1                              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"
D48V5, binary
                                 cls
clus                                0   1
  AMP PEAK 51(20Q13.11) MUTATED     9   1
  AMP PEAK 51(20Q13.11) WILD-TYPE 216 223
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 51(20Q13.11) MUTATED      9    1
  AMP PEAK 51(20Q13.11) WILD-TYPE  216  223
   clus
vv  AMP PEAK 51(20Q13.11) MUTATED AMP PEAK 51(20Q13.11) WILD-TYPE
  0                             9                             216
  1                             1                             223
[1] 2 2
[1] FALSE
D48V6, binary
                                 cls
clus                                0   1
  AMP PEAK 51(20Q13.11) MUTATED     2   0
  AMP PEAK 51(20Q13.11) WILD-TYPE 276   9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 51(20Q13.11) MUTATED      2    0
  AMP PEAK 51(20Q13.11) WILD-TYPE  276    9
   clus
vv  AMP PEAK 51(20Q13.11) MUTATED AMP PEAK 51(20Q13.11) WILD-TYPE
  0                             2                             276
  1                             0                               9
[1] 2 2
[1] FALSE
D48V7, binary
                                 cls
clus                                0   1
  AMP PEAK 51(20Q13.11) MUTATED    10   4
  AMP PEAK 51(20Q13.11) WILD-TYPE 355 130
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 51(20Q13.11) MUTATED     10    4
  AMP PEAK 51(20Q13.11) WILD-TYPE  355  130
        clus
vv       AMP PEAK 51(20Q13.11) MUTATED AMP PEAK 51(20Q13.11) WILD-TYPE
  FEMALE                            10                             355
  MALE                               4                             130
[1] 2 2
[1] FALSE
D48V8, binary
                                 cls
clus                                0   1
  AMP PEAK 51(20Q13.11) MUTATED     4   8
  AMP PEAK 51(20Q13.11) WILD-TYPE 181 282
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 51(20Q13.11) MUTATED      4    8
  AMP PEAK 51(20Q13.11) WILD-TYPE  181  282
     clus
vv    AMP PEAK 51(20Q13.11) MUTATED AMP PEAK 51(20Q13.11) WILD-TYPE
  NO                              4                             181
  YES                             8                             282
[1] 2 2
[1] FALSE
                                 vv
clus                              OTHER  SPECIFY
  AMP PEAK 51(20Q13.11) MUTATED                0
  AMP PEAK 51(20Q13.11) WILD-TYPE              8
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 51(20Q13.11) MUTATED                                               5
  AMP PEAK 51(20Q13.11) WILD-TYPE                                           350
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 51(20Q13.11) MUTATED                                                                        9
  AMP PEAK 51(20Q13.11) WILD-TYPE                                                                     91
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 51(20Q13.11) MUTATED                                                                     0
  AMP PEAK 51(20Q13.11) WILD-TYPE                                                                  36
D48V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 51(20Q13.11) MUTATED
  OTHER  SPECIFY                                                                                     0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      5
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             9
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                0
                                                                        clus
vv                                                                       AMP PEAK 51(20Q13.11) WILD-TYPE
  OTHER  SPECIFY                                                                                       8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                              91
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V10, binary
                                 cls
clus                                0   1
  AMP PEAK 51(20Q13.11) MUTATED    13   0
  AMP PEAK 51(20Q13.11) WILD-TYPE 407  17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 51(20Q13.11) MUTATED     13    0
  AMP PEAK 51(20Q13.11) WILD-TYPE  407   17
     clus
vv    AMP PEAK 51(20Q13.11) MUTATED AMP PEAK 51(20Q13.11) WILD-TYPE
  NO                             13                             407
  YES                             0                              17
[1] 2 2
[1] FALSE
                                 vv
clus                              MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 51(20Q13.11) MUTATED              1                       0   12
  AMP PEAK 51(20Q13.11) WILD-TYPE          131                      18  318
                                 vv
clus                              VERY ADVANCED (T4B)
  AMP PEAK 51(20Q13.11) MUTATED                     1
  AMP PEAK 51(20Q13.11) WILD-TYPE                   0
D48V11, multiclass
                         clus
vv                        AMP PEAK 51(20Q13.11) MUTATED
  MINIMAL (T3)                                        1
  MODERATE/ADVANCED (T4A)                             0
  NONE                                               12
  VERY ADVANCED (T4B)                                 1
                         clus
vv                        AMP PEAK 51(20Q13.11) WILD-TYPE
  MINIMAL (T3)                                        131
  MODERATE/ADVANCED (T4A)                              18
  NONE                                                318
  VERY ADVANCED (T4B)                                   0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 51(20Q13.11) MUTATED    12   1   0   1
  AMP PEAK 51(20Q13.11) WILD-TYPE 371  50   4  29
D48V12, multiclass
    clus
vv   AMP PEAK 51(20Q13.11) MUTATED AMP PEAK 51(20Q13.11) WILD-TYPE
  R0                            12                             371
  R1                             1                              50
  R2                             0                               4
  RX                             1                              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"
D48V13, continuous
D48V14, binary
                                 cls
clus                                0   1
  AMP PEAK 51(20Q13.11) MUTATED     6   8
  AMP PEAK 51(20Q13.11) WILD-TYPE 219 256
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 51(20Q13.11) MUTATED      6    8
  AMP PEAK 51(20Q13.11) WILD-TYPE  219  256
            clus
vv           AMP PEAK 51(20Q13.11) MUTATED AMP PEAK 51(20Q13.11) WILD-TYPE
  MULTIFOCAL                             6                             219
  UNIFOCAL                               8                             256
[1] 2 2
[1] FALSE
D48V15, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 51(20Q13.11) MUTATED                                  0     0
  AMP PEAK 51(20Q13.11) WILD-TYPE                                1    52
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 51(20Q13.11) MUTATED                           0     7
  AMP PEAK 51(20Q13.11) WILD-TYPE                        27   321
D48V16, multiclass
                                  clus
vv                                 AMP PEAK 51(20Q13.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                    0
  WHITE                                                        7
                                  clus
vv                                 AMP PEAK 51(20Q13.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         52
  BLACK OR AFRICAN AMERICAN                                     27
  WHITE                                                        321
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V17, binary
                                 cls
clus                                0   1
  AMP PEAK 51(20Q13.11) MUTATED     2   6
  AMP PEAK 51(20Q13.11) WILD-TYPE  36 353
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 51(20Q13.11) MUTATED      2    6
  AMP PEAK 51(20Q13.11) WILD-TYPE   36  353
                        clus
vv                       AMP PEAK 51(20Q13.11) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                             6
                        clus
vv                       AMP PEAK 51(20Q13.11) WILD-TYPE
  HISPANIC OR LATINO                                  36
  NOT HISPANIC OR LATINO                             353
[1] 2 2
[1] FALSE

Clustering(49) Variable = AMP PEAK 52(20Q13.2) MUTATION ANALYSIS
D49V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 52(20Q13.2) MUTATED    13   1
  AMP PEAK 52(20Q13.2) WILD-TYPE 468  15
  AMP PEAK 52(20Q13.2) MUTATED AMP PEAK 52(20Q13.2) WILD-TYPE 
                            14                            483 
  AMP PEAK 52(20Q13.2) MUTATED AMP PEAK 52(20Q13.2) WILD-TYPE 
                             1                             15 
$`AMP PEAK 52(20Q13.2) MUTATED`
TCGA-DE-A4MD TCGA-DJ-A1QG TCGA-EL-A3T9 TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A1YD 
       25.12        44.98         5.72        23.90        78.61        57.01 
TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A2MZ 
        6.05        32.32        22.52         9.24        13.51        37.25 
TCGA-ET-A39N TCGA-FY-A3I5 
      123.32         7.82 

$`AMP PEAK 52(20Q13.2) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       11.57        30.02        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       30.61        42.51        14.96        17.59         6.02        42.58 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
       47.41        17.56        10.09         7.82        30.58        35.41 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       27.45        26.20        38.83        33.96        31.99        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       28.96         8.78         8.42        34.36        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24        33.93        37.48        36.46        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        33.53        35.18        15.88        36.92        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       32.42        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        17.69        59.57        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        42.54        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL 
        7.76        35.67         3.12        36.43        24.76        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        21.34        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        52.44        39.95        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA 
       32.48       132.07        98.24        41.29       107.47        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM 
       82.82        89.56        78.97        51.78        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        65.49        61.22        60.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       34.39        30.51        53.36        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       43.59        24.30        27.06        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I 
       48.49        18.05        19.79        19.46        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O 
       14.50        15.75        10.45        14.53        10.65        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       19.73        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
       15.06         7.33         0.49        13.91        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       29.95        29.85        12.79        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        5.33        26.37        26.37        22.45        21.53        60.49 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       24.46        13.68        81.93        81.70        77.56        70.42 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       56.58        60.20        63.39        65.29        18.38        63.45 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       88.41        58.75        52.60        54.35        83.34         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       80.88        33.24       106.09       107.41       108.46        84.89 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
      100.57        95.34        94.13        55.10        98.20        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
       50.40        79.10        76.64         5.79        87.62        77.82 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       75.42        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       117.40        66.77       112.80        39.95        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.11         1.05        13.28         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25        20.42        17.82         0.99        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08         0.30         0.76 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16         6.58        22.49        19.04 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35        21.60         1.68        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46         2.99        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       18.51        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       17.23        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY 
       24.69        22.29         5.75         2.47         2.60         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.40        40.37        21.83         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       30.21        23.93        12.89 

  AMP PEAK 52(20Q13.2) MUTATED AMP PEAK 52(20Q13.2) WILD-TYPE 
                          5.72                           0.16 
  AMP PEAK 52(20Q13.2) MUTATED AMP PEAK 52(20Q13.2) WILD-TYPE 
                        123.32                         169.32 
  AMP PEAK 52(20Q13.2) MUTATED AMP PEAK 52(20Q13.2) WILD-TYPE 
                         24.51                          30.61 
[1] "5.7 - 123.3 (24.5)" "0.2 - 169.3 (30.6)"
[1] "hr=" "2.7"
D49V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 52(20Q13.2) MUTATED         5        4         3        1         1
  AMP PEAK 52(20Q13.2) WILD-TYPE     277       46       108        1        45
                                vv
clus                             STAGE IVC
  AMP PEAK 52(20Q13.2) MUTATED           0
  AMP PEAK 52(20Q13.2) WILD-TYPE         6
D49V3, multiclass
           clus
vv          AMP PEAK 52(20Q13.2) MUTATED AMP PEAK 52(20Q13.2) WILD-TYPE
  STAGE I                              5                            277
  STAGE II                             4                             46
  STAGE III                            3                            108
  STAGE IV                             1                              1
  STAGE IVA                            1                             45
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 52(20Q13.2) MUTATED     3   4   6   1
  AMP PEAK 52(20Q13.2) WILD-TYPE 139 161 161  22
D49V4, multiclass
    clus
vv   AMP PEAK 52(20Q13.2) MUTATED AMP PEAK 52(20Q13.2) WILD-TYPE
  T1                            3                            139
  T2                            4                            161
  T3                            6                            161
  T4                            1                             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"
D49V5, binary
                                cls
clus                               0   1
  AMP PEAK 52(20Q13.2) MUTATED     8   2
  AMP PEAK 52(20Q13.2) WILD-TYPE 217 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 52(20Q13.2) MUTATED      8    2
  AMP PEAK 52(20Q13.2) WILD-TYPE  217  222
   clus
vv  AMP PEAK 52(20Q13.2) MUTATED AMP PEAK 52(20Q13.2) WILD-TYPE
  0                            8                            217
  1                            2                            222
[1] 2 2
[1] FALSE
D49V6, binary
                                cls
clus                               0   1
  AMP PEAK 52(20Q13.2) MUTATED     2   0
  AMP PEAK 52(20Q13.2) WILD-TYPE 276   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 52(20Q13.2) MUTATED      2    0
  AMP PEAK 52(20Q13.2) WILD-TYPE  276    9
   clus
vv  AMP PEAK 52(20Q13.2) MUTATED AMP PEAK 52(20Q13.2) WILD-TYPE
  0                            2                            276
  1                            0                              9
[1] 2 2
[1] FALSE
D49V7, binary
                                cls
clus                               0   1
  AMP PEAK 52(20Q13.2) MUTATED     8   6
  AMP PEAK 52(20Q13.2) WILD-TYPE 357 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 52(20Q13.2) MUTATED      8    6
  AMP PEAK 52(20Q13.2) WILD-TYPE  357  128
        clus
vv       AMP PEAK 52(20Q13.2) MUTATED AMP PEAK 52(20Q13.2) WILD-TYPE
  FEMALE                            8                            357
  MALE                              6                            128
[1] 2 2
[1] FALSE
D49V8, binary
                                cls
clus                               0   1
  AMP PEAK 52(20Q13.2) MUTATED     4   8
  AMP PEAK 52(20Q13.2) WILD-TYPE 181 282
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 52(20Q13.2) MUTATED      4    8
  AMP PEAK 52(20Q13.2) WILD-TYPE  181  282
     clus
vv    AMP PEAK 52(20Q13.2) MUTATED AMP PEAK 52(20Q13.2) WILD-TYPE
  NO                             4                            181
  YES                            8                            282
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 52(20Q13.2) MUTATED                0
  AMP PEAK 52(20Q13.2) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 52(20Q13.2) MUTATED                                               5
  AMP PEAK 52(20Q13.2) WILD-TYPE                                           350
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 52(20Q13.2) MUTATED                                                                        9
  AMP PEAK 52(20Q13.2) WILD-TYPE                                                                     91
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 52(20Q13.2) MUTATED                                                                     0
  AMP PEAK 52(20Q13.2) WILD-TYPE                                                                  36
D49V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 52(20Q13.2) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     5
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            9
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       AMP PEAK 52(20Q13.2) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             91
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V10, binary
                                cls
clus                               0   1
  AMP PEAK 52(20Q13.2) MUTATED    13   0
  AMP PEAK 52(20Q13.2) WILD-TYPE 407  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 52(20Q13.2) MUTATED     13    0
  AMP PEAK 52(20Q13.2) WILD-TYPE  407   17
     clus
vv    AMP PEAK 52(20Q13.2) MUTATED AMP PEAK 52(20Q13.2) WILD-TYPE
  NO                            13                            407
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 52(20Q13.2) MUTATED              1                       0   12
  AMP PEAK 52(20Q13.2) WILD-TYPE          131                      18  318
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 52(20Q13.2) MUTATED                     1
  AMP PEAK 52(20Q13.2) WILD-TYPE                   0
D49V11, multiclass
                         clus
vv                        AMP PEAK 52(20Q13.2) MUTATED
  MINIMAL (T3)                                       1
  MODERATE/ADVANCED (T4A)                            0
  NONE                                              12
  VERY ADVANCED (T4B)                                1
                         clus
vv                        AMP PEAK 52(20Q13.2) WILD-TYPE
  MINIMAL (T3)                                       131
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               318
  VERY ADVANCED (T4B)                                  0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 52(20Q13.2) MUTATED    12   1   0   1
  AMP PEAK 52(20Q13.2) WILD-TYPE 371  50   4  29
D49V12, multiclass
    clus
vv   AMP PEAK 52(20Q13.2) MUTATED AMP PEAK 52(20Q13.2) WILD-TYPE
  R0                           12                            371
  R1                            1                             50
  R2                            0                              4
  RX                            1                             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"
D49V13, continuous
D49V14, binary
                                cls
clus                               0   1
  AMP PEAK 52(20Q13.2) MUTATED     7   7
  AMP PEAK 52(20Q13.2) WILD-TYPE 218 257
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 52(20Q13.2) MUTATED      7    7
  AMP PEAK 52(20Q13.2) WILD-TYPE  218  257
            clus
vv           AMP PEAK 52(20Q13.2) MUTATED AMP PEAK 52(20Q13.2) WILD-TYPE
  MULTIFOCAL                            7                            218
  UNIFOCAL                              7                            257
[1] 2 2
[1] FALSE
D49V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 52(20Q13.2) MUTATED                                  0     0
  AMP PEAK 52(20Q13.2) WILD-TYPE                                1    52
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 52(20Q13.2) MUTATED                           0     8
  AMP PEAK 52(20Q13.2) WILD-TYPE                        27   320
D49V16, multiclass
                                  clus
vv                                 AMP PEAK 52(20Q13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       8
                                  clus
vv                                 AMP PEAK 52(20Q13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        52
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       320
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V17, binary
                                cls
clus                               0   1
  AMP PEAK 52(20Q13.2) MUTATED     0   8
  AMP PEAK 52(20Q13.2) WILD-TYPE  38 351
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 52(20Q13.2) MUTATED      0    8
  AMP PEAK 52(20Q13.2) WILD-TYPE   38  351
                        clus
vv                       AMP PEAK 52(20Q13.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            8
                        clus
vv                       AMP PEAK 52(20Q13.2) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            351
[1] 2 2
[1] FALSE

Clustering(50) Variable = AMP PEAK 53(20Q13.2) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 53(20Q13.2) MUTATED    12   1
  AMP PEAK 53(20Q13.2) WILD-TYPE 469  15
  AMP PEAK 53(20Q13.2) MUTATED AMP PEAK 53(20Q13.2) WILD-TYPE 
                            13                            484 
  AMP PEAK 53(20Q13.2) MUTATED AMP PEAK 53(20Q13.2) WILD-TYPE 
                             1                             15 
$`AMP PEAK 53(20Q13.2) MUTATED`
TCGA-EL-A3T9 TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A2CO TCGA-EM-A2OY 
        5.72        23.90        78.61        57.01         6.05        32.32 
TCGA-EM-A3AI TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FY-A3I5 
       22.52         9.24        13.51        37.25       123.32         7.82 
TCGA-L6-A4EU 
        9.50 

$`AMP PEAK 53(20Q13.2) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
       30.58        35.41        27.45        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74         6.77        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        36.33        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       35.87        40.96        36.99        20.22        30.61        42.54 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20        23.21        21.27        20.48        24.82        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ 
       21.01        18.97         7.76        35.67         3.12        36.43 
TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       24.76        17.23        27.62        30.87        21.34        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        80.52        63.19        52.44        39.95        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04         0.72 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
        0.26         3.02        25.45        30.61         0.16         0.23 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        33.50         0.39         0.39        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS 
       26.73       155.54        97.74       158.83         7.66        45.53 
TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY 
       60.95       157.15        37.94        57.01       106.62         4.18 
TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 
       79.50       139.86        98.53        69.57        57.11       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
       64.87        49.51        50.24       115.10        65.39       136.01 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        50.20       147.75       101.13       139.99        49.32 
TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 
       33.50        43.36        49.71        83.57       139.00       150.48 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 
      108.66        57.63        17.52        52.50        29.65       147.42 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
      107.47        66.90        82.82        89.56        78.97        51.78 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        47.38        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       60.16         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS 
       41.13        47.84        43.59        24.30        27.06        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       54.08        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.65        44.19        41.29        14.24        47.57        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU 
       13.18        23.51         2.99        12.30        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        40.34        19.73        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       17.29        14.60        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        29.72        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA 
       15.02        14.50        15.06         7.33         0.49        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.66        38.86        29.95        29.85        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        63.45        88.41        58.75        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       83.34         2.66        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
      108.46        84.89       100.57        95.34        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       98.20        28.24        50.40        79.10        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       87.62        77.82        75.42        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       94.59        84.85        80.58        66.84        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      166.62        24.72        43.99        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        13.28         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM 
       48.10       116.09         1.25        20.42        17.82         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
        0.30         0.76        17.06        17.36        15.16         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
       22.49        19.04         1.35        21.60         1.68        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46         2.99        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        8.22        25.64        17.23        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
       26.70        43.69        18.64        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-MK-A4N6 
       35.28        33.24        33.40        40.37        21.83        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45        30.21        23.93        12.89 

  AMP PEAK 53(20Q13.2) MUTATED AMP PEAK 53(20Q13.2) WILD-TYPE 
                          5.72                           0.16 
  AMP PEAK 53(20Q13.2) MUTATED AMP PEAK 53(20Q13.2) WILD-TYPE 
                        123.32                         169.32 
  AMP PEAK 53(20Q13.2) MUTATED AMP PEAK 53(20Q13.2) WILD-TYPE 
                         22.52                          30.74 
[1] "5.7 - 123.3 (22.5)" "0.2 - 169.3 (30.7)"
[1] "hr=" "2.9"
D50V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 53(20Q13.2) MUTATED         4        4         4        1         0
  AMP PEAK 53(20Q13.2) WILD-TYPE     278       46       107        1        46
                                vv
clus                             STAGE IVC
  AMP PEAK 53(20Q13.2) MUTATED           0
  AMP PEAK 53(20Q13.2) WILD-TYPE         6
D50V3, multiclass
           clus
vv          AMP PEAK 53(20Q13.2) MUTATED AMP PEAK 53(20Q13.2) WILD-TYPE
  STAGE I                              4                            278
  STAGE II                             4                             46
  STAGE III                            4                            107
  STAGE IV                             1                              1
  STAGE IVA                            0                             46
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 53(20Q13.2) MUTATED     2   4   6   1
  AMP PEAK 53(20Q13.2) WILD-TYPE 140 161 161  22
D50V4, multiclass
    clus
vv   AMP PEAK 53(20Q13.2) MUTATED AMP PEAK 53(20Q13.2) WILD-TYPE
  T1                            2                            140
  T2                            4                            161
  T3                            6                            161
  T4                            1                             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"
D50V5, binary
                                cls
clus                               0   1
  AMP PEAK 53(20Q13.2) MUTATED     7   2
  AMP PEAK 53(20Q13.2) WILD-TYPE 218 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 53(20Q13.2) MUTATED      7    2
  AMP PEAK 53(20Q13.2) WILD-TYPE  218  222
   clus
vv  AMP PEAK 53(20Q13.2) MUTATED AMP PEAK 53(20Q13.2) WILD-TYPE
  0                            7                            218
  1                            2                            222
[1] 2 2
[1] FALSE
D50V6, binary
                                cls
clus                               0   1
  AMP PEAK 53(20Q13.2) MUTATED     1   0
  AMP PEAK 53(20Q13.2) WILD-TYPE 277   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 53(20Q13.2) MUTATED      1    0
  AMP PEAK 53(20Q13.2) WILD-TYPE  277    9
   clus
vv  AMP PEAK 53(20Q13.2) MUTATED AMP PEAK 53(20Q13.2) WILD-TYPE
  0                            1                            277
  1                            0                              9
[1] 2 2
[1] FALSE
D50V7, binary
                                cls
clus                               0   1
  AMP PEAK 53(20Q13.2) MUTATED     9   4
  AMP PEAK 53(20Q13.2) WILD-TYPE 356 130
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 53(20Q13.2) MUTATED      9    4
  AMP PEAK 53(20Q13.2) WILD-TYPE  356  130
        clus
vv       AMP PEAK 53(20Q13.2) MUTATED AMP PEAK 53(20Q13.2) WILD-TYPE
  FEMALE                            9                            356
  MALE                              4                            130
[1] 2 2
[1] FALSE
D50V8, binary
                                cls
clus                               0   1
  AMP PEAK 53(20Q13.2) MUTATED     3   8
  AMP PEAK 53(20Q13.2) WILD-TYPE 182 282
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 53(20Q13.2) MUTATED      3    8
  AMP PEAK 53(20Q13.2) WILD-TYPE  182  282
     clus
vv    AMP PEAK 53(20Q13.2) MUTATED AMP PEAK 53(20Q13.2) WILD-TYPE
  NO                             3                            182
  YES                            8                            282
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 53(20Q13.2) MUTATED                0
  AMP PEAK 53(20Q13.2) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 53(20Q13.2) MUTATED                                               4
  AMP PEAK 53(20Q13.2) WILD-TYPE                                           351
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 53(20Q13.2) MUTATED                                                                        8
  AMP PEAK 53(20Q13.2) WILD-TYPE                                                                     92
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 53(20Q13.2) MUTATED                                                                     1
  AMP PEAK 53(20Q13.2) WILD-TYPE                                                                  35
D50V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 53(20Q13.2) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            8
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               1
                                                                        clus
vv                                                                       AMP PEAK 53(20Q13.2) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             92
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V10, binary
                                cls
clus                               0   1
  AMP PEAK 53(20Q13.2) MUTATED    12   0
  AMP PEAK 53(20Q13.2) WILD-TYPE 408  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 53(20Q13.2) MUTATED     12    0
  AMP PEAK 53(20Q13.2) WILD-TYPE  408   17
     clus
vv    AMP PEAK 53(20Q13.2) MUTATED AMP PEAK 53(20Q13.2) WILD-TYPE
  NO                            12                            408
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 53(20Q13.2) MUTATED              2                       0   10
  AMP PEAK 53(20Q13.2) WILD-TYPE          130                      18  320
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 53(20Q13.2) MUTATED                     1
  AMP PEAK 53(20Q13.2) WILD-TYPE                   0
D50V11, multiclass
                         clus
vv                        AMP PEAK 53(20Q13.2) MUTATED
  MINIMAL (T3)                                       2
  MODERATE/ADVANCED (T4A)                            0
  NONE                                              10
  VERY ADVANCED (T4B)                                1
                         clus
vv                        AMP PEAK 53(20Q13.2) WILD-TYPE
  MINIMAL (T3)                                       130
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               320
  VERY ADVANCED (T4B)                                  0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 53(20Q13.2) MUTATED    10   2   0   1
  AMP PEAK 53(20Q13.2) WILD-TYPE 373  49   4  29
D50V12, multiclass
    clus
vv   AMP PEAK 53(20Q13.2) MUTATED AMP PEAK 53(20Q13.2) WILD-TYPE
  R0                           10                            373
  R1                            2                             49
  R2                            0                              4
  RX                            1                             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"
D50V13, continuous
D50V14, binary
                                cls
clus                               0   1
  AMP PEAK 53(20Q13.2) MUTATED     7   6
  AMP PEAK 53(20Q13.2) WILD-TYPE 218 258
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 53(20Q13.2) MUTATED      7    6
  AMP PEAK 53(20Q13.2) WILD-TYPE  218  258
            clus
vv           AMP PEAK 53(20Q13.2) MUTATED AMP PEAK 53(20Q13.2) WILD-TYPE
  MULTIFOCAL                            7                            218
  UNIFOCAL                              6                            258
[1] 2 2
[1] FALSE
D50V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 53(20Q13.2) MUTATED                                  0     0
  AMP PEAK 53(20Q13.2) WILD-TYPE                                1    52
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 53(20Q13.2) MUTATED                           1     6
  AMP PEAK 53(20Q13.2) WILD-TYPE                        26   322
D50V16, multiclass
                                  clus
vv                                 AMP PEAK 53(20Q13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                       6
                                  clus
vv                                 AMP PEAK 53(20Q13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        52
  BLACK OR AFRICAN AMERICAN                                    26
  WHITE                                                       322
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V17, binary
                                cls
clus                               0   1
  AMP PEAK 53(20Q13.2) MUTATED     0   7
  AMP PEAK 53(20Q13.2) WILD-TYPE  38 352
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 53(20Q13.2) MUTATED      0    7
  AMP PEAK 53(20Q13.2) WILD-TYPE   38  352
                        clus
vv                       AMP PEAK 53(20Q13.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            7
                        clus
vv                       AMP PEAK 53(20Q13.2) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            352
[1] 2 2
[1] FALSE

Clustering(51) Variable = AMP PEAK 54(21Q21.3) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 54(21Q21.3) MUTATED     6   0
  AMP PEAK 54(21Q21.3) WILD-TYPE 475  16
  AMP PEAK 54(21Q21.3) MUTATED AMP PEAK 54(21Q21.3) WILD-TYPE 
                             6                            491 
  AMP PEAK 54(21Q21.3) MUTATED AMP PEAK 54(21Q21.3) WILD-TYPE 
                             0                             16 
$`AMP PEAK 54(21Q21.3) MUTATED`
TCGA-BJ-A45E TCGA-E8-A242 TCGA-EL-A3ZR TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N 
       21.01        31.23        60.16        13.51        37.25       123.32 

$`AMP PEAK 54(21Q21.3) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G 
       23.31        18.64         7.99        10.88         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A2EA TCGA-E8-A3X7 
       80.52        63.19        52.44        39.95        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS 
       36.03        53.06        47.38        65.49        61.22         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       34.39        30.51        53.36        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       43.59        24.30        27.06        23.90        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        48.49        18.05        19.79        19.46        78.61 
TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       57.01        54.08        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       14.53        10.65        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
       17.88        13.18        23.51         6.05         2.99        12.30 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       48.46        13.15        22.16        40.34        19.73        32.32 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       33.96        17.59        17.46        17.29        14.60        22.52 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.06         7.33         0.49         9.24        13.91        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       38.86        29.95        29.85        12.79        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
       21.34         5.33        26.37        26.37        22.45        21.53 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       60.49        24.46        13.68        81.93        81.70        77.56 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       70.42        56.58        60.20        63.39        65.29        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       63.45        88.41        58.75        52.60        54.35        83.34 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89       100.57        95.34        94.13        55.10        98.20 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24        50.40        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       77.82        75.42        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       71.08         4.11         1.05        13.28         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
      116.09         1.25        20.42        17.82         7.82         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
        0.30         0.76        17.06        17.36        15.16         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
       22.49        19.04         1.35        21.60         1.68        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46         2.99        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        8.22        25.64        17.23        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
       26.70        43.69        18.64        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       36.10        32.45        30.21        23.93        12.89 

  AMP PEAK 54(21Q21.3) MUTATED AMP PEAK 54(21Q21.3) WILD-TYPE 
                         13.51                           0.16 
  AMP PEAK 54(21Q21.3) MUTATED AMP PEAK 54(21Q21.3) WILD-TYPE 
                        123.32                         169.32 
  AMP PEAK 54(21Q21.3) MUTATED AMP PEAK 54(21Q21.3) WILD-TYPE 
                         34.24                          30.61 
[1] "13.5 - 123.3 (34.2)" "0.2 - 169.3 (30.6)" 
[1] "hr="     "9100000"
D51V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 54(21Q21.3) MUTATED         4        1         1        0         0
  AMP PEAK 54(21Q21.3) WILD-TYPE     278       49       110        2        46
                                vv
clus                             STAGE IVC
  AMP PEAK 54(21Q21.3) MUTATED           0
  AMP PEAK 54(21Q21.3) WILD-TYPE         6
D51V3, multiclass
           clus
vv          AMP PEAK 54(21Q21.3) MUTATED AMP PEAK 54(21Q21.3) WILD-TYPE
  STAGE I                              4                            278
  STAGE II                             1                             49
  STAGE III                            1                            110
  STAGE IV                             0                              2
  STAGE IVA                            0                             46
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 54(21Q21.3) MUTATED     3   1   2   0
  AMP PEAK 54(21Q21.3) WILD-TYPE 139 164 165  23
D51V4, multiclass
    clus
vv   AMP PEAK 54(21Q21.3) MUTATED AMP PEAK 54(21Q21.3) WILD-TYPE
  T1                            3                            139
  T2                            1                            164
  T3                            2                            165
  T4                            0                             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"
D51V5, binary
                                cls
clus                               0   1
  AMP PEAK 54(21Q21.3) MUTATED     4   0
  AMP PEAK 54(21Q21.3) WILD-TYPE 221 224
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 54(21Q21.3) MUTATED      4    0
  AMP PEAK 54(21Q21.3) WILD-TYPE  221  224
   clus
vv  AMP PEAK 54(21Q21.3) MUTATED AMP PEAK 54(21Q21.3) WILD-TYPE
  0                            4                            221
  1                            0                            224
[1] 2 2
[1] FALSE
D51V6, binary
                                cls
clus                               0   1
  AMP PEAK 54(21Q21.3) MUTATED     2   0
  AMP PEAK 54(21Q21.3) WILD-TYPE 276   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 54(21Q21.3) MUTATED      2    0
  AMP PEAK 54(21Q21.3) WILD-TYPE  276    9
   clus
vv  AMP PEAK 54(21Q21.3) MUTATED AMP PEAK 54(21Q21.3) WILD-TYPE
  0                            2                            276
  1                            0                              9
[1] 2 2
[1] FALSE
D51V7, binary
                                cls
clus                               0   1
  AMP PEAK 54(21Q21.3) MUTATED     4   2
  AMP PEAK 54(21Q21.3) WILD-TYPE 361 132
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 54(21Q21.3) MUTATED      4    2
  AMP PEAK 54(21Q21.3) WILD-TYPE  361  132
        clus
vv       AMP PEAK 54(21Q21.3) MUTATED AMP PEAK 54(21Q21.3) WILD-TYPE
  FEMALE                            4                            361
  MALE                              2                            132
[1] 2 2
[1] FALSE
D51V8, binary
                                cls
clus                               0   1
  AMP PEAK 54(21Q21.3) MUTATED     4   2
  AMP PEAK 54(21Q21.3) WILD-TYPE 181 288
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 54(21Q21.3) MUTATED      4    2
  AMP PEAK 54(21Q21.3) WILD-TYPE  181  288
     clus
vv    AMP PEAK 54(21Q21.3) MUTATED AMP PEAK 54(21Q21.3) WILD-TYPE
  NO                             4                            181
  YES                            2                            288
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 54(21Q21.3) MUTATED                0
  AMP PEAK 54(21Q21.3) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 54(21Q21.3) MUTATED                                               5
  AMP PEAK 54(21Q21.3) WILD-TYPE                                           350
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 54(21Q21.3) MUTATED                                                                        1
  AMP PEAK 54(21Q21.3) WILD-TYPE                                                                     99
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 54(21Q21.3) MUTATED                                                                     0
  AMP PEAK 54(21Q21.3) WILD-TYPE                                                                  36
D51V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 54(21Q21.3) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     5
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       AMP PEAK 54(21Q21.3) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             99
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V10, binary
                                cls
clus                               0   1
  AMP PEAK 54(21Q21.3) MUTATED     5   0
  AMP PEAK 54(21Q21.3) WILD-TYPE 415  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 54(21Q21.3) MUTATED      5    0
  AMP PEAK 54(21Q21.3) WILD-TYPE  415   17
     clus
vv    AMP PEAK 54(21Q21.3) MUTATED AMP PEAK 54(21Q21.3) WILD-TYPE
  NO                             5                            415
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 54(21Q21.3) MUTATED              1                       0    4
  AMP PEAK 54(21Q21.3) WILD-TYPE          131                      18  326
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 54(21Q21.3) MUTATED                     0
  AMP PEAK 54(21Q21.3) WILD-TYPE                   1
D51V11, multiclass
                         clus
vv                        AMP PEAK 54(21Q21.3) MUTATED
  MINIMAL (T3)                                       1
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               4
  VERY ADVANCED (T4B)                                0
                         clus
vv                        AMP PEAK 54(21Q21.3) WILD-TYPE
  MINIMAL (T3)                                       131
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               326
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 54(21Q21.3) MUTATED     3   1   0   1
  AMP PEAK 54(21Q21.3) WILD-TYPE 380  50   4  29
D51V12, multiclass
    clus
vv   AMP PEAK 54(21Q21.3) MUTATED AMP PEAK 54(21Q21.3) WILD-TYPE
  R0                            3                            380
  R1                            1                             50
  R2                            0                              4
  RX                            1                             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"
D51V13, continuous
D51V14, binary
                                cls
clus                               0   1
  AMP PEAK 54(21Q21.3) MUTATED     0   6
  AMP PEAK 54(21Q21.3) WILD-TYPE 225 258
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 54(21Q21.3) MUTATED      0    6
  AMP PEAK 54(21Q21.3) WILD-TYPE  225  258
            clus
vv           AMP PEAK 54(21Q21.3) MUTATED AMP PEAK 54(21Q21.3) WILD-TYPE
  MULTIFOCAL                            0                            225
  UNIFOCAL                              6                            258
[1] 2 2
[1] FALSE
D51V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 54(21Q21.3) MUTATED                                  0     0
  AMP PEAK 54(21Q21.3) WILD-TYPE                                1    52
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 54(21Q21.3) MUTATED                           0     5
  AMP PEAK 54(21Q21.3) WILD-TYPE                        27   323
D51V16, multiclass
                                  clus
vv                                 AMP PEAK 54(21Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       5
                                  clus
vv                                 AMP PEAK 54(21Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        52
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       323
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V17, binary
                                cls
clus                               0   1
  AMP PEAK 54(21Q21.3) MUTATED     0   5
  AMP PEAK 54(21Q21.3) WILD-TYPE  38 354
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 54(21Q21.3) MUTATED      0    5
  AMP PEAK 54(21Q21.3) WILD-TYPE   38  354
                        clus
vv                       AMP PEAK 54(21Q21.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            5
                        clus
vv                       AMP PEAK 54(21Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            354
[1] 2 2
[1] FALSE

Clustering(52) Variable = AMP PEAK 55(22Q11.21) MUTATION ANALYSIS
D52V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 55(22Q11.21) MUTATED     7   0
  AMP PEAK 55(22Q11.21) WILD-TYPE 474  16
  AMP PEAK 55(22Q11.21) MUTATED AMP PEAK 55(22Q11.21) WILD-TYPE 
                              7                             490 
  AMP PEAK 55(22Q11.21) MUTATED AMP PEAK 55(22Q11.21) WILD-TYPE 
                              0                              16 
$`AMP PEAK 55(22Q11.21) MUTATED`
TCGA-BJ-A45E TCGA-DJ-A3UP TCGA-EM-A22K TCGA-EM-A22N TCGA-ET-A3DT TCGA-FY-A3W9 
       21.01        16.41        15.75        10.65        43.73         0.76 
TCGA-QD-A8IV 
       12.89 

$`AMP PEAK 55(22Q11.21) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G 
       23.31        18.64         7.99        10.88         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       31.04        32.42        31.46        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        17.69        59.57        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        42.54        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL 
        7.76        35.67         3.12        36.43        24.76        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        21.34        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        52.44        39.95        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       47.84        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22L 
       78.61        57.01        54.08        14.73        14.50        10.45 
TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       14.53        44.19        41.29        14.24        47.57        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       13.18        23.51         6.05         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        40.34        19.73        32.32        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ 
       17.59        17.46        17.29        14.60        22.52        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        33.07        13.38         8.35        29.72 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        47.38        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 
       17.49        17.39        16.18        15.02        14.50        15.06 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33         0.49         9.24        13.91        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       29.95        29.85        13.51        12.79        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
       21.34         5.33        26.37        26.37        22.45        21.53 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       60.49        24.46        13.68        81.93        81.70        77.56 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       70.42        56.58        60.20        63.39        65.29        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       63.45        88.41        58.75        37.25        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       83.34         2.66        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      108.46        84.89       123.32       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        98.20        28.24        50.40        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.79        87.62        77.82        75.42        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DU 
      116.78        94.59        84.85        80.58        66.84        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      166.62        24.72        43.99        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        13.28         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 
       48.10       116.09         1.25        20.42        17.82         7.82 
TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
        0.99        19.56        13.91        16.27        15.68        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
       18.08         0.30        17.06        17.36        15.16         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
       22.49        19.04         1.35        21.60         1.68        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46         2.99        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        8.22        25.64        17.23        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
       26.70        43.69        18.64        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       36.10        32.45        30.21        23.93 

  AMP PEAK 55(22Q11.21) MUTATED AMP PEAK 55(22Q11.21) WILD-TYPE 
                           0.76                            0.16 
  AMP PEAK 55(22Q11.21) MUTATED AMP PEAK 55(22Q11.21) WILD-TYPE 
                          43.73                          169.32 
  AMP PEAK 55(22Q11.21) MUTATED AMP PEAK 55(22Q11.21) WILD-TYPE 
                         15.750                          30.905 
[1] "0.8 - 43.7 (15.8)"  "0.2 - 169.3 (30.9)"
[1] "hr="     "3300000"
D52V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 55(22Q11.21) MUTATED         4        1         0        0         2
  AMP PEAK 55(22Q11.21) WILD-TYPE     278       49       111        2        44
                                 vv
clus                              STAGE IVC
  AMP PEAK 55(22Q11.21) MUTATED           0
  AMP PEAK 55(22Q11.21) WILD-TYPE         6
D52V3, multiclass
           clus
vv          AMP PEAK 55(22Q11.21) MUTATED AMP PEAK 55(22Q11.21) WILD-TYPE
  STAGE I                               4                             278
  STAGE II                              1                              49
  STAGE III                             0                             111
  STAGE IV                              0                               2
  STAGE IVA                             2                              44
  STAGE IVC                             0                               6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 55(22Q11.21) MUTATED     3   3   1   0
  AMP PEAK 55(22Q11.21) WILD-TYPE 139 162 166  23
D52V4, multiclass
    clus
vv   AMP PEAK 55(22Q11.21) MUTATED AMP PEAK 55(22Q11.21) WILD-TYPE
  T1                             3                             139
  T2                             3                             162
  T3                             1                             166
  T4                             0                              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"
D52V5, binary
                                 cls
clus                                0   1
  AMP PEAK 55(22Q11.21) MUTATED     4   3
  AMP PEAK 55(22Q11.21) WILD-TYPE 221 221
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 55(22Q11.21) MUTATED      4    3
  AMP PEAK 55(22Q11.21) WILD-TYPE  221  221
   clus
vv  AMP PEAK 55(22Q11.21) MUTATED AMP PEAK 55(22Q11.21) WILD-TYPE
  0                             4                             221
  1                             3                             221
[1] 2 2
[1] FALSE
D52V6, binary
                                 cls
clus                                0   1
  AMP PEAK 55(22Q11.21) MUTATED     2   0
  AMP PEAK 55(22Q11.21) WILD-TYPE 276   9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 55(22Q11.21) MUTATED      2    0
  AMP PEAK 55(22Q11.21) WILD-TYPE  276    9
   clus
vv  AMP PEAK 55(22Q11.21) MUTATED AMP PEAK 55(22Q11.21) WILD-TYPE
  0                             2                             276
  1                             0                               9
[1] 2 2
[1] FALSE
D52V7, binary
                                 cls
clus                                0   1
  AMP PEAK 55(22Q11.21) MUTATED     7   0
  AMP PEAK 55(22Q11.21) WILD-TYPE 358 134
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 55(22Q11.21) MUTATED      7    0
  AMP PEAK 55(22Q11.21) WILD-TYPE  358  134
        clus
vv       AMP PEAK 55(22Q11.21) MUTATED AMP PEAK 55(22Q11.21) WILD-TYPE
  FEMALE                             7                             358
  MALE                               0                             134
[1] 2 2
[1] FALSE
D52V8, binary
                                 cls
clus                                0   1
  AMP PEAK 55(22Q11.21) MUTATED     2   4
  AMP PEAK 55(22Q11.21) WILD-TYPE 183 286
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 55(22Q11.21) MUTATED      2    4
  AMP PEAK 55(22Q11.21) WILD-TYPE  183  286
     clus
vv    AMP PEAK 55(22Q11.21) MUTATED AMP PEAK 55(22Q11.21) WILD-TYPE
  NO                              2                             183
  YES                             4                             286
[1] 2 2
[1] FALSE
                                 vv
clus                              OTHER  SPECIFY
  AMP PEAK 55(22Q11.21) MUTATED                0
  AMP PEAK 55(22Q11.21) WILD-TYPE              8
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 55(22Q11.21) MUTATED                                               4
  AMP PEAK 55(22Q11.21) WILD-TYPE                                           351
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 55(22Q11.21) MUTATED                                                                        3
  AMP PEAK 55(22Q11.21) WILD-TYPE                                                                     97
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 55(22Q11.21) MUTATED                                                                     0
  AMP PEAK 55(22Q11.21) WILD-TYPE                                                                  36
D52V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 55(22Q11.21) MUTATED
  OTHER  SPECIFY                                                                                     0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             3
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                0
                                                                        clus
vv                                                                       AMP PEAK 55(22Q11.21) WILD-TYPE
  OTHER  SPECIFY                                                                                       8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                              97
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V10, binary
                                 cls
clus                                0   1
  AMP PEAK 55(22Q11.21) MUTATED     6   0
  AMP PEAK 55(22Q11.21) WILD-TYPE 414  17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 55(22Q11.21) MUTATED      6    0
  AMP PEAK 55(22Q11.21) WILD-TYPE  414   17
     clus
vv    AMP PEAK 55(22Q11.21) MUTATED AMP PEAK 55(22Q11.21) WILD-TYPE
  NO                              6                             414
  YES                             0                              17
[1] 2 2
[1] FALSE
                                 vv
clus                              MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 55(22Q11.21) MUTATED              1                       0    5
  AMP PEAK 55(22Q11.21) WILD-TYPE          131                      18  325
                                 vv
clus                              VERY ADVANCED (T4B)
  AMP PEAK 55(22Q11.21) MUTATED                     0
  AMP PEAK 55(22Q11.21) WILD-TYPE                   1
D52V11, multiclass
                         clus
vv                        AMP PEAK 55(22Q11.21) MUTATED
  MINIMAL (T3)                                        1
  MODERATE/ADVANCED (T4A)                             0
  NONE                                                5
  VERY ADVANCED (T4B)                                 0
                         clus
vv                        AMP PEAK 55(22Q11.21) WILD-TYPE
  MINIMAL (T3)                                        131
  MODERATE/ADVANCED (T4A)                              18
  NONE                                                325
  VERY ADVANCED (T4B)                                   1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 55(22Q11.21) MUTATED     2   2   0   2
  AMP PEAK 55(22Q11.21) WILD-TYPE 381  49   4  28
D52V12, multiclass
    clus
vv   AMP PEAK 55(22Q11.21) MUTATED AMP PEAK 55(22Q11.21) WILD-TYPE
  R0                             2                             381
  R1                             2                              49
  R2                             0                               4
  RX                             2                              28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V13, continuous
D52V14, binary
                                 cls
clus                                0   1
  AMP PEAK 55(22Q11.21) MUTATED     3   4
  AMP PEAK 55(22Q11.21) WILD-TYPE 222 260
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 55(22Q11.21) MUTATED      3    4
  AMP PEAK 55(22Q11.21) WILD-TYPE  222  260
            clus
vv           AMP PEAK 55(22Q11.21) MUTATED AMP PEAK 55(22Q11.21) WILD-TYPE
  MULTIFOCAL                             3                             222
  UNIFOCAL                               4                             260
[1] 2 2
[1] FALSE
D52V15, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 55(22Q11.21) MUTATED                                  0     0
  AMP PEAK 55(22Q11.21) WILD-TYPE                                1    52
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 55(22Q11.21) MUTATED                           1     3
  AMP PEAK 55(22Q11.21) WILD-TYPE                        26   325
D52V16, multiclass
                                  clus
vv                                 AMP PEAK 55(22Q11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                    1
  WHITE                                                        3
                                  clus
vv                                 AMP PEAK 55(22Q11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         52
  BLACK OR AFRICAN AMERICAN                                     26
  WHITE                                                        325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V17, binary
                                 cls
clus                                0   1
  AMP PEAK 55(22Q11.21) MUTATED     1   4
  AMP PEAK 55(22Q11.21) WILD-TYPE  37 355
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 55(22Q11.21) MUTATED      1    4
  AMP PEAK 55(22Q11.21) WILD-TYPE   37  355
                        clus
vv                       AMP PEAK 55(22Q11.21) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                             4
                        clus
vv                       AMP PEAK 55(22Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                  37
  NOT HISPANIC OR LATINO                             355
[1] 2 2
[1] FALSE

Clustering(53) Variable = AMP PEAK 56(XP22.12) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 56(XP22.12) MUTATED     9   1
  AMP PEAK 56(XP22.12) WILD-TYPE 472  15
  AMP PEAK 56(XP22.12) MUTATED AMP PEAK 56(XP22.12) WILD-TYPE 
                            10                            487 
  AMP PEAK 56(XP22.12) MUTATED AMP PEAK 56(XP22.12) WILD-TYPE 
                             1                             15 
$`AMP PEAK 56(XP22.12) MUTATED`
TCGA-BJ-A0Z0 TCGA-BJ-A2N9 TCGA-EL-A3T9 TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N 
       13.78        20.48         5.72        78.61        57.01        10.65 
TCGA-EM-A3AI TCGA-ET-A40S TCGA-FY-A3NM TCGA-QD-A8IV 
       22.52        40.21         0.99        12.89 

$`AMP PEAK 56(XP22.12) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
        4.24        24.79        49.78        16.34        14.73        41.33 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73        25.48        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       42.08        51.39        41.52        20.58         4.83        44.35 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
       42.15        21.04        35.54        32.45        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
       11.08        30.21        22.88        18.38        16.57        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        7.99        10.88        21.01         3.45        23.84        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
       15.45        21.63        23.18        19.43        23.47        12.66 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
       12.43        12.66        35.84        21.63        50.17        37.64 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M 
       25.12        14.70        14.27         2.76         9.96        48.79 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       38.17       169.32        18.58         8.71        56.19        23.38 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       43.17        52.37         8.32        11.01       135.91        30.61 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       44.98        42.51        14.96        17.59         6.02        42.58 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
       47.41        17.56        10.09         7.82        30.58        35.41 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       27.45        26.20        38.83        33.96        31.99        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       28.96         8.78         8.42        34.36        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24        33.93        37.48        36.46        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        33.53        35.18        15.88        36.92        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       32.42        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        17.69        59.57        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        42.54        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL 
        7.76        35.67         3.12        36.43        24.76        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        21.34        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        52.44        39.95        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA 
       32.48       132.07        98.24        41.29       107.47        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM 
       82.82        89.56        78.97        51.78        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        65.49        61.22        60.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       34.39        30.51        53.36        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       43.59        24.30        27.06        23.90        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE 
       20.91        48.49        18.05        19.79        19.46        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O 
       14.73        14.50        15.75        10.45        14.53        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        6.05         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       40.34        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       17.29        14.60        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        29.72        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 
       15.02        14.50        15.06         7.33         0.49         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       13.91        38.66        38.86        29.95        29.85        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        84.59        29.33        21.34         5.33        26.37 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
       26.37        22.45        21.53        60.49        24.46        13.68 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       81.93        81.70        77.56        70.42        56.58        60.20 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       63.39        65.29        18.38        63.45        88.41        58.75 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       37.25        52.60        54.35        83.34         2.66        80.88 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
       33.24       106.09       107.41       108.46        84.89       123.32 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
      100.57        95.34        94.13        55.10        98.20        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
       50.40        79.10        76.64         5.79        87.62        77.82 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       75.42        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
       43.99        46.26        44.38        37.48        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      117.40        66.77       112.80        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        1.05        13.28         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       20.42        17.82         7.82        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83        31.10         8.22        25.64        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z 
       23.93 

  AMP PEAK 56(XP22.12) MUTATED AMP PEAK 56(XP22.12) WILD-TYPE 
                          0.99                           0.16 
  AMP PEAK 56(XP22.12) MUTATED AMP PEAK 56(XP22.12) WILD-TYPE 
                         78.61                         169.32 
  AMP PEAK 56(XP22.12) MUTATED AMP PEAK 56(XP22.12) WILD-TYPE 
                         17.13                          30.87 
[1] "1.0 - 78.6 (17.1)"  "0.2 - 169.3 (30.9)"
[1] "hr=" "4.8"
D53V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 56(XP22.12) MUTATED         2        4         2        1         1
  AMP PEAK 56(XP22.12) WILD-TYPE     280       46       109        1        45
                                vv
clus                             STAGE IVC
  AMP PEAK 56(XP22.12) MUTATED           0
  AMP PEAK 56(XP22.12) WILD-TYPE         6
D53V3, multiclass
           clus
vv          AMP PEAK 56(XP22.12) MUTATED AMP PEAK 56(XP22.12) WILD-TYPE
  STAGE I                              2                            280
  STAGE II                             4                             46
  STAGE III                            2                            109
  STAGE IV                             1                              1
  STAGE IVA                            1                             45
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 56(XP22.12) MUTATED     1   5   3   1
  AMP PEAK 56(XP22.12) WILD-TYPE 141 160 164  22
D53V4, multiclass
    clus
vv   AMP PEAK 56(XP22.12) MUTATED AMP PEAK 56(XP22.12) WILD-TYPE
  T1                            1                            141
  T2                            5                            160
  T3                            3                            164
  T4                            1                             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"
D53V5, binary
                                cls
clus                               0   1
  AMP PEAK 56(XP22.12) MUTATED     7   2
  AMP PEAK 56(XP22.12) WILD-TYPE 218 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 56(XP22.12) MUTATED      7    2
  AMP PEAK 56(XP22.12) WILD-TYPE  218  222
   clus
vv  AMP PEAK 56(XP22.12) MUTATED AMP PEAK 56(XP22.12) WILD-TYPE
  0                            7                            218
  1                            2                            222
[1] 2 2
[1] FALSE
D53V6, binary
                                cls
clus                               0   1
  AMP PEAK 56(XP22.12) MUTATED     1   0
  AMP PEAK 56(XP22.12) WILD-TYPE 277   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 56(XP22.12) MUTATED      1    0
  AMP PEAK 56(XP22.12) WILD-TYPE  277    9
   clus
vv  AMP PEAK 56(XP22.12) MUTATED AMP PEAK 56(XP22.12) WILD-TYPE
  0                            1                            277
  1                            0                              9
[1] 2 2
[1] FALSE
D53V7, binary
                                cls
clus                               0   1
  AMP PEAK 56(XP22.12) MUTATED     8   2
  AMP PEAK 56(XP22.12) WILD-TYPE 357 132
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 56(XP22.12) MUTATED      8    2
  AMP PEAK 56(XP22.12) WILD-TYPE  357  132
        clus
vv       AMP PEAK 56(XP22.12) MUTATED AMP PEAK 56(XP22.12) WILD-TYPE
  FEMALE                            8                            357
  MALE                              2                            132
[1] 2 2
[1] FALSE
D53V8, binary
                                cls
clus                               0   1
  AMP PEAK 56(XP22.12) MUTATED     2   6
  AMP PEAK 56(XP22.12) WILD-TYPE 183 284
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 56(XP22.12) MUTATED      2    6
  AMP PEAK 56(XP22.12) WILD-TYPE  183  284
     clus
vv    AMP PEAK 56(XP22.12) MUTATED AMP PEAK 56(XP22.12) WILD-TYPE
  NO                             2                            183
  YES                            6                            284
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 56(XP22.12) MUTATED                0
  AMP PEAK 56(XP22.12) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 56(XP22.12) MUTATED                                               6
  AMP PEAK 56(XP22.12) WILD-TYPE                                           349
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 56(XP22.12) MUTATED                                                                        4
  AMP PEAK 56(XP22.12) WILD-TYPE                                                                     96
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 56(XP22.12) MUTATED                                                                     0
  AMP PEAK 56(XP22.12) WILD-TYPE                                                                  36
D53V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 56(XP22.12) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     6
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            4
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       AMP PEAK 56(XP22.12) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     349
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V10, binary
                                cls
clus                               0   1
  AMP PEAK 56(XP22.12) MUTATED     8   1
  AMP PEAK 56(XP22.12) WILD-TYPE 412  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 56(XP22.12) MUTATED      8    1
  AMP PEAK 56(XP22.12) WILD-TYPE  412   16
     clus
vv    AMP PEAK 56(XP22.12) MUTATED AMP PEAK 56(XP22.12) WILD-TYPE
  NO                             8                            412
  YES                            1                             16
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 56(XP22.12) MUTATED              2                       0    7
  AMP PEAK 56(XP22.12) WILD-TYPE          130                      18  323
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 56(XP22.12) MUTATED                     1
  AMP PEAK 56(XP22.12) WILD-TYPE                   0
D53V11, multiclass
                         clus
vv                        AMP PEAK 56(XP22.12) MUTATED
  MINIMAL (T3)                                       2
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               7
  VERY ADVANCED (T4B)                                1
                         clus
vv                        AMP PEAK 56(XP22.12) WILD-TYPE
  MINIMAL (T3)                                       130
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               323
  VERY ADVANCED (T4B)                                  0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 56(XP22.12) MUTATED     5   2   0   3
  AMP PEAK 56(XP22.12) WILD-TYPE 378  49   4  27
D53V12, multiclass
    clus
vv   AMP PEAK 56(XP22.12) MUTATED AMP PEAK 56(XP22.12) WILD-TYPE
  R0                            5                            378
  R1                            2                             49
  R2                            0                              4
  RX                            3                             27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V13, continuous
D53V14, binary
                                cls
clus                               0   1
  AMP PEAK 56(XP22.12) MUTATED     6   4
  AMP PEAK 56(XP22.12) WILD-TYPE 219 260
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 56(XP22.12) MUTATED      6    4
  AMP PEAK 56(XP22.12) WILD-TYPE  219  260
            clus
vv           AMP PEAK 56(XP22.12) MUTATED AMP PEAK 56(XP22.12) WILD-TYPE
  MULTIFOCAL                            6                            219
  UNIFOCAL                              4                            260
[1] 2 2
[1] FALSE
D53V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 56(XP22.12) MUTATED                                  0     0
  AMP PEAK 56(XP22.12) WILD-TYPE                                1    52
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 56(XP22.12) MUTATED                           1     5
  AMP PEAK 56(XP22.12) WILD-TYPE                        26   323
D53V16, multiclass
                                  clus
vv                                 AMP PEAK 56(XP22.12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                       5
                                  clus
vv                                 AMP PEAK 56(XP22.12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        52
  BLACK OR AFRICAN AMERICAN                                    26
  WHITE                                                       323
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V17, binary
                                cls
clus                               0   1
  AMP PEAK 56(XP22.12) MUTATED     0   7
  AMP PEAK 56(XP22.12) WILD-TYPE  38 352
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 56(XP22.12) MUTATED      0    7
  AMP PEAK 56(XP22.12) WILD-TYPE   38  352
                        clus
vv                       AMP PEAK 56(XP22.12) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            7
                        clus
vv                       AMP PEAK 56(XP22.12) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            352
[1] 2 2
[1] FALSE

Clustering(54) Variable = AMP PEAK 57(XP11.4) MUTATION ANALYSIS
D54V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 57(XP11.4) MUTATED     8   1
  AMP PEAK 57(XP11.4) WILD-TYPE 473  15
  AMP PEAK 57(XP11.4) MUTATED AMP PEAK 57(XP11.4) WILD-TYPE 
                            9                           488 
  AMP PEAK 57(XP11.4) MUTATED AMP PEAK 57(XP11.4) WILD-TYPE 
                            1                            15 
$`AMP PEAK 57(XP11.4) MUTATED`
TCGA-BJ-A2N9 TCGA-DE-A4MD TCGA-EL-A3T9 TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N 
       20.48        25.12         5.72        78.61        57.01        10.65 
TCGA-EM-A3AI TCGA-ET-A40S TCGA-FY-A3NM 
       22.52        40.21         0.99 

$`AMP PEAK 57(XP11.4) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M 
       30.02        14.70        14.27         2.76         9.96        48.79 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       38.17       169.32        18.58         8.71        56.19        23.38 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       43.17        52.37         8.32        11.01       135.91        30.61 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       44.98        42.51        14.96        17.59         6.02        42.58 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
       47.41        17.56        10.09         7.82        30.58        35.41 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       27.45        26.20        38.83        33.96        31.99        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       28.96         8.78         8.42        34.36        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24        33.93        37.48        36.46        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        33.53        35.18        15.88        36.92        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       32.42        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        17.69        59.57        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        42.54        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL 
        7.76        35.67         3.12        36.43        24.76        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        21.34        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        52.44        39.95        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA 
       32.48       132.07        98.24        41.29       107.47        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM 
       82.82        89.56        78.97        51.78        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        65.49        61.22        60.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       34.39        30.51        53.36        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       43.59        24.30        27.06        23.90        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE 
       20.91        48.49        18.05        19.79        19.46        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O 
       14.73        14.50        15.75        10.45        14.53        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        6.05         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       40.34        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       17.29        14.60        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        29.72        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 
       15.02        14.50        15.06         7.33         0.49         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       13.91        38.66        38.86        29.95        29.85        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        84.59        29.33        21.34         5.33        26.37 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
       26.37        22.45        21.53        60.49        24.46        13.68 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       81.93        81.70        77.56        70.42        56.58        60.20 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       63.39        65.29        18.38        63.45        88.41        58.75 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       37.25        52.60        54.35        83.34         2.66        80.88 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
       33.24       106.09       107.41       108.46        84.89       123.32 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
      100.57        95.34        94.13        55.10        98.20        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
       50.40        79.10        76.64         5.79        87.62        77.82 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       75.42        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
       43.99        46.26        44.38        37.48        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      117.40        66.77       112.80        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        1.05        13.28         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       20.42        17.82         7.82        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83        31.10         8.22        25.64        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       23.93        12.89 

  AMP PEAK 57(XP11.4) MUTATED AMP PEAK 57(XP11.4) WILD-TYPE 
                         0.99                          0.16 
  AMP PEAK 57(XP11.4) MUTATED AMP PEAK 57(XP11.4) WILD-TYPE 
                        78.61                        169.32 
  AMP PEAK 57(XP11.4) MUTATED AMP PEAK 57(XP11.4) WILD-TYPE 
                        22.52                         30.74 
[1] "1.0 - 78.6 (22.5)"  "0.2 - 169.3 (30.7)"
[1] "hr=" "4.9"
D54V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 57(XP11.4) MUTATED         2        3         2        1         1
  AMP PEAK 57(XP11.4) WILD-TYPE     280       47       109        1        45
                               vv
clus                            STAGE IVC
  AMP PEAK 57(XP11.4) MUTATED           0
  AMP PEAK 57(XP11.4) WILD-TYPE         6
D54V3, multiclass
           clus
vv          AMP PEAK 57(XP11.4) MUTATED AMP PEAK 57(XP11.4) WILD-TYPE
  STAGE I                             2                           280
  STAGE II                            3                            47
  STAGE III                           2                           109
  STAGE IV                            1                             1
  STAGE IVA                           1                            45
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 57(XP11.4) MUTATED     1   4   3   1
  AMP PEAK 57(XP11.4) WILD-TYPE 141 161 164  22
D54V4, multiclass
    clus
vv   AMP PEAK 57(XP11.4) MUTATED AMP PEAK 57(XP11.4) WILD-TYPE
  T1                           1                           141
  T2                           4                           161
  T3                           3                           164
  T4                           1                            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"
D54V5, binary
                               cls
clus                              0   1
  AMP PEAK 57(XP11.4) MUTATED     6   2
  AMP PEAK 57(XP11.4) WILD-TYPE 219 222
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 57(XP11.4) MUTATED      6    2
  AMP PEAK 57(XP11.4) WILD-TYPE  219  222
   clus
vv  AMP PEAK 57(XP11.4) MUTATED AMP PEAK 57(XP11.4) WILD-TYPE
  0                           6                           219
  1                           2                           222
[1] 2 2
[1] FALSE
D54V6, binary
                               cls
clus                              0   1
  AMP PEAK 57(XP11.4) MUTATED     2   0
  AMP PEAK 57(XP11.4) WILD-TYPE 276   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 57(XP11.4) MUTATED      2    0
  AMP PEAK 57(XP11.4) WILD-TYPE  276    9
   clus
vv  AMP PEAK 57(XP11.4) MUTATED AMP PEAK 57(XP11.4) WILD-TYPE
  0                           2                           276
  1                           0                             9
[1] 2 2
[1] FALSE
D54V7, binary
                               cls
clus                              0   1
  AMP PEAK 57(XP11.4) MUTATED     7   2
  AMP PEAK 57(XP11.4) WILD-TYPE 358 132
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 57(XP11.4) MUTATED      7    2
  AMP PEAK 57(XP11.4) WILD-TYPE  358  132
        clus
vv       AMP PEAK 57(XP11.4) MUTATED AMP PEAK 57(XP11.4) WILD-TYPE
  FEMALE                           7                           358
  MALE                             2                           132
[1] 2 2
[1] FALSE
D54V8, binary
                               cls
clus                              0   1
  AMP PEAK 57(XP11.4) MUTATED     2   5
  AMP PEAK 57(XP11.4) WILD-TYPE 183 285
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 57(XP11.4) MUTATED      2    5
  AMP PEAK 57(XP11.4) WILD-TYPE  183  285
     clus
vv    AMP PEAK 57(XP11.4) MUTATED AMP PEAK 57(XP11.4) WILD-TYPE
  NO                            2                           183
  YES                           5                           285
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 57(XP11.4) MUTATED                0
  AMP PEAK 57(XP11.4) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 57(XP11.4) MUTATED                                               5
  AMP PEAK 57(XP11.4) WILD-TYPE                                           350
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 57(XP11.4) MUTATED                                                                        4
  AMP PEAK 57(XP11.4) WILD-TYPE                                                                     96
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 57(XP11.4) MUTATED                                                                     0
  AMP PEAK 57(XP11.4) WILD-TYPE                                                                  36
D54V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 57(XP11.4) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    5
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           4
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       AMP PEAK 57(XP11.4) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V10, binary
                               cls
clus                              0   1
  AMP PEAK 57(XP11.4) MUTATED     8   1
  AMP PEAK 57(XP11.4) WILD-TYPE 412  16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 57(XP11.4) MUTATED      8    1
  AMP PEAK 57(XP11.4) WILD-TYPE  412   16
     clus
vv    AMP PEAK 57(XP11.4) MUTATED AMP PEAK 57(XP11.4) WILD-TYPE
  NO                            8                           412
  YES                           1                            16
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 57(XP11.4) MUTATED              1                       0    7
  AMP PEAK 57(XP11.4) WILD-TYPE          131                      18  323
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 57(XP11.4) MUTATED                     1
  AMP PEAK 57(XP11.4) WILD-TYPE                   0
D54V11, multiclass
                         clus
vv                        AMP PEAK 57(XP11.4) MUTATED
  MINIMAL (T3)                                      1
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              7
  VERY ADVANCED (T4B)                               1
                         clus
vv                        AMP PEAK 57(XP11.4) WILD-TYPE
  MINIMAL (T3)                                      131
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              323
  VERY ADVANCED (T4B)                                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 57(XP11.4) MUTATED     5   2   0   2
  AMP PEAK 57(XP11.4) WILD-TYPE 378  49   4  28
D54V12, multiclass
    clus
vv   AMP PEAK 57(XP11.4) MUTATED AMP PEAK 57(XP11.4) WILD-TYPE
  R0                           5                           378
  R1                           2                            49
  R2                           0                             4
  RX                           2                            28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V13, continuous
D54V14, binary
                               cls
clus                              0   1
  AMP PEAK 57(XP11.4) MUTATED     5   4
  AMP PEAK 57(XP11.4) WILD-TYPE 220 260
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 57(XP11.4) MUTATED      5    4
  AMP PEAK 57(XP11.4) WILD-TYPE  220  260
            clus
vv           AMP PEAK 57(XP11.4) MUTATED AMP PEAK 57(XP11.4) WILD-TYPE
  MULTIFOCAL                           5                           220
  UNIFOCAL                             4                           260
[1] 2 2
[1] FALSE
D54V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 57(XP11.4) MUTATED                                  0     0
  AMP PEAK 57(XP11.4) WILD-TYPE                                1    52
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 57(XP11.4) MUTATED                           0     6
  AMP PEAK 57(XP11.4) WILD-TYPE                        27   322
D54V16, multiclass
                                  clus
vv                                 AMP PEAK 57(XP11.4) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      6
                                  clus
vv                                 AMP PEAK 57(XP11.4) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       52
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      322
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V17, binary
                               cls
clus                              0   1
  AMP PEAK 57(XP11.4) MUTATED     0   6
  AMP PEAK 57(XP11.4) WILD-TYPE  38 353
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 57(XP11.4) MUTATED      0    6
  AMP PEAK 57(XP11.4) WILD-TYPE   38  353
                        clus
vv                       AMP PEAK 57(XP11.4) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           6
                        clus
vv                       AMP PEAK 57(XP11.4) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           353
[1] 2 2
[1] FALSE

Clustering(55) Variable = AMP PEAK 58(XP11.22) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 58(XP11.22) MUTATED     7   1
  AMP PEAK 58(XP11.22) WILD-TYPE 474  15
  AMP PEAK 58(XP11.22) MUTATED AMP PEAK 58(XP11.22) WILD-TYPE 
                             8                            489 
  AMP PEAK 58(XP11.22) MUTATED AMP PEAK 58(XP11.22) WILD-TYPE 
                             1                             15 
$`AMP PEAK 58(XP11.22) MUTATED`
TCGA-BJ-A2N9 TCGA-EL-A3T9 TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A3AI 
       20.48         5.72        78.61        57.01        10.65        22.52 
TCGA-ET-A3BS TCGA-FY-A3NM 
        5.79         0.99 

$`AMP PEAK 58(XP11.22) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        30.61         0.16         0.23        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        33.50         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        69.57        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       49.51        50.24       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       150.48       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       47.84        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       54.08        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       44.19        41.29        14.24        47.57        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         6.05         2.99        12.30        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        40.34        19.73        32.32        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.46        17.29        14.60        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       33.07        13.38         8.35        29.72        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        47.38        21.01        12.07        17.49        17.39 
TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 
       16.18        15.02        14.50        15.06         7.33         0.49 
TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
        9.24        13.91        38.66        38.86        29.95        29.85 
TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       13.51        12.79        84.59        29.33        21.34         5.33 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
       26.37        26.37        22.45        21.53        60.49        24.46 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
       13.68        81.93        81.70        77.56        70.42        56.58 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       60.20        63.39        65.29        18.38        63.45        88.41 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       58.75        37.25        52.60        54.35        83.34         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       80.88        33.24       106.09       107.41       108.46        84.89 
TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
      123.32       100.57        95.34        94.13        55.10        98.20 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BT TCGA-ET-A3BU 
       28.24        50.40        79.10        76.64        87.62        77.82 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       75.42        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       117.40        66.77       112.80        39.95        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.11         1.05        13.28         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25        20.42        17.82         7.82        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08         0.30         0.76 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16         6.58        22.49        19.04 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35        21.60         1.68        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46         2.99        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       18.51        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       17.23        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY 
       24.69        22.29         5.75         2.47         2.60         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.40        40.37        21.83         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       30.21        23.93        12.89 

  AMP PEAK 58(XP11.22) MUTATED AMP PEAK 58(XP11.22) WILD-TYPE 
                          0.99                           0.16 
  AMP PEAK 58(XP11.22) MUTATED AMP PEAK 58(XP11.22) WILD-TYPE 
                         78.61                         169.32 
  AMP PEAK 58(XP11.22) MUTATED AMP PEAK 58(XP11.22) WILD-TYPE 
                        15.565                         30.870 
[1] "1.0 - 78.6 (15.6)"  "0.2 - 169.3 (30.9)"
[1] "hr=" "5.9"
D55V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 58(XP11.22) MUTATED         3        2         2        1         0
  AMP PEAK 58(XP11.22) WILD-TYPE     279       48       109        1        46
                                vv
clus                             STAGE IVC
  AMP PEAK 58(XP11.22) MUTATED           0
  AMP PEAK 58(XP11.22) WILD-TYPE         6
D55V3, multiclass
           clus
vv          AMP PEAK 58(XP11.22) MUTATED AMP PEAK 58(XP11.22) WILD-TYPE
  STAGE I                              3                            279
  STAGE II                             2                             48
  STAGE III                            2                            109
  STAGE IV                             1                              1
  STAGE IVA                            0                             46
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 58(XP11.22) MUTATED     1   3   3   1
  AMP PEAK 58(XP11.22) WILD-TYPE 141 162 164  22
D55V4, multiclass
    clus
vv   AMP PEAK 58(XP11.22) MUTATED AMP PEAK 58(XP11.22) WILD-TYPE
  T1                            1                            141
  T2                            3                            162
  T3                            3                            164
  T4                            1                             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"
D55V5, binary
                                cls
clus                               0   1
  AMP PEAK 58(XP11.22) MUTATED     5   2
  AMP PEAK 58(XP11.22) WILD-TYPE 220 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 58(XP11.22) MUTATED      5    2
  AMP PEAK 58(XP11.22) WILD-TYPE  220  222
   clus
vv  AMP PEAK 58(XP11.22) MUTATED AMP PEAK 58(XP11.22) WILD-TYPE
  0                            5                            220
  1                            2                            222
[1] 2 2
[1] FALSE
D55V6, binary
                                cls
clus                               0   1
  AMP PEAK 58(XP11.22) MUTATED     1   0
  AMP PEAK 58(XP11.22) WILD-TYPE 277   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 58(XP11.22) MUTATED      1    0
  AMP PEAK 58(XP11.22) WILD-TYPE  277    9
   clus
vv  AMP PEAK 58(XP11.22) MUTATED AMP PEAK 58(XP11.22) WILD-TYPE
  0                            1                            277
  1                            0                              9
[1] 2 2
[1] FALSE
D55V7, binary
                                cls
clus                               0   1
  AMP PEAK 58(XP11.22) MUTATED     7   1
  AMP PEAK 58(XP11.22) WILD-TYPE 358 133
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 58(XP11.22) MUTATED      7    1
  AMP PEAK 58(XP11.22) WILD-TYPE  358  133
        clus
vv       AMP PEAK 58(XP11.22) MUTATED AMP PEAK 58(XP11.22) WILD-TYPE
  FEMALE                            7                            358
  MALE                              1                            133
[1] 2 2
[1] FALSE
D55V8, binary
                                cls
clus                               0   1
  AMP PEAK 58(XP11.22) MUTATED     2   4
  AMP PEAK 58(XP11.22) WILD-TYPE 183 286
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 58(XP11.22) MUTATED      2    4
  AMP PEAK 58(XP11.22) WILD-TYPE  183  286
     clus
vv    AMP PEAK 58(XP11.22) MUTATED AMP PEAK 58(XP11.22) WILD-TYPE
  NO                             2                            183
  YES                            4                            286
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 58(XP11.22) MUTATED                0
  AMP PEAK 58(XP11.22) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 58(XP11.22) MUTATED                                               4
  AMP PEAK 58(XP11.22) WILD-TYPE                                           351
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 58(XP11.22) MUTATED                                                                        4
  AMP PEAK 58(XP11.22) WILD-TYPE                                                                     96
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 58(XP11.22) MUTATED                                                                     0
  AMP PEAK 58(XP11.22) WILD-TYPE                                                                  36
D55V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 58(XP11.22) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            4
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       AMP PEAK 58(XP11.22) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V10, binary
                                cls
clus                               0   1
  AMP PEAK 58(XP11.22) MUTATED     7   1
  AMP PEAK 58(XP11.22) WILD-TYPE 413  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 58(XP11.22) MUTATED      7    1
  AMP PEAK 58(XP11.22) WILD-TYPE  413   16
     clus
vv    AMP PEAK 58(XP11.22) MUTATED AMP PEAK 58(XP11.22) WILD-TYPE
  NO                             7                            413
  YES                            1                             16
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 58(XP11.22) MUTATED              2                       0    5
  AMP PEAK 58(XP11.22) WILD-TYPE          130                      18  325
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 58(XP11.22) MUTATED                     1
  AMP PEAK 58(XP11.22) WILD-TYPE                   0
D55V11, multiclass
                         clus
vv                        AMP PEAK 58(XP11.22) MUTATED
  MINIMAL (T3)                                       2
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               5
  VERY ADVANCED (T4B)                                1
                         clus
vv                        AMP PEAK 58(XP11.22) WILD-TYPE
  MINIMAL (T3)                                       130
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               325
  VERY ADVANCED (T4B)                                  0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 58(XP11.22) MUTATED     5   2   0   1
  AMP PEAK 58(XP11.22) WILD-TYPE 378  49   4  29
D55V12, multiclass
    clus
vv   AMP PEAK 58(XP11.22) MUTATED AMP PEAK 58(XP11.22) WILD-TYPE
  R0                            5                            378
  R1                            2                             49
  R2                            0                              4
  RX                            1                             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"
D55V13, continuous
D55V14, binary
                                cls
clus                               0   1
  AMP PEAK 58(XP11.22) MUTATED     5   3
  AMP PEAK 58(XP11.22) WILD-TYPE 220 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 58(XP11.22) MUTATED      5    3
  AMP PEAK 58(XP11.22) WILD-TYPE  220  261
            clus
vv           AMP PEAK 58(XP11.22) MUTATED AMP PEAK 58(XP11.22) WILD-TYPE
  MULTIFOCAL                            5                            220
  UNIFOCAL                              3                            261
[1] 2 2
[1] FALSE
D55V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 58(XP11.22) MUTATED                                  0     1
  AMP PEAK 58(XP11.22) WILD-TYPE                                1    51
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 58(XP11.22) MUTATED                           0     4
  AMP PEAK 58(XP11.22) WILD-TYPE                        27   324
D55V16, multiclass
                                  clus
vv                                 AMP PEAK 58(XP11.22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       4
                                  clus
vv                                 AMP PEAK 58(XP11.22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        51
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V17, binary
                                cls
clus                               0   1
  AMP PEAK 58(XP11.22) MUTATED     0   5
  AMP PEAK 58(XP11.22) WILD-TYPE  38 354
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 58(XP11.22) MUTATED      0    5
  AMP PEAK 58(XP11.22) WILD-TYPE   38  354
                        clus
vv                       AMP PEAK 58(XP11.22) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            5
                        clus
vv                       AMP PEAK 58(XP11.22) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            354
[1] 2 2
[1] FALSE

Clustering(56) Variable = AMP PEAK 59(XP11.21) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 59(XP11.21) MUTATED     8   1
  AMP PEAK 59(XP11.21) WILD-TYPE 473  15
  AMP PEAK 59(XP11.21) MUTATED AMP PEAK 59(XP11.21) WILD-TYPE 
                             9                            488 
  AMP PEAK 59(XP11.21) MUTATED AMP PEAK 59(XP11.21) WILD-TYPE 
                             1                             15 
$`AMP PEAK 59(XP11.21) MUTATED`
TCGA-BJ-A2N9 TCGA-EL-A3GU TCGA-EL-A3T9 TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N 
       20.48       136.01         5.72        78.61        57.01        10.65 
TCGA-EM-A3AI TCGA-ET-A2N3 TCGA-FY-A3NM 
       22.52        83.34         0.99 

$`AMP PEAK 59(XP11.21) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        30.61         0.16         0.23        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        33.50         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        69.57        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GV TCGA-EL-A3GW 
       49.51        50.24       115.10        65.39        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA 
       32.48       132.07        98.24        41.29       107.47        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM 
       82.82        89.56        78.97        51.78        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        65.49        61.22        60.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       34.39        30.51        53.36        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       43.59        24.30        27.06        23.90        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE 
       20.91        48.49        18.05        19.79        19.46        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O 
       14.73        14.50        15.75        10.45        14.53        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        6.05         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       40.34        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       17.29        14.60        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        29.72        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 
       15.02        14.50        15.06         7.33         0.49         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       13.91        38.66        38.86        29.95        29.85        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        84.59        29.33        21.34         5.33        26.37 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
       26.37        22.45        21.53        60.49        24.46        13.68 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       81.93        81.70        77.56        70.42        56.58        60.20 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       63.39        65.29        18.38        63.45        88.41        58.75 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       37.25        52.60        54.35         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
      106.09       107.41       108.46        84.89       123.32       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       95.34        94.13        55.10        98.20        28.24        50.40 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
       79.10        76.64         5.79        87.62        77.82        75.42 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
       46.65        52.47       116.78        94.59        84.85        80.58 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
       66.84        43.73        62.83       166.62        24.72        43.99 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
       46.26        44.38        40.21        37.48        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      117.40        66.77       112.80        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        1.05        13.28         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       20.42        17.82         7.82        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83        31.10         8.22        25.64        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       23.93        12.89 

  AMP PEAK 59(XP11.21) MUTATED AMP PEAK 59(XP11.21) WILD-TYPE 
                          0.99                           0.16 
  AMP PEAK 59(XP11.21) MUTATED AMP PEAK 59(XP11.21) WILD-TYPE 
                        136.01                         169.32 
  AMP PEAK 59(XP11.21) MUTATED AMP PEAK 59(XP11.21) WILD-TYPE 
                         22.52                          30.61 
[1] "1.0 - 136.0 (22.5)" "0.2 - 169.3 (30.6)"
[1] "hr=" "2.8"
D56V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 59(XP11.21) MUTATED         3        2         3        1         0
  AMP PEAK 59(XP11.21) WILD-TYPE     279       48       108        1        46
                                vv
clus                             STAGE IVC
  AMP PEAK 59(XP11.21) MUTATED           0
  AMP PEAK 59(XP11.21) WILD-TYPE         6
D56V3, multiclass
           clus
vv          AMP PEAK 59(XP11.21) MUTATED AMP PEAK 59(XP11.21) WILD-TYPE
  STAGE I                              3                            279
  STAGE II                             2                             48
  STAGE III                            3                            108
  STAGE IV                             1                              1
  STAGE IVA                            0                             46
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 59(XP11.21) MUTATED     1   4   3   1
  AMP PEAK 59(XP11.21) WILD-TYPE 141 161 164  22
D56V4, multiclass
    clus
vv   AMP PEAK 59(XP11.21) MUTATED AMP PEAK 59(XP11.21) WILD-TYPE
  T1                            1                            141
  T2                            4                            161
  T3                            3                            164
  T4                            1                             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"
D56V5, binary
                                cls
clus                               0   1
  AMP PEAK 59(XP11.21) MUTATED     5   2
  AMP PEAK 59(XP11.21) WILD-TYPE 220 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 59(XP11.21) MUTATED      5    2
  AMP PEAK 59(XP11.21) WILD-TYPE  220  222
   clus
vv  AMP PEAK 59(XP11.21) MUTATED AMP PEAK 59(XP11.21) WILD-TYPE
  0                            5                            220
  1                            2                            222
[1] 2 2
[1] FALSE
D56V6, binary
                                cls
clus                               0   1
  AMP PEAK 59(XP11.21) MUTATED     2   0
  AMP PEAK 59(XP11.21) WILD-TYPE 276   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 59(XP11.21) MUTATED      2    0
  AMP PEAK 59(XP11.21) WILD-TYPE  276    9
   clus
vv  AMP PEAK 59(XP11.21) MUTATED AMP PEAK 59(XP11.21) WILD-TYPE
  0                            2                            276
  1                            0                              9
[1] 2 2
[1] FALSE
D56V7, binary
                                cls
clus                               0   1
  AMP PEAK 59(XP11.21) MUTATED     9   0
  AMP PEAK 59(XP11.21) WILD-TYPE 356 134
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 59(XP11.21) MUTATED      9    0
  AMP PEAK 59(XP11.21) WILD-TYPE  356  134
        clus
vv       AMP PEAK 59(XP11.21) MUTATED AMP PEAK 59(XP11.21) WILD-TYPE
  FEMALE                            9                            356
  MALE                              0                            134
[1] 2 2
[1] FALSE
D56V8, binary
                                cls
clus                               0   1
  AMP PEAK 59(XP11.21) MUTATED     3   4
  AMP PEAK 59(XP11.21) WILD-TYPE 182 286
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 59(XP11.21) MUTATED      3    4
  AMP PEAK 59(XP11.21) WILD-TYPE  182  286
     clus
vv    AMP PEAK 59(XP11.21) MUTATED AMP PEAK 59(XP11.21) WILD-TYPE
  NO                             3                            182
  YES                            4                            286
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 59(XP11.21) MUTATED                0
  AMP PEAK 59(XP11.21) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 59(XP11.21) MUTATED                                               4
  AMP PEAK 59(XP11.21) WILD-TYPE                                           351
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 59(XP11.21) MUTATED                                                                        5
  AMP PEAK 59(XP11.21) WILD-TYPE                                                                     95
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 59(XP11.21) MUTATED                                                                     0
  AMP PEAK 59(XP11.21) WILD-TYPE                                                                  36
D56V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 59(XP11.21) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            5
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       AMP PEAK 59(XP11.21) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             95
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V10, binary
                                cls
clus                               0   1
  AMP PEAK 59(XP11.21) MUTATED     9   0
  AMP PEAK 59(XP11.21) WILD-TYPE 411  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 59(XP11.21) MUTATED      9    0
  AMP PEAK 59(XP11.21) WILD-TYPE  411   17
     clus
vv    AMP PEAK 59(XP11.21) MUTATED AMP PEAK 59(XP11.21) WILD-TYPE
  NO                             9                            411
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 59(XP11.21) MUTATED              2                       0    6
  AMP PEAK 59(XP11.21) WILD-TYPE          130                      18  324
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 59(XP11.21) MUTATED                     1
  AMP PEAK 59(XP11.21) WILD-TYPE                   0
D56V11, multiclass
                         clus
vv                        AMP PEAK 59(XP11.21) MUTATED
  MINIMAL (T3)                                       2
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               6
  VERY ADVANCED (T4B)                                1
                         clus
vv                        AMP PEAK 59(XP11.21) WILD-TYPE
  MINIMAL (T3)                                       130
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               324
  VERY ADVANCED (T4B)                                  0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 59(XP11.21) MUTATED     5   2   0   2
  AMP PEAK 59(XP11.21) WILD-TYPE 378  49   4  28
D56V12, multiclass
    clus
vv   AMP PEAK 59(XP11.21) MUTATED AMP PEAK 59(XP11.21) WILD-TYPE
  R0                            5                            378
  R1                            2                             49
  R2                            0                              4
  RX                            2                             28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V13, continuous
D56V14, binary
                                cls
clus                               0   1
  AMP PEAK 59(XP11.21) MUTATED     4   5
  AMP PEAK 59(XP11.21) WILD-TYPE 221 259
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 59(XP11.21) MUTATED      4    5
  AMP PEAK 59(XP11.21) WILD-TYPE  221  259
            clus
vv           AMP PEAK 59(XP11.21) MUTATED AMP PEAK 59(XP11.21) WILD-TYPE
  MULTIFOCAL                            4                            221
  UNIFOCAL                              5                            259
[1] 2 2
[1] FALSE
D56V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 59(XP11.21) MUTATED                                  0     0
  AMP PEAK 59(XP11.21) WILD-TYPE                                1    52
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 59(XP11.21) MUTATED                           0     6
  AMP PEAK 59(XP11.21) WILD-TYPE                        27   322
D56V16, multiclass
                                  clus
vv                                 AMP PEAK 59(XP11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       6
                                  clus
vv                                 AMP PEAK 59(XP11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        52
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       322
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V17, binary
                                cls
clus                               0   1
  AMP PEAK 59(XP11.21) MUTATED     1   5
  AMP PEAK 59(XP11.21) WILD-TYPE  37 354
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 59(XP11.21) MUTATED      1    5
  AMP PEAK 59(XP11.21) WILD-TYPE   37  354
                        clus
vv                       AMP PEAK 59(XP11.21) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                            5
                        clus
vv                       AMP PEAK 59(XP11.21) WILD-TYPE
  HISPANIC OR LATINO                                 37
  NOT HISPANIC OR LATINO                            354
[1] 2 2
[1] FALSE

Clustering(57) Variable = AMP PEAK 60(XQ21.2) MUTATION ANALYSIS
D57V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 60(XQ21.2) MUTATED     8   1
  AMP PEAK 60(XQ21.2) WILD-TYPE 473  15
  AMP PEAK 60(XQ21.2) MUTATED AMP PEAK 60(XQ21.2) WILD-TYPE 
                            9                           488 
  AMP PEAK 60(XQ21.2) MUTATED AMP PEAK 60(XQ21.2) WILD-TYPE 
                            1                            15 
$`AMP PEAK 60(XQ21.2) MUTATED`
TCGA-BJ-A2N9 TCGA-EL-A3T9 TCGA-EL-A3ZM TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N 
       20.48         5.72        36.03        78.61        57.01        10.65 
TCGA-EM-A3AI TCGA-EM-A3FK TCGA-FY-A3NM 
       22.52        23.77         0.99 

$`AMP PEAK 60(XQ21.2) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        30.61         0.16         0.23        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        33.50         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        69.57        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       49.51        50.24       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       150.48       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        65.49        61.22        60.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       34.39        30.51        53.36        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       43.59        24.30        27.06        23.90        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE 
       20.91        48.49        18.05        19.79        19.46        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O 
       14.73        14.50        15.75        10.45        14.53        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        6.05         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       40.34        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       17.29        14.60        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FL 
       13.38         8.35        29.72        37.25        27.95        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33         0.49         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
      106.09       107.41       108.46        84.89       123.32       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       95.34        94.13        55.10        98.20        28.24        50.40 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
       79.10        76.64         5.79        87.62        77.82        75.42 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
       46.65        52.47       116.78        94.59        84.85        80.58 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
       66.84        43.73        62.83       166.62        24.72        43.99 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
       46.26        44.38        40.21        37.48        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      117.40        66.77       112.80        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        1.05        13.28         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       20.42        17.82         7.82        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83        31.10         8.22        25.64        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       23.93        12.89 

  AMP PEAK 60(XQ21.2) MUTATED AMP PEAK 60(XQ21.2) WILD-TYPE 
                         0.99                          0.16 
  AMP PEAK 60(XQ21.2) MUTATED AMP PEAK 60(XQ21.2) WILD-TYPE 
                        78.61                        169.32 
  AMP PEAK 60(XQ21.2) MUTATED AMP PEAK 60(XQ21.2) WILD-TYPE 
                        22.52                         30.74 
[1] "1.0 - 78.6 (22.5)"  "0.2 - 169.3 (30.7)"
[1] "hr=" "4.9"
D57V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 60(XQ21.2) MUTATED         3        2         2        1         1
  AMP PEAK 60(XQ21.2) WILD-TYPE     279       48       109        1        45
                               vv
clus                            STAGE IVC
  AMP PEAK 60(XQ21.2) MUTATED           0
  AMP PEAK 60(XQ21.2) WILD-TYPE         6
D57V3, multiclass
           clus
vv          AMP PEAK 60(XQ21.2) MUTATED AMP PEAK 60(XQ21.2) WILD-TYPE
  STAGE I                             3                           279
  STAGE II                            2                            48
  STAGE III                           2                           109
  STAGE IV                            1                             1
  STAGE IVA                           1                            45
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 60(XQ21.2) MUTATED     2   3   2   2
  AMP PEAK 60(XQ21.2) WILD-TYPE 140 162 165  21
D57V4, multiclass
    clus
vv   AMP PEAK 60(XQ21.2) MUTATED AMP PEAK 60(XQ21.2) WILD-TYPE
  T1                           2                           140
  T2                           3                           162
  T3                           2                           165
  T4                           2                            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"
D57V5, binary
                               cls
clus                              0   1
  AMP PEAK 60(XQ21.2) MUTATED     5   3
  AMP PEAK 60(XQ21.2) WILD-TYPE 220 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 60(XQ21.2) MUTATED      5    3
  AMP PEAK 60(XQ21.2) WILD-TYPE  220  221
   clus
vv  AMP PEAK 60(XQ21.2) MUTATED AMP PEAK 60(XQ21.2) WILD-TYPE
  0                           5                           220
  1                           3                           221
[1] 2 2
[1] FALSE
D57V6, binary
                               cls
clus                              0   1
  AMP PEAK 60(XQ21.2) MUTATED     2   0
  AMP PEAK 60(XQ21.2) WILD-TYPE 276   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 60(XQ21.2) MUTATED      2    0
  AMP PEAK 60(XQ21.2) WILD-TYPE  276    9
   clus
vv  AMP PEAK 60(XQ21.2) MUTATED AMP PEAK 60(XQ21.2) WILD-TYPE
  0                           2                           276
  1                           0                             9
[1] 2 2
[1] FALSE
D57V7, binary
                               cls
clus                              0   1
  AMP PEAK 60(XQ21.2) MUTATED     8   1
  AMP PEAK 60(XQ21.2) WILD-TYPE 357 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 60(XQ21.2) MUTATED      8    1
  AMP PEAK 60(XQ21.2) WILD-TYPE  357  133
        clus
vv       AMP PEAK 60(XQ21.2) MUTATED AMP PEAK 60(XQ21.2) WILD-TYPE
  FEMALE                           8                           357
  MALE                             1                           133
[1] 2 2
[1] FALSE
D57V8, binary
                               cls
clus                              0   1
  AMP PEAK 60(XQ21.2) MUTATED     2   5
  AMP PEAK 60(XQ21.2) WILD-TYPE 183 285
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 60(XQ21.2) MUTATED      2    5
  AMP PEAK 60(XQ21.2) WILD-TYPE  183  285
     clus
vv    AMP PEAK 60(XQ21.2) MUTATED AMP PEAK 60(XQ21.2) WILD-TYPE
  NO                            2                           183
  YES                           5                           285
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 60(XQ21.2) MUTATED                0
  AMP PEAK 60(XQ21.2) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 60(XQ21.2) MUTATED                                               5
  AMP PEAK 60(XQ21.2) WILD-TYPE                                           350
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 60(XQ21.2) MUTATED                                                                        4
  AMP PEAK 60(XQ21.2) WILD-TYPE                                                                     96
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 60(XQ21.2) MUTATED                                                                     0
  AMP PEAK 60(XQ21.2) WILD-TYPE                                                                  36
D57V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 60(XQ21.2) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    5
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           4
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       AMP PEAK 60(XQ21.2) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V10, binary
                               cls
clus                              0   1
  AMP PEAK 60(XQ21.2) MUTATED     9   0
  AMP PEAK 60(XQ21.2) WILD-TYPE 411  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 60(XQ21.2) MUTATED      9    0
  AMP PEAK 60(XQ21.2) WILD-TYPE  411   17
     clus
vv    AMP PEAK 60(XQ21.2) MUTATED AMP PEAK 60(XQ21.2) WILD-TYPE
  NO                            9                           411
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 60(XQ21.2) MUTATED              1                       1    6
  AMP PEAK 60(XQ21.2) WILD-TYPE          131                      17  324
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 60(XQ21.2) MUTATED                     1
  AMP PEAK 60(XQ21.2) WILD-TYPE                   0
D57V11, multiclass
                         clus
vv                        AMP PEAK 60(XQ21.2) MUTATED
  MINIMAL (T3)                                      1
  MODERATE/ADVANCED (T4A)                           1
  NONE                                              6
  VERY ADVANCED (T4B)                               1
                         clus
vv                        AMP PEAK 60(XQ21.2) WILD-TYPE
  MINIMAL (T3)                                      131
  MODERATE/ADVANCED (T4A)                            17
  NONE                                              324
  VERY ADVANCED (T4B)                                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 60(XQ21.2) MUTATED     5   3   0   1
  AMP PEAK 60(XQ21.2) WILD-TYPE 378  48   4  29
D57V12, multiclass
    clus
vv   AMP PEAK 60(XQ21.2) MUTATED AMP PEAK 60(XQ21.2) WILD-TYPE
  R0                           5                           378
  R1                           3                            48
  R2                           0                             4
  RX                           1                            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"
D57V13, continuous
D57V14, binary
                               cls
clus                              0   1
  AMP PEAK 60(XQ21.2) MUTATED     5   4
  AMP PEAK 60(XQ21.2) WILD-TYPE 220 260
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 60(XQ21.2) MUTATED      5    4
  AMP PEAK 60(XQ21.2) WILD-TYPE  220  260
            clus
vv           AMP PEAK 60(XQ21.2) MUTATED AMP PEAK 60(XQ21.2) WILD-TYPE
  MULTIFOCAL                           5                           220
  UNIFOCAL                             4                           260
[1] 2 2
[1] FALSE
D57V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 60(XQ21.2) MUTATED                                  0     0
  AMP PEAK 60(XQ21.2) WILD-TYPE                                1    52
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 60(XQ21.2) MUTATED                           0     4
  AMP PEAK 60(XQ21.2) WILD-TYPE                        27   324
D57V16, multiclass
                                  clus
vv                                 AMP PEAK 60(XQ21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      4
                                  clus
vv                                 AMP PEAK 60(XQ21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       52
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V17, binary
                               cls
clus                              0   1
  AMP PEAK 60(XQ21.2) MUTATED     0   4
  AMP PEAK 60(XQ21.2) WILD-TYPE  38 355
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 60(XQ21.2) MUTATED      0    4
  AMP PEAK 60(XQ21.2) WILD-TYPE   38  355
                        clus
vv                       AMP PEAK 60(XQ21.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           4
                        clus
vv                       AMP PEAK 60(XQ21.2) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           355
[1] 2 2
[1] FALSE

Clustering(58) Variable = AMP PEAK 61(XQ22.3) MUTATION ANALYSIS
D58V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 61(XQ22.3) MUTATED    14   1
  AMP PEAK 61(XQ22.3) WILD-TYPE 467  15
  AMP PEAK 61(XQ22.3) MUTATED AMP PEAK 61(XQ22.3) WILD-TYPE 
                           15                           482 
  AMP PEAK 61(XQ22.3) MUTATED AMP PEAK 61(XQ22.3) WILD-TYPE 
                            1                            15 
$`AMP PEAK 61(XQ22.3) MUTATED`
TCGA-BJ-A2N9 TCGA-DJ-A4UT TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-EL-A3T9 TCGA-EL-A4K1 
       20.48        27.06         3.12        15.81         5.72        34.39 
TCGA-EL-A4KH TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A3AI TCGA-EM-A3FK 
       27.06        78.61        57.01        10.65        22.52        23.77 
TCGA-EM-A4FQ TCGA-FY-A3NM TCGA-KS-A4I5 
       22.45         0.99        18.64 

$`AMP PEAK 61(XQ22.3) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
       26.93        35.54        35.38        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       92.55        47.21        66.38        80.52        63.19        52.44 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       39.95        31.23        35.67        31.27        29.98        31.50 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 
       31.04         0.72         0.26         3.02        25.45        30.61 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
        0.16         0.23        14.96         7.69        33.50         0.39 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
        0.39        31.66        26.73       155.54        97.74       158.83 
TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
        7.66        45.53        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 
      106.62         4.18        79.50       139.86        98.53        69.57 
TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR 
       57.11       108.36        64.87        49.51        50.24       115.10 
TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY 
       65.39       136.01        50.37        50.20       147.75       101.13 
TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 
      139.99        49.32        33.50        43.36        49.71        83.57 
TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ 
      139.00       150.48       108.66        57.63        17.52        52.50 
TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       29.65       147.42       142.52       129.57        32.48       132.07 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       98.24        41.29       107.47        66.90        82.82        89.56 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO 
       78.97        51.78        62.30        36.03        53.06        47.38 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       65.49        61.22        60.16         7.07        59.44        57.47 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K2 TCGA-EL-A4K4 
       34.72        45.96        37.94        31.04        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KI 
       44.15        41.13        47.84        43.59        24.30        23.90 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       19.46        54.08        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       14.53        44.19        41.29        14.24        47.57        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       13.18        23.51         6.05         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        40.34        19.73        32.32        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.59        17.46        17.29        14.60        30.94        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR 
       14.14        33.07        13.38         8.35        29.72        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       27.95        47.38        21.01        12.07        17.49        17.39 
TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 
       16.18        15.02        14.50        15.06         7.33         0.49 
TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
        9.24        13.91        38.66        38.86        29.95        29.85 
TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       13.51        12.79        84.59        29.33        21.34         5.33 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
       26.37        26.37        21.53        60.49        24.46        13.68 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       81.93        81.70        77.56        70.42        56.58        60.20 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       63.39        65.29        18.38        63.45        88.41        58.75 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       37.25        52.60        54.35        83.34         2.66        80.88 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
       33.24       106.09       107.41       108.46        84.89       123.32 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
      100.57        95.34        94.13        55.10        98.20        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
       50.40        79.10        76.64         5.79        87.62        77.82 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       75.42        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       117.40        66.77       112.80        39.95        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.11         1.05        13.28         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25        20.42        17.82         7.82        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08         0.30         0.76 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16         6.58        22.49        19.04 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35        21.60         1.68        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46         2.99        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       18.51        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       17.23        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY 
       24.69        22.29         5.75         2.47         2.60         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       23.93        12.89 

  AMP PEAK 61(XQ22.3) MUTATED AMP PEAK 61(XQ22.3) WILD-TYPE 
                         0.99                          0.16 
  AMP PEAK 61(XQ22.3) MUTATED AMP PEAK 61(XQ22.3) WILD-TYPE 
                        78.61                        169.32 
  AMP PEAK 61(XQ22.3) MUTATED AMP PEAK 61(XQ22.3) WILD-TYPE 
                       22.450                        31.005 
[1] "1.0 - 78.6 (22.4)"  "0.2 - 169.3 (31.0)"
[1] "hr=" "3.9"
D58V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 61(XQ22.3) MUTATED         8        2         3        1         1
  AMP PEAK 61(XQ22.3) WILD-TYPE     274       48       108        1        45
                               vv
clus                            STAGE IVC
  AMP PEAK 61(XQ22.3) MUTATED           0
  AMP PEAK 61(XQ22.3) WILD-TYPE         6
D58V3, multiclass
           clus
vv          AMP PEAK 61(XQ22.3) MUTATED AMP PEAK 61(XQ22.3) WILD-TYPE
  STAGE I                             8                           274
  STAGE II                            2                            48
  STAGE III                           3                           108
  STAGE IV                            1                             1
  STAGE IVA                           1                            45
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 61(XQ22.3) MUTATED     5   6   3   1
  AMP PEAK 61(XQ22.3) WILD-TYPE 137 159 164  22
D58V4, multiclass
    clus
vv   AMP PEAK 61(XQ22.3) MUTATED AMP PEAK 61(XQ22.3) WILD-TYPE
  T1                           5                           137
  T2                           6                           159
  T3                           3                           164
  T4                           1                            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"
D58V5, binary
                               cls
clus                              0   1
  AMP PEAK 61(XQ22.3) MUTATED     9   5
  AMP PEAK 61(XQ22.3) WILD-TYPE 216 219
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 61(XQ22.3) MUTATED      9    5
  AMP PEAK 61(XQ22.3) WILD-TYPE  216  219
   clus
vv  AMP PEAK 61(XQ22.3) MUTATED AMP PEAK 61(XQ22.3) WILD-TYPE
  0                           9                           216
  1                           5                           219
[1] 2 2
[1] FALSE
D58V6, binary
                               cls
clus                              0   1
  AMP PEAK 61(XQ22.3) MUTATED     7   0
  AMP PEAK 61(XQ22.3) WILD-TYPE 271   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 61(XQ22.3) MUTATED      7    0
  AMP PEAK 61(XQ22.3) WILD-TYPE  271    9
   clus
vv  AMP PEAK 61(XQ22.3) MUTATED AMP PEAK 61(XQ22.3) WILD-TYPE
  0                           7                           271
  1                           0                             9
[1] 2 2
[1] FALSE
D58V7, binary
                               cls
clus                              0   1
  AMP PEAK 61(XQ22.3) MUTATED    15   0
  AMP PEAK 61(XQ22.3) WILD-TYPE 350 134
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 61(XQ22.3) MUTATED     15    0
  AMP PEAK 61(XQ22.3) WILD-TYPE  350  134
        clus
vv       AMP PEAK 61(XQ22.3) MUTATED AMP PEAK 61(XQ22.3) WILD-TYPE
  FEMALE                          15                           350
  MALE                             0                           134
[1] 2 2
[1] FALSE
D58V8, binary
                               cls
clus                              0   1
  AMP PEAK 61(XQ22.3) MUTATED     6   7
  AMP PEAK 61(XQ22.3) WILD-TYPE 179 283
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 61(XQ22.3) MUTATED      6    7
  AMP PEAK 61(XQ22.3) WILD-TYPE  179  283
     clus
vv    AMP PEAK 61(XQ22.3) MUTATED AMP PEAK 61(XQ22.3) WILD-TYPE
  NO                            6                           179
  YES                           7                           283
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 61(XQ22.3) MUTATED                0
  AMP PEAK 61(XQ22.3) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 61(XQ22.3) MUTATED                                               9
  AMP PEAK 61(XQ22.3) WILD-TYPE                                           346
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 61(XQ22.3) MUTATED                                                                        5
  AMP PEAK 61(XQ22.3) WILD-TYPE                                                                     95
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 61(XQ22.3) MUTATED                                                                     1
  AMP PEAK 61(XQ22.3) WILD-TYPE                                                                  35
D58V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 61(XQ22.3) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    9
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           5
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              1
                                                                        clus
vv                                                                       AMP PEAK 61(XQ22.3) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    346
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            95
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V10, binary
                               cls
clus                              0   1
  AMP PEAK 61(XQ22.3) MUTATED    15   0
  AMP PEAK 61(XQ22.3) WILD-TYPE 405  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 61(XQ22.3) MUTATED     15    0
  AMP PEAK 61(XQ22.3) WILD-TYPE  405   17
     clus
vv    AMP PEAK 61(XQ22.3) MUTATED AMP PEAK 61(XQ22.3) WILD-TYPE
  NO                           15                           405
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 61(XQ22.3) MUTATED              1                       0   13
  AMP PEAK 61(XQ22.3) WILD-TYPE          131                      18  317
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 61(XQ22.3) MUTATED                     1
  AMP PEAK 61(XQ22.3) WILD-TYPE                   0
D58V11, multiclass
                         clus
vv                        AMP PEAK 61(XQ22.3) MUTATED
  MINIMAL (T3)                                      1
  MODERATE/ADVANCED (T4A)                           0
  NONE                                             13
  VERY ADVANCED (T4B)                               1
                         clus
vv                        AMP PEAK 61(XQ22.3) WILD-TYPE
  MINIMAL (T3)                                      131
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              317
  VERY ADVANCED (T4B)                                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 61(XQ22.3) MUTATED    12   2   0   1
  AMP PEAK 61(XQ22.3) WILD-TYPE 371  49   4  29
D58V12, multiclass
    clus
vv   AMP PEAK 61(XQ22.3) MUTATED AMP PEAK 61(XQ22.3) WILD-TYPE
  R0                          12                           371
  R1                           2                            49
  R2                           0                             4
  RX                           1                            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"
D58V13, continuous
D58V14, binary
                               cls
clus                              0   1
  AMP PEAK 61(XQ22.3) MUTATED     9   6
  AMP PEAK 61(XQ22.3) WILD-TYPE 216 258
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 61(XQ22.3) MUTATED      9    6
  AMP PEAK 61(XQ22.3) WILD-TYPE  216  258
            clus
vv           AMP PEAK 61(XQ22.3) MUTATED AMP PEAK 61(XQ22.3) WILD-TYPE
  MULTIFOCAL                           9                           216
  UNIFOCAL                             6                           258
[1] 2 2
[1] FALSE
D58V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 61(XQ22.3) MUTATED                                  0     0
  AMP PEAK 61(XQ22.3) WILD-TYPE                                1    52
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 61(XQ22.3) MUTATED                           0     9
  AMP PEAK 61(XQ22.3) WILD-TYPE                        27   319
D58V16, multiclass
                                  clus
vv                                 AMP PEAK 61(XQ22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      9
                                  clus
vv                                 AMP PEAK 61(XQ22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       52
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      319
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V17, binary
                               cls
clus                              0   1
  AMP PEAK 61(XQ22.3) MUTATED     0   9
  AMP PEAK 61(XQ22.3) WILD-TYPE  38 350
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 61(XQ22.3) MUTATED      0    9
  AMP PEAK 61(XQ22.3) WILD-TYPE   38  350
                        clus
vv                       AMP PEAK 61(XQ22.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           9
                        clus
vv                       AMP PEAK 61(XQ22.3) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           350
[1] 2 2
[1] FALSE

Clustering(59) Variable = AMP PEAK 62(XQ23) MUTATION ANALYSIS
D59V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 62(XQ23) MUTATED     8   1
  AMP PEAK 62(XQ23) WILD-TYPE 473  15
  AMP PEAK 62(XQ23) MUTATED AMP PEAK 62(XQ23) WILD-TYPE 
                          9                         488 
  AMP PEAK 62(XQ23) MUTATED AMP PEAK 62(XQ23) WILD-TYPE 
                          1                          15 
$`AMP PEAK 62(XQ23) MUTATED`
TCGA-BJ-A2N9 TCGA-EL-A3T9 TCGA-EM-A1CU TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N 
       20.48         5.72        20.91        78.61        57.01        10.65 
TCGA-EM-A3AI TCGA-EM-A3FK TCGA-FY-A3NM 
       22.52        23.77         0.99 

$`AMP PEAK 62(XQ23) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        30.61         0.16         0.23        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        33.50         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        69.57        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       49.51        50.24       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       150.48       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       47.84        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE 
       18.18        48.49        18.05        19.79        19.46        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O 
       14.73        14.50        15.75        10.45        14.53        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        6.05         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       40.34        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       17.29        14.60        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FL 
       13.38         8.35        29.72        37.25        27.95        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33         0.49         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
      106.09       107.41       108.46        84.89       123.32       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       95.34        94.13        55.10        98.20        28.24        50.40 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
       79.10        76.64         5.79        87.62        77.82        75.42 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
       46.65        52.47       116.78        94.59        84.85        80.58 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
       66.84        43.73        62.83       166.62        24.72        43.99 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
       46.26        44.38        40.21        37.48        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      117.40        66.77       112.80        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        1.05        13.28         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       20.42        17.82         7.82        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83        31.10         8.22        25.64        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       23.93        12.89 

  AMP PEAK 62(XQ23) MUTATED AMP PEAK 62(XQ23) WILD-TYPE 
                       0.99                        0.16 
  AMP PEAK 62(XQ23) MUTATED AMP PEAK 62(XQ23) WILD-TYPE 
                      78.61                      169.32 
  AMP PEAK 62(XQ23) MUTATED AMP PEAK 62(XQ23) WILD-TYPE 
                     20.910                      30.905 
[1] "1.0 - 78.6 (20.9)"  "0.2 - 169.3 (30.9)"
[1] "hr=" "5.4"
D59V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 62(XQ23) MUTATED         4        2         2        1         0
  AMP PEAK 62(XQ23) WILD-TYPE     278       48       109        1        46
                             vv
clus                          STAGE IVC
  AMP PEAK 62(XQ23) MUTATED           0
  AMP PEAK 62(XQ23) WILD-TYPE         6
D59V3, multiclass
           clus
vv          AMP PEAK 62(XQ23) MUTATED AMP PEAK 62(XQ23) WILD-TYPE
  STAGE I                           4                         278
  STAGE II                          2                          48
  STAGE III                         2                         109
  STAGE IV                          1                           1
  STAGE IVA                         0                          46
  STAGE IVC                         0                           6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK 62(XQ23) MUTATED     2   3   3   1
  AMP PEAK 62(XQ23) WILD-TYPE 140 162 164  22
D59V4, multiclass
    clus
vv   AMP PEAK 62(XQ23) MUTATED AMP PEAK 62(XQ23) WILD-TYPE
  T1                         2                         140
  T2                         3                         162
  T3                         3                         164
  T4                         1                          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"
D59V5, binary
                             cls
clus                            0   1
  AMP PEAK 62(XQ23) MUTATED     5   3
  AMP PEAK 62(XQ23) WILD-TYPE 220 221
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 62(XQ23) MUTATED      5    3
  AMP PEAK 62(XQ23) WILD-TYPE  220  221
   clus
vv  AMP PEAK 62(XQ23) MUTATED AMP PEAK 62(XQ23) WILD-TYPE
  0                         5                         220
  1                         3                         221
[1] 2 2
[1] FALSE
D59V6, binary
                             cls
clus                            0   1
  AMP PEAK 62(XQ23) MUTATED     2   0
  AMP PEAK 62(XQ23) WILD-TYPE 276   9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 62(XQ23) MUTATED      2    0
  AMP PEAK 62(XQ23) WILD-TYPE  276    9
   clus
vv  AMP PEAK 62(XQ23) MUTATED AMP PEAK 62(XQ23) WILD-TYPE
  0                         2                         276
  1                         0                           9
[1] 2 2
[1] FALSE
D59V7, binary
                             cls
clus                            0   1
  AMP PEAK 62(XQ23) MUTATED     8   1
  AMP PEAK 62(XQ23) WILD-TYPE 357 133
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 62(XQ23) MUTATED      8    1
  AMP PEAK 62(XQ23) WILD-TYPE  357  133
        clus
vv       AMP PEAK 62(XQ23) MUTATED AMP PEAK 62(XQ23) WILD-TYPE
  FEMALE                         8                         357
  MALE                           1                         133
[1] 2 2
[1] FALSE
D59V8, binary
                             cls
clus                            0   1
  AMP PEAK 62(XQ23) MUTATED     2   5
  AMP PEAK 62(XQ23) WILD-TYPE 183 285
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 62(XQ23) MUTATED      2    5
  AMP PEAK 62(XQ23) WILD-TYPE  183  285
     clus
vv    AMP PEAK 62(XQ23) MUTATED AMP PEAK 62(XQ23) WILD-TYPE
  NO                          2                         183
  YES                         5                         285
[1] 2 2
[1] FALSE
                             vv
clus                          OTHER  SPECIFY
  AMP PEAK 62(XQ23) MUTATED                0
  AMP PEAK 62(XQ23) WILD-TYPE              8
                             vv
clus                          THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 62(XQ23) MUTATED                                               5
  AMP PEAK 62(XQ23) WILD-TYPE                                           350
                             vv
clus                          THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 62(XQ23) MUTATED                                                                        4
  AMP PEAK 62(XQ23) WILD-TYPE                                                                     96
                             vv
clus                          THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 62(XQ23) MUTATED                                                                     0
  AMP PEAK 62(XQ23) WILD-TYPE                                                                  36
D59V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 62(XQ23) MUTATED
  OTHER  SPECIFY                                                                                 0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  5
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                         4
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                            0
                                                                        clus
vv                                                                       AMP PEAK 62(XQ23) WILD-TYPE
  OTHER  SPECIFY                                                                                   8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                             36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V10, binary
                             cls
clus                            0   1
  AMP PEAK 62(XQ23) MUTATED     8   0
  AMP PEAK 62(XQ23) WILD-TYPE 412  17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 62(XQ23) MUTATED      8    0
  AMP PEAK 62(XQ23) WILD-TYPE  412   17
     clus
vv    AMP PEAK 62(XQ23) MUTATED AMP PEAK 62(XQ23) WILD-TYPE
  NO                          8                         412
  YES                         0                          17
[1] 2 2
[1] FALSE
                             vv
clus                          MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 62(XQ23) MUTATED              1                       0    7
  AMP PEAK 62(XQ23) WILD-TYPE          131                      18  323
                             vv
clus                          VERY ADVANCED (T4B)
  AMP PEAK 62(XQ23) MUTATED                     1
  AMP PEAK 62(XQ23) WILD-TYPE                   0
D59V11, multiclass
                         clus
vv                        AMP PEAK 62(XQ23) MUTATED AMP PEAK 62(XQ23) WILD-TYPE
  MINIMAL (T3)                                    1                         131
  MODERATE/ADVANCED (T4A)                         0                          18
  NONE                                            7                         323
  VERY ADVANCED (T4B)                             1                           0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK 62(XQ23) MUTATED     5   2   0   1
  AMP PEAK 62(XQ23) WILD-TYPE 378  49   4  29
D59V12, multiclass
    clus
vv   AMP PEAK 62(XQ23) MUTATED AMP PEAK 62(XQ23) WILD-TYPE
  R0                         5                         378
  R1                         2                          49
  R2                         0                           4
  RX                         1                          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"
D59V13, continuous
D59V14, binary
                             cls
clus                            0   1
  AMP PEAK 62(XQ23) MUTATED     6   3
  AMP PEAK 62(XQ23) WILD-TYPE 219 261
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 62(XQ23) MUTATED      6    3
  AMP PEAK 62(XQ23) WILD-TYPE  219  261
            clus
vv           AMP PEAK 62(XQ23) MUTATED AMP PEAK 62(XQ23) WILD-TYPE
  MULTIFOCAL                         6                         219
  UNIFOCAL                           3                         261
[1] 2 2
[1] FALSE
D59V15, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 62(XQ23) MUTATED                                  0     0
  AMP PEAK 62(XQ23) WILD-TYPE                                1    52
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 62(XQ23) MUTATED                           0     4
  AMP PEAK 62(XQ23) WILD-TYPE                        27   324
D59V16, multiclass
                                  clus
vv                                 AMP PEAK 62(XQ23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                0
  WHITE                                                    4
                                  clus
vv                                 AMP PEAK 62(XQ23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     52
  BLACK OR AFRICAN AMERICAN                                 27
  WHITE                                                    324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V17, binary
                             cls
clus                            0   1
  AMP PEAK 62(XQ23) MUTATED     0   4
  AMP PEAK 62(XQ23) WILD-TYPE  38 355
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 62(XQ23) MUTATED      0    4
  AMP PEAK 62(XQ23) WILD-TYPE   38  355
                        clus
vv                       AMP PEAK 62(XQ23) MUTATED AMP PEAK 62(XQ23) WILD-TYPE
  HISPANIC OR LATINO                             0                          38
  NOT HISPANIC OR LATINO                         4                         355
[1] 2 2
[1] FALSE

Clustering(60) Variable = AMP PEAK 63(XQ24) MUTATION ANALYSIS
D60V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 63(XQ24) MUTATED     8   1
  AMP PEAK 63(XQ24) WILD-TYPE 473  15
  AMP PEAK 63(XQ24) MUTATED AMP PEAK 63(XQ24) WILD-TYPE 
                          9                         488 
  AMP PEAK 63(XQ24) MUTATED AMP PEAK 63(XQ24) WILD-TYPE 
                          1                          15 
$`AMP PEAK 63(XQ24) MUTATED`
TCGA-BJ-A2N9 TCGA-EL-A3T9 TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A3AI 
       20.48         5.72        78.61        57.01        10.65        22.52 
TCGA-EM-A3FK TCGA-ET-A25G TCGA-FY-A3NM 
       23.77        81.93         0.99 

$`AMP PEAK 63(XQ24) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        30.61         0.16         0.23        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        33.50         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        69.57        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       49.51        50.24       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       150.48       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       47.84        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       54.08        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       44.19        41.29        14.24        47.57        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         6.05         2.99        12.30        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        40.34        19.73        32.32        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.46        17.29        14.60        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       33.07        13.38         8.35        29.72        37.25        27.95 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 
       15.02        14.50        15.06         7.33         0.49         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       13.91        38.66        38.86        29.95        29.85        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        84.59        29.33        21.34         5.33        26.37 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
       26.37        22.45        21.53        60.49        24.46        13.68 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
      106.09       107.41       108.46        84.89       123.32       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       95.34        94.13        55.10        98.20        28.24        50.40 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
       79.10        76.64         5.79        87.62        77.82        75.42 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
       46.65        52.47       116.78        94.59        84.85        80.58 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
       66.84        43.73        62.83       166.62        24.72        43.99 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
       46.26        44.38        40.21        37.48        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      117.40        66.77       112.80        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        1.05        13.28         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       20.42        17.82         7.82        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83        31.10         8.22        25.64        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       23.93        12.89 

  AMP PEAK 63(XQ24) MUTATED AMP PEAK 63(XQ24) WILD-TYPE 
                       0.99                        0.16 
  AMP PEAK 63(XQ24) MUTATED AMP PEAK 63(XQ24) WILD-TYPE 
                      81.93                      169.32 
  AMP PEAK 63(XQ24) MUTATED AMP PEAK 63(XQ24) WILD-TYPE 
                      22.52                       30.74 
[1] "1.0 - 81.9 (22.5)"  "0.2 - 169.3 (30.7)"
[1] "hr=" "3.9"
D60V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 63(XQ24) MUTATED         3        2         3        1         0
  AMP PEAK 63(XQ24) WILD-TYPE     279       48       108        1        46
                             vv
clus                          STAGE IVC
  AMP PEAK 63(XQ24) MUTATED           0
  AMP PEAK 63(XQ24) WILD-TYPE         6
D60V3, multiclass
           clus
vv          AMP PEAK 63(XQ24) MUTATED AMP PEAK 63(XQ24) WILD-TYPE
  STAGE I                           3                         279
  STAGE II                          2                          48
  STAGE III                         3                         108
  STAGE IV                          1                           1
  STAGE IVA                         0                          46
  STAGE IVC                         0                           6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK 63(XQ24) MUTATED     2   3   3   1
  AMP PEAK 63(XQ24) WILD-TYPE 140 162 164  22
D60V4, multiclass
    clus
vv   AMP PEAK 63(XQ24) MUTATED AMP PEAK 63(XQ24) WILD-TYPE
  T1                         2                         140
  T2                         3                         162
  T3                         3                         164
  T4                         1                          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"
D60V5, binary
                             cls
clus                            0   1
  AMP PEAK 63(XQ24) MUTATED     6   2
  AMP PEAK 63(XQ24) WILD-TYPE 219 222
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 63(XQ24) MUTATED      6    2
  AMP PEAK 63(XQ24) WILD-TYPE  219  222
   clus
vv  AMP PEAK 63(XQ24) MUTATED AMP PEAK 63(XQ24) WILD-TYPE
  0                         6                         219
  1                         2                         222
[1] 2 2
[1] FALSE
D60V6, binary
                             cls
clus                            0   1
  AMP PEAK 63(XQ24) MUTATED     1   0
  AMP PEAK 63(XQ24) WILD-TYPE 277   9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 63(XQ24) MUTATED      1    0
  AMP PEAK 63(XQ24) WILD-TYPE  277    9
   clus
vv  AMP PEAK 63(XQ24) MUTATED AMP PEAK 63(XQ24) WILD-TYPE
  0                         1                         277
  1                         0                           9
[1] 2 2
[1] FALSE
D60V7, binary
                             cls
clus                            0   1
  AMP PEAK 63(XQ24) MUTATED     9   0
  AMP PEAK 63(XQ24) WILD-TYPE 356 134
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 63(XQ24) MUTATED      9    0
  AMP PEAK 63(XQ24) WILD-TYPE  356  134
        clus
vv       AMP PEAK 63(XQ24) MUTATED AMP PEAK 63(XQ24) WILD-TYPE
  FEMALE                         9                         356
  MALE                           0                         134
[1] 2 2
[1] FALSE
D60V8, binary
                             cls
clus                            0   1
  AMP PEAK 63(XQ24) MUTATED     2   5
  AMP PEAK 63(XQ24) WILD-TYPE 183 285
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 63(XQ24) MUTATED      2    5
  AMP PEAK 63(XQ24) WILD-TYPE  183  285
     clus
vv    AMP PEAK 63(XQ24) MUTATED AMP PEAK 63(XQ24) WILD-TYPE
  NO                          2                         183
  YES                         5                         285
[1] 2 2
[1] FALSE
                             vv
clus                          OTHER  SPECIFY
  AMP PEAK 63(XQ24) MUTATED                0
  AMP PEAK 63(XQ24) WILD-TYPE              8
                             vv
clus                          THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 63(XQ24) MUTATED                                               4
  AMP PEAK 63(XQ24) WILD-TYPE                                           351
                             vv
clus                          THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 63(XQ24) MUTATED                                                                        4
  AMP PEAK 63(XQ24) WILD-TYPE                                                                     96
                             vv
clus                          THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 63(XQ24) MUTATED                                                                     1
  AMP PEAK 63(XQ24) WILD-TYPE                                                                  35
D60V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 63(XQ24) MUTATED
  OTHER  SPECIFY                                                                                 0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                         4
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                            1
                                                                        clus
vv                                                                       AMP PEAK 63(XQ24) WILD-TYPE
  OTHER  SPECIFY                                                                                   8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                             35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V10, binary
                             cls
clus                            0   1
  AMP PEAK 63(XQ24) MUTATED     9   0
  AMP PEAK 63(XQ24) WILD-TYPE 411  17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 63(XQ24) MUTATED      9    0
  AMP PEAK 63(XQ24) WILD-TYPE  411   17
     clus
vv    AMP PEAK 63(XQ24) MUTATED AMP PEAK 63(XQ24) WILD-TYPE
  NO                          9                         411
  YES                         0                          17
[1] 2 2
[1] FALSE
                             vv
clus                          MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 63(XQ24) MUTATED              2                       0    6
  AMP PEAK 63(XQ24) WILD-TYPE          130                      18  324
                             vv
clus                          VERY ADVANCED (T4B)
  AMP PEAK 63(XQ24) MUTATED                     1
  AMP PEAK 63(XQ24) WILD-TYPE                   0
D60V11, multiclass
                         clus
vv                        AMP PEAK 63(XQ24) MUTATED AMP PEAK 63(XQ24) WILD-TYPE
  MINIMAL (T3)                                    2                         130
  MODERATE/ADVANCED (T4A)                         0                          18
  NONE                                            6                         324
  VERY ADVANCED (T4B)                             1                           0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK 63(XQ24) MUTATED     6   2   0   1
  AMP PEAK 63(XQ24) WILD-TYPE 377  49   4  29
D60V12, multiclass
    clus
vv   AMP PEAK 63(XQ24) MUTATED AMP PEAK 63(XQ24) WILD-TYPE
  R0                         6                         377
  R1                         2                          49
  R2                         0                           4
  RX                         1                          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"
D60V13, continuous
D60V14, binary
                             cls
clus                            0   1
  AMP PEAK 63(XQ24) MUTATED     5   4
  AMP PEAK 63(XQ24) WILD-TYPE 220 260
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 63(XQ24) MUTATED      5    4
  AMP PEAK 63(XQ24) WILD-TYPE  220  260
            clus
vv           AMP PEAK 63(XQ24) MUTATED AMP PEAK 63(XQ24) WILD-TYPE
  MULTIFOCAL                         5                         220
  UNIFOCAL                           4                         260
[1] 2 2
[1] FALSE
D60V15, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 63(XQ24) MUTATED                                  0     0
  AMP PEAK 63(XQ24) WILD-TYPE                                1    52
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 63(XQ24) MUTATED                           0     5
  AMP PEAK 63(XQ24) WILD-TYPE                        27   323
D60V16, multiclass
                                  clus
vv                                 AMP PEAK 63(XQ24) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                0
  WHITE                                                    5
                                  clus
vv                                 AMP PEAK 63(XQ24) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     52
  BLACK OR AFRICAN AMERICAN                                 27
  WHITE                                                    323
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V17, binary
                             cls
clus                            0   1
  AMP PEAK 63(XQ24) MUTATED     0   5
  AMP PEAK 63(XQ24) WILD-TYPE  38 354
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 63(XQ24) MUTATED      0    5
  AMP PEAK 63(XQ24) WILD-TYPE   38  354
                        clus
vv                       AMP PEAK 63(XQ24) MUTATED AMP PEAK 63(XQ24) WILD-TYPE
  HISPANIC OR LATINO                             0                          38
  NOT HISPANIC OR LATINO                         5                         354
[1] 2 2
[1] FALSE

Clustering(61) Variable = AMP PEAK 64(XQ24) MUTATION ANALYSIS
D61V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 64(XQ24) MUTATED     8   1
  AMP PEAK 64(XQ24) WILD-TYPE 473  15
  AMP PEAK 64(XQ24) MUTATED AMP PEAK 64(XQ24) WILD-TYPE 
                          9                         488 
  AMP PEAK 64(XQ24) MUTATED AMP PEAK 64(XQ24) WILD-TYPE 
                          1                          15 
$`AMP PEAK 64(XQ24) MUTATED`
TCGA-BJ-A2N9 TCGA-DJ-A2Q6 TCGA-EL-A3T9 TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N 
       20.48        36.46         5.72        78.61        57.01        10.65 
TCGA-EM-A3AI TCGA-EM-A3FK TCGA-FY-A3NM 
       22.52        23.77         0.99 

$`AMP PEAK 64(XQ24) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
        6.77        40.24        33.93        37.48        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        33.53        35.18        15.88        36.92        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       32.42        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        17.69        59.57        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        42.54        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL 
        7.76        35.67         3.12        36.43        24.76        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        21.34        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        52.44        39.95        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA 
       32.48       132.07        98.24        41.29       107.47        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM 
       82.82        89.56        78.97        51.78        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        65.49        61.22        60.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       34.39        30.51        53.36        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       43.59        24.30        27.06        23.90        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE 
       20.91        48.49        18.05        19.79        19.46        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O 
       14.73        14.50        15.75        10.45        14.53        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        6.05         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       40.34        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       17.29        14.60        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FL 
       13.38         8.35        29.72        37.25        27.95        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33         0.49         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
      106.09       107.41       108.46        84.89       123.32       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       95.34        94.13        55.10        98.20        28.24        50.40 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
       79.10        76.64         5.79        87.62        77.82        75.42 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
       46.65        52.47       116.78        94.59        84.85        80.58 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
       66.84        43.73        62.83       166.62        24.72        43.99 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
       46.26        44.38        40.21        37.48        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      117.40        66.77       112.80        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        1.05        13.28         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       20.42        17.82         7.82        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83        31.10         8.22        25.64        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       23.93        12.89 

  AMP PEAK 64(XQ24) MUTATED AMP PEAK 64(XQ24) WILD-TYPE 
                       0.99                        0.16 
  AMP PEAK 64(XQ24) MUTATED AMP PEAK 64(XQ24) WILD-TYPE 
                      78.61                      169.32 
  AMP PEAK 64(XQ24) MUTATED AMP PEAK 64(XQ24) WILD-TYPE 
                      22.52                       30.74 
[1] "1.0 - 78.6 (22.5)"  "0.2 - 169.3 (30.7)"
[1] "hr=" "4.9"
D61V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 64(XQ24) MUTATED         4        2         2        1         0
  AMP PEAK 64(XQ24) WILD-TYPE     278       48       109        1        46
                             vv
clus                          STAGE IVC
  AMP PEAK 64(XQ24) MUTATED           0
  AMP PEAK 64(XQ24) WILD-TYPE         6
D61V3, multiclass
           clus
vv          AMP PEAK 64(XQ24) MUTATED AMP PEAK 64(XQ24) WILD-TYPE
  STAGE I                           4                         278
  STAGE II                          2                          48
  STAGE III                         2                         109
  STAGE IV                          1                           1
  STAGE IVA                         0                          46
  STAGE IVC                         0                           6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK 64(XQ24) MUTATED     3   3   2   1
  AMP PEAK 64(XQ24) WILD-TYPE 139 162 165  22
D61V4, multiclass
    clus
vv   AMP PEAK 64(XQ24) MUTATED AMP PEAK 64(XQ24) WILD-TYPE
  T1                         3                         139
  T2                         3                         162
  T3                         2                         165
  T4                         1                          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"
D61V5, binary
                             cls
clus                            0   1
  AMP PEAK 64(XQ24) MUTATED     5   3
  AMP PEAK 64(XQ24) WILD-TYPE 220 221
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 64(XQ24) MUTATED      5    3
  AMP PEAK 64(XQ24) WILD-TYPE  220  221
   clus
vv  AMP PEAK 64(XQ24) MUTATED AMP PEAK 64(XQ24) WILD-TYPE
  0                         5                         220
  1                         3                         221
[1] 2 2
[1] FALSE
D61V6, binary
                             cls
clus                            0   1
  AMP PEAK 64(XQ24) MUTATED     2   0
  AMP PEAK 64(XQ24) WILD-TYPE 276   9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 64(XQ24) MUTATED      2    0
  AMP PEAK 64(XQ24) WILD-TYPE  276    9
   clus
vv  AMP PEAK 64(XQ24) MUTATED AMP PEAK 64(XQ24) WILD-TYPE
  0                         2                         276
  1                         0                           9
[1] 2 2
[1] FALSE
D61V7, binary
                             cls
clus                            0   1
  AMP PEAK 64(XQ24) MUTATED     9   0
  AMP PEAK 64(XQ24) WILD-TYPE 356 134
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 64(XQ24) MUTATED      9    0
  AMP PEAK 64(XQ24) WILD-TYPE  356  134
        clus
vv       AMP PEAK 64(XQ24) MUTATED AMP PEAK 64(XQ24) WILD-TYPE
  FEMALE                         9                         356
  MALE                           0                         134
[1] 2 2
[1] FALSE
D61V8, binary
                             cls
clus                            0   1
  AMP PEAK 64(XQ24) MUTATED     2   5
  AMP PEAK 64(XQ24) WILD-TYPE 183 285
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 64(XQ24) MUTATED      2    5
  AMP PEAK 64(XQ24) WILD-TYPE  183  285
     clus
vv    AMP PEAK 64(XQ24) MUTATED AMP PEAK 64(XQ24) WILD-TYPE
  NO                          2                         183
  YES                         5                         285
[1] 2 2
[1] FALSE
                             vv
clus                          OTHER  SPECIFY
  AMP PEAK 64(XQ24) MUTATED                0
  AMP PEAK 64(XQ24) WILD-TYPE              8
                             vv
clus                          THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 64(XQ24) MUTATED                                               5
  AMP PEAK 64(XQ24) WILD-TYPE                                           350
                             vv
clus                          THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 64(XQ24) MUTATED                                                                        4
  AMP PEAK 64(XQ24) WILD-TYPE                                                                     96
                             vv
clus                          THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 64(XQ24) MUTATED                                                                     0
  AMP PEAK 64(XQ24) WILD-TYPE                                                                  36
D61V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 64(XQ24) MUTATED
  OTHER  SPECIFY                                                                                 0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  5
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                         4
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                            0
                                                                        clus
vv                                                                       AMP PEAK 64(XQ24) WILD-TYPE
  OTHER  SPECIFY                                                                                   8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                             36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V10, binary
                             cls
clus                            0   1
  AMP PEAK 64(XQ24) MUTATED     9   0
  AMP PEAK 64(XQ24) WILD-TYPE 411  17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 64(XQ24) MUTATED      9    0
  AMP PEAK 64(XQ24) WILD-TYPE  411   17
     clus
vv    AMP PEAK 64(XQ24) MUTATED AMP PEAK 64(XQ24) WILD-TYPE
  NO                          9                         411
  YES                         0                          17
[1] 2 2
[1] FALSE
                             vv
clus                          MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 64(XQ24) MUTATED              2                       0    6
  AMP PEAK 64(XQ24) WILD-TYPE          130                      18  324
                             vv
clus                          VERY ADVANCED (T4B)
  AMP PEAK 64(XQ24) MUTATED                     1
  AMP PEAK 64(XQ24) WILD-TYPE                   0
D61V11, multiclass
                         clus
vv                        AMP PEAK 64(XQ24) MUTATED AMP PEAK 64(XQ24) WILD-TYPE
  MINIMAL (T3)                                    2                         130
  MODERATE/ADVANCED (T4A)                         0                          18
  NONE                                            6                         324
  VERY ADVANCED (T4B)                             1                           0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK 64(XQ24) MUTATED     6   2   0   1
  AMP PEAK 64(XQ24) WILD-TYPE 377  49   4  29
D61V12, multiclass
    clus
vv   AMP PEAK 64(XQ24) MUTATED AMP PEAK 64(XQ24) WILD-TYPE
  R0                         6                         377
  R1                         2                          49
  R2                         0                           4
  RX                         1                          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"
D61V13, continuous
D61V14, binary
                             cls
clus                            0   1
  AMP PEAK 64(XQ24) MUTATED     6   3
  AMP PEAK 64(XQ24) WILD-TYPE 219 261
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 64(XQ24) MUTATED      6    3
  AMP PEAK 64(XQ24) WILD-TYPE  219  261
            clus
vv           AMP PEAK 64(XQ24) MUTATED AMP PEAK 64(XQ24) WILD-TYPE
  MULTIFOCAL                         6                         219
  UNIFOCAL                           3                         261
[1] 2 2
[1] FALSE
D61V15, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 64(XQ24) MUTATED                                  0     0
  AMP PEAK 64(XQ24) WILD-TYPE                                1    52
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 64(XQ24) MUTATED                           0     5
  AMP PEAK 64(XQ24) WILD-TYPE                        27   323
D61V16, multiclass
                                  clus
vv                                 AMP PEAK 64(XQ24) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                0
  WHITE                                                    5
                                  clus
vv                                 AMP PEAK 64(XQ24) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     52
  BLACK OR AFRICAN AMERICAN                                 27
  WHITE                                                    323
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V17, binary
                             cls
clus                            0   1
  AMP PEAK 64(XQ24) MUTATED     0   5
  AMP PEAK 64(XQ24) WILD-TYPE  38 354
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 64(XQ24) MUTATED      0    5
  AMP PEAK 64(XQ24) WILD-TYPE   38  354
                        clus
vv                       AMP PEAK 64(XQ24) MUTATED AMP PEAK 64(XQ24) WILD-TYPE
  HISPANIC OR LATINO                             0                          38
  NOT HISPANIC OR LATINO                         5                         354
[1] 2 2
[1] FALSE

Clustering(62) Variable = AMP PEAK 65(XQ28) MUTATION ANALYSIS
D62V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 65(XQ28) MUTATED     9   1
  AMP PEAK 65(XQ28) WILD-TYPE 472  15
  AMP PEAK 65(XQ28) MUTATED AMP PEAK 65(XQ28) WILD-TYPE 
                         10                         487 
  AMP PEAK 65(XQ28) MUTATED AMP PEAK 65(XQ28) WILD-TYPE 
                          1                          15 
$`AMP PEAK 65(XQ28) MUTATED`
TCGA-BJ-A2N9 TCGA-EL-A3T9 TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A3AI 
       20.48         5.72        78.61        57.01        10.65        22.52 
TCGA-EM-A3AQ TCGA-EM-A3FK TCGA-FE-A22Z TCGA-FY-A3NM 
       29.72        23.77        73.74         0.99 

$`AMP PEAK 65(XQ28) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        30.61         0.16         0.23        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        33.50         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        69.57        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       49.51        50.24       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       150.48       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       47.84        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       54.08        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       44.19        41.29        14.24        47.57        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         6.05         2.99        12.30        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        40.34        19.73        32.32        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.46        17.29        14.60        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FL 
       33.07        13.38         8.35        37.25        27.95        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33         0.49         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
      106.09       107.41       108.46        84.89       123.32       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       95.34        94.13        55.10        98.20        28.24        50.40 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
       79.10        76.64         5.79        87.62        77.82        75.42 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
       46.65        52.47       116.78        94.59        84.85        80.58 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
       66.84        43.73        62.83       166.62        24.72        43.99 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
       46.26        44.38        40.21        37.48        33.17        31.40 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       71.44        31.59        79.69        24.69        68.22       117.40 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77       112.80        39.95        33.63        81.83       106.36 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD 
       85.15        85.68        78.77        71.08         4.11         1.05 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       13.28         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       17.82         7.82        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08         0.30         0.76        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       15.16         6.58        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83        31.10         8.22        25.64        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        23.93 
TCGA-QD-A8IV 
       12.89 

  AMP PEAK 65(XQ28) MUTATED AMP PEAK 65(XQ28) WILD-TYPE 
                       0.99                        0.16 
  AMP PEAK 65(XQ28) MUTATED AMP PEAK 65(XQ28) WILD-TYPE 
                      78.61                      169.32 
  AMP PEAK 65(XQ28) MUTATED AMP PEAK 65(XQ28) WILD-TYPE 
                     23.145                      30.870 
[1] "1.0 - 78.6 (23.1)"  "0.2 - 169.3 (30.9)"
[1] "hr=" "3.7"
D62V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 65(XQ28) MUTATED         4        2         2        1         1
  AMP PEAK 65(XQ28) WILD-TYPE     278       48       109        1        45
                             vv
clus                          STAGE IVC
  AMP PEAK 65(XQ28) MUTATED           0
  AMP PEAK 65(XQ28) WILD-TYPE         6
D62V3, multiclass
           clus
vv          AMP PEAK 65(XQ28) MUTATED AMP PEAK 65(XQ28) WILD-TYPE
  STAGE I                           4                         278
  STAGE II                          2                          48
  STAGE III                         2                         109
  STAGE IV                          1                           1
  STAGE IVA                         1                          45
  STAGE IVC                         0                           6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK 65(XQ28) MUTATED     3   3   2   2
  AMP PEAK 65(XQ28) WILD-TYPE 139 162 165  21
D62V4, multiclass
    clus
vv   AMP PEAK 65(XQ28) MUTATED AMP PEAK 65(XQ28) WILD-TYPE
  T1                         3                         139
  T2                         3                         162
  T3                         2                         165
  T4                         2                          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"
D62V5, binary
                             cls
clus                            0   1
  AMP PEAK 65(XQ28) MUTATED     6   3
  AMP PEAK 65(XQ28) WILD-TYPE 219 221
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 65(XQ28) MUTATED      6    3
  AMP PEAK 65(XQ28) WILD-TYPE  219  221
   clus
vv  AMP PEAK 65(XQ28) MUTATED AMP PEAK 65(XQ28) WILD-TYPE
  0                         6                         219
  1                         3                         221
[1] 2 2
[1] FALSE
D62V6, binary
                             cls
clus                            0   1
  AMP PEAK 65(XQ28) MUTATED     1   0
  AMP PEAK 65(XQ28) WILD-TYPE 277   9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 65(XQ28) MUTATED      1    0
  AMP PEAK 65(XQ28) WILD-TYPE  277    9
   clus
vv  AMP PEAK 65(XQ28) MUTATED AMP PEAK 65(XQ28) WILD-TYPE
  0                         1                         277
  1                         0                           9
[1] 2 2
[1] FALSE
D62V7, binary
                             cls
clus                            0   1
  AMP PEAK 65(XQ28) MUTATED    10   0
  AMP PEAK 65(XQ28) WILD-TYPE 355 134
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 65(XQ28) MUTATED     10    0
  AMP PEAK 65(XQ28) WILD-TYPE  355  134
        clus
vv       AMP PEAK 65(XQ28) MUTATED AMP PEAK 65(XQ28) WILD-TYPE
  FEMALE                        10                         355
  MALE                           0                         134
[1] 2 2
[1] FALSE
D62V8, binary
                             cls
clus                            0   1
  AMP PEAK 65(XQ28) MUTATED     4   4
  AMP PEAK 65(XQ28) WILD-TYPE 181 286
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 65(XQ28) MUTATED      4    4
  AMP PEAK 65(XQ28) WILD-TYPE  181  286
     clus
vv    AMP PEAK 65(XQ28) MUTATED AMP PEAK 65(XQ28) WILD-TYPE
  NO                          4                         181
  YES                         4                         286
[1] 2 2
[1] FALSE
                             vv
clus                          OTHER  SPECIFY
  AMP PEAK 65(XQ28) MUTATED                0
  AMP PEAK 65(XQ28) WILD-TYPE              8
                             vv
clus                          THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 65(XQ28) MUTATED                                               5
  AMP PEAK 65(XQ28) WILD-TYPE                                           350
                             vv
clus                          THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 65(XQ28) MUTATED                                                                        5
  AMP PEAK 65(XQ28) WILD-TYPE                                                                     95
                             vv
clus                          THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 65(XQ28) MUTATED                                                                     0
  AMP PEAK 65(XQ28) WILD-TYPE                                                                  36
D62V9, multiclass
                                                                        clus
vv                                                                       AMP PEAK 65(XQ28) MUTATED
  OTHER  SPECIFY                                                                                 0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  5
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                         5
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                            0
                                                                        clus
vv                                                                       AMP PEAK 65(XQ28) WILD-TYPE
  OTHER  SPECIFY                                                                                   8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          95
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                             36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V10, binary
                             cls
clus                            0   1
  AMP PEAK 65(XQ28) MUTATED    10   0
  AMP PEAK 65(XQ28) WILD-TYPE 410  17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 65(XQ28) MUTATED     10    0
  AMP PEAK 65(XQ28) WILD-TYPE  410   17
     clus
vv    AMP PEAK 65(XQ28) MUTATED AMP PEAK 65(XQ28) WILD-TYPE
  NO                         10                         410
  YES                         0                          17
[1] 2 2
[1] FALSE
                             vv
clus                          MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 65(XQ28) MUTATED              1                       1    7
  AMP PEAK 65(XQ28) WILD-TYPE          131                      17  323
                             vv
clus                          VERY ADVANCED (T4B)
  AMP PEAK 65(XQ28) MUTATED                     1
  AMP PEAK 65(XQ28) WILD-TYPE                   0
D62V11, multiclass
                         clus
vv                        AMP PEAK 65(XQ28) MUTATED AMP PEAK 65(XQ28) WILD-TYPE
  MINIMAL (T3)                                    1                         131
  MODERATE/ADVANCED (T4A)                         1                          17
  NONE                                            7                         323
  VERY ADVANCED (T4B)                             1                           0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK 65(XQ28) MUTATED     7   2   0   1
  AMP PEAK 65(XQ28) WILD-TYPE 376  49   4  29
D62V12, multiclass
    clus
vv   AMP PEAK 65(XQ28) MUTATED AMP PEAK 65(XQ28) WILD-TYPE
  R0                         7                         376
  R1                         2                          49
  R2                         0                           4
  RX                         1                          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"
D62V13, continuous
D62V14, binary
                             cls
clus                            0   1
  AMP PEAK 65(XQ28) MUTATED     6   4
  AMP PEAK 65(XQ28) WILD-TYPE 219 260
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 65(XQ28) MUTATED      6    4
  AMP PEAK 65(XQ28) WILD-TYPE  219  260
            clus
vv           AMP PEAK 65(XQ28) MUTATED AMP PEAK 65(XQ28) WILD-TYPE
  MULTIFOCAL                         6                         219
  UNIFOCAL                           4                         260
[1] 2 2
[1] FALSE
D62V15, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 65(XQ28) MUTATED                                  0     0
  AMP PEAK 65(XQ28) WILD-TYPE                                1    52
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 65(XQ28) MUTATED                           0     5
  AMP PEAK 65(XQ28) WILD-TYPE                        27   323
D62V16, multiclass
                                  clus
vv                                 AMP PEAK 65(XQ28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                0
  WHITE                                                    5
                                  clus
vv                                 AMP PEAK 65(XQ28) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     52
  BLACK OR AFRICAN AMERICAN                                 27
  WHITE                                                    323
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V17, binary
                             cls
clus                            0   1
  AMP PEAK 65(XQ28) MUTATED     0   5
  AMP PEAK 65(XQ28) WILD-TYPE  38 354
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 65(XQ28) MUTATED      0    5
  AMP PEAK 65(XQ28) WILD-TYPE   38  354
                        clus
vv                       AMP PEAK 65(XQ28) MUTATED AMP PEAK 65(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             0                          38
  NOT HISPANIC OR LATINO                         5                         354
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK  1(1Q24.2) MUTATION ANALYSIS
D63V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  1(1Q24.2) MUTATED     3   0
  DEL PEAK  1(1Q24.2) WILD-TYPE 478  16
  DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE 
                            3                           494 
  DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE 
                            0                            16 
$`DEL PEAK  1(1Q24.2) MUTATED`
TCGA-EM-A1YE TCGA-ET-A39N TCGA-FY-A3I5 
       54.08       123.32         7.82 

$`DEL PEAK  1(1Q24.2) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
       30.58        35.41        27.45        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74         6.77        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        36.33        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       35.87        40.96        36.99        20.22        30.61        42.54 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20        23.21        21.27        20.48        24.82        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ 
       21.01        18.97         7.76        35.67         3.12        36.43 
TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       24.76        17.23        27.62        30.87        21.34        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        80.52        63.19        52.44        39.95        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04         0.72 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
        0.26         3.02        25.45        30.61         0.16         0.23 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        33.50         0.39         0.39        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS 
       26.73       155.54        97.74       158.83         7.66        45.53 
TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY 
       60.95       157.15        37.94        57.01       106.62         4.18 
TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 
       79.50       139.86        98.53        69.57        57.11       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
       64.87        49.51        50.24       115.10        65.39       136.01 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        50.20       147.75       101.13       139.99        49.32 
TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 
       33.50        43.36        49.71        83.57       139.00       150.48 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 
      108.66        57.63        17.52        52.50        29.65       147.42 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        47.38        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        37.94        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J 
       19.79        19.46        78.61        57.01        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P 
       15.75        10.45        14.53        10.65        44.19        41.29 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        47.57        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        32.32        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        29.72        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 
       15.02        14.50        15.06         7.33         0.49         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       13.91        38.66        38.86        29.95        29.85        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        84.59        29.33        21.34         5.33        26.37 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
       26.37        22.45        21.53        60.49        24.46        13.68 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       81.93        81.70        77.56        70.42        56.58        60.20 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       63.39        65.29        18.38        63.45        88.41        58.75 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       37.25        52.60        54.35        83.34         2.66        80.88 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O 
       33.24       106.09       107.41       108.46        84.89       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       95.34        94.13        55.10        98.20        28.24        50.40 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
       79.10        76.64         5.79        87.62        77.82        75.42 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
       46.65        52.47       116.78        94.59        84.85        80.58 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
       66.84        43.73        62.83       166.62        24.72        43.99 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
       46.26        44.38        40.21        37.48        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      117.40        66.77       112.80        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        1.05        13.28         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       20.42        17.82         0.99        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83        31.10         8.22        25.64        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       23.93        12.89 

  DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE 
                         7.82                          0.16 
  DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE 
                       123.32                        169.32 
  DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE 
                        54.08                         30.61 
[1] "7.8 - 123.3 (54.1)" "0.2 - 169.3 (30.6)"
[1] "hr="     "9100000"
D63V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK  1(1Q24.2) MUTATED         1        1         1        0         0
  DEL PEAK  1(1Q24.2) WILD-TYPE     281       49       110        2        46
                               vv
clus                            STAGE IVC
  DEL PEAK  1(1Q24.2) MUTATED           0
  DEL PEAK  1(1Q24.2) WILD-TYPE         6
D63V3, multiclass
           clus
vv          DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE
  STAGE I                             1                           281
  STAGE II                            1                            49
  STAGE III                           1                           110
  STAGE IV                            0                             2
  STAGE IVA                           0                            46
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  1(1Q24.2) MUTATED     0   1   2   0
  DEL PEAK  1(1Q24.2) WILD-TYPE 142 164 165  23
D63V4, multiclass
    clus
vv   DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE
  T1                           0                           142
  T2                           1                           164
  T3                           2                           165
  T4                           0                            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"
D63V5, binary
                               cls
clus                              0   1
  DEL PEAK  1(1Q24.2) MUTATED     2   0
  DEL PEAK  1(1Q24.2) WILD-TYPE 223 224
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(1Q24.2) MUTATED      2    0
  DEL PEAK  1(1Q24.2) WILD-TYPE  223  224
   clus
vv  DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE
  0                           2                           223
  1                           0                           224
[1] 2 2
[1] FALSE
D63V6, binary
                               cls
clus                              0   1
  DEL PEAK  1(1Q24.2) MUTATED     0   0
  DEL PEAK  1(1Q24.2) WILD-TYPE 278   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(1Q24.2) MUTATED      0    0
  DEL PEAK  1(1Q24.2) WILD-TYPE  278    9
D63V7, binary
                               cls
clus                              0   1
  DEL PEAK  1(1Q24.2) MUTATED     3   0
  DEL PEAK  1(1Q24.2) WILD-TYPE 362 134
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(1Q24.2) MUTATED      3    0
  DEL PEAK  1(1Q24.2) WILD-TYPE  362  134
        clus
vv       DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE
  FEMALE                           3                           362
  MALE                             0                           134
[1] 2 2
[1] FALSE
D63V8, binary
                               cls
clus                              0   1
  DEL PEAK  1(1Q24.2) MUTATED     0   2
  DEL PEAK  1(1Q24.2) WILD-TYPE 185 288
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(1Q24.2) MUTATED      0    2
  DEL PEAK  1(1Q24.2) WILD-TYPE  185  288
     clus
vv    DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE
  NO                            0                           185
  YES                           2                           288
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  DEL PEAK  1(1Q24.2) MUTATED                0
  DEL PEAK  1(1Q24.2) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK  1(1Q24.2) MUTATED                                               1
  DEL PEAK  1(1Q24.2) WILD-TYPE                                           354
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK  1(1Q24.2) MUTATED                                                                        2
  DEL PEAK  1(1Q24.2) WILD-TYPE                                                                     98
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK  1(1Q24.2) MUTATED                                                                     0
  DEL PEAK  1(1Q24.2) WILD-TYPE                                                                  36
D63V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK  1(1Q24.2) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    1
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       DEL PEAK  1(1Q24.2) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    354
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V10, binary
                               cls
clus                              0   1
  DEL PEAK  1(1Q24.2) MUTATED     2   0
  DEL PEAK  1(1Q24.2) WILD-TYPE 418  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(1Q24.2) MUTATED      2    0
  DEL PEAK  1(1Q24.2) WILD-TYPE  418   17
     clus
vv    DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE
  NO                            2                           418
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK  1(1Q24.2) MUTATED              0                       0    3
  DEL PEAK  1(1Q24.2) WILD-TYPE          132                      18  327
                               vv
clus                            VERY ADVANCED (T4B)
  DEL PEAK  1(1Q24.2) MUTATED                     0
  DEL PEAK  1(1Q24.2) WILD-TYPE                   1
D63V11, multiclass
                         clus
vv                        DEL PEAK  1(1Q24.2) MUTATED
  MINIMAL (T3)                                      0
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              3
  VERY ADVANCED (T4B)                               0
                         clus
vv                        DEL PEAK  1(1Q24.2) WILD-TYPE
  MINIMAL (T3)                                      132
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              327
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  1(1Q24.2) MUTATED     3   0   0   0
  DEL PEAK  1(1Q24.2) WILD-TYPE 380  51   4  30
D63V12, multiclass
    clus
vv   DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE
  R0                           3                           380
  R1                           0                            51
  R2                           0                             4
  RX                           0                            30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V13, continuous
[1] "Remove cluster labels:"      "DEL PEAK  1(1Q24.2) MUTATED"
clus
  DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE 
                            2                           383 
                   TCGA-4C-A93U                    TCGA-BJ-A0Z0 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A0Z3                    TCGA-BJ-A0Z9 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A0ZA                    TCGA-BJ-A0ZB 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A0ZH                    TCGA-BJ-A0ZJ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A18Y                    TCGA-BJ-A18Z 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A190                    TCGA-BJ-A191 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A28R                    TCGA-BJ-A28T 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A28W                    TCGA-BJ-A28X 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A28Z                    TCGA-BJ-A290 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A291                    TCGA-BJ-A2N8 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A2N9                    TCGA-BJ-A2NA 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A3EZ                    TCGA-BJ-A3PR 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A3PU                    TCGA-BJ-A45C 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A45D                    TCGA-BJ-A45E 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A45G                    TCGA-BJ-A45I 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A45J                    TCGA-BJ-A45K 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A4O8                    TCGA-BJ-A4O9 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-CE-A13K                    TCGA-CE-A3MD 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-CE-A483                    TCGA-CE-A484 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-CE-A485                    TCGA-DE-A0XZ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DE-A0Y2                    TCGA-DE-A0Y3 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DE-A3KN                    TCGA-DE-A4M8 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DE-A4MA                    TCGA-DE-A4MB 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DE-A4MC                    TCGA-DE-A4MD 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DE-A69K                    TCGA-DE-A7U5 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A13M                    TCGA-DJ-A13O 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A13R                    TCGA-DJ-A13T 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A13V                    TCGA-DJ-A13W 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A13X                    TCGA-DJ-A1QG 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A1QH                    TCGA-DJ-A1QM 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A2PO                    TCGA-DJ-A2PP 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A2PQ                    TCGA-DJ-A2PR 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A2PS                    TCGA-DJ-A2PT 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A2PU                    TCGA-DJ-A2PV 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A2PW                    TCGA-DJ-A2PX 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A2PY                    TCGA-DJ-A2PZ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A2Q0                    TCGA-DJ-A2Q1 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A2Q2                    TCGA-DJ-A2Q3 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A2Q4                    TCGA-DJ-A2Q5 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A2Q6                    TCGA-DJ-A2Q7 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A2Q8                    TCGA-DJ-A2Q9 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A2QA                    TCGA-DJ-A2QB 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3UK                    TCGA-DJ-A3UM 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3UN                    TCGA-DJ-A3UO 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3UP                    TCGA-DJ-A3UQ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3UR                    TCGA-DJ-A3UU 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3UW                    TCGA-DJ-A3UX 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3UZ                    TCGA-DJ-A3V0 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3V2                    TCGA-DJ-A3V3 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3V4                    TCGA-DJ-A3V5 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3V7                    TCGA-DJ-A3V8 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3V9                    TCGA-DJ-A3VA 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3VB                    TCGA-DJ-A3VD 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3VF                    TCGA-DJ-A3VG 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3VI                    TCGA-DJ-A3VJ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3VK                    TCGA-DJ-A3VL 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A4UL                    TCGA-DJ-A4UP 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A4UQ                    TCGA-DJ-A4UR 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A4UW                    TCGA-DJ-A4V2 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A4V5                    TCGA-DO-A1K0 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DO-A2HM                    TCGA-E3-A3DY 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E3-A3DZ                    TCGA-E3-A3E0 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E3-A3E1                    TCGA-E3-A3E2 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E3-A3E3                    TCGA-E3-A3E5 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E8-A242                    TCGA-E8-A2EA 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E8-A414                    TCGA-E8-A415 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E8-A417                    TCGA-E8-A419 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E8-A433                    TCGA-E8-A436 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E8-A438                    TCGA-E8-A44K 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3CM                    TCGA-EL-A3CN 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3CO                    TCGA-EL-A3CR 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3CS                    TCGA-EL-A3CT 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3CU                    TCGA-EL-A3CV 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3CW                    TCGA-EL-A3CX 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3CY                    TCGA-EL-A3CZ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3D0                    TCGA-EL-A3D1 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3D4                    TCGA-EL-A3D5 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3D6                    TCGA-EL-A3GO 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3GP                    TCGA-EL-A3GQ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3GS                    TCGA-EL-A3GU 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3GV                    TCGA-EL-A3GX 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3H3                    TCGA-EL-A3H4 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3H5                    TCGA-EL-A3H7 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3H8                    TCGA-EL-A3MW 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3MX                    TCGA-EL-A3MZ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3N2                    TCGA-EL-A3T0 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3T1                    TCGA-EL-A3T2 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3TB                    TCGA-EL-A3ZH 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3ZK                    TCGA-EL-A3ZL 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3ZM                    TCGA-EL-A3ZN 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3ZO                    TCGA-EL-A3ZP 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3ZS                    TCGA-EL-A4JV 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A4JW                    TCGA-EL-A4JX 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A4JZ                    TCGA-EL-A4K0 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A4K1                    TCGA-EL-A4K2 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A4K4                    TCGA-EL-A4K6 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A4K7                    TCGA-EL-A4KD 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A4KG                    TCGA-EL-A4KI 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A1CS                    TCGA-EM-A1CT 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A1CU                    TCGA-EM-A1CV 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A1CW                    TCGA-EM-A1YC 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A1YD                    TCGA-EM-A22I 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A22J                    TCGA-EM-A22K 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A22L                    TCGA-EM-A22M 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A22N                    TCGA-EM-A22O 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A22P                    TCGA-EM-A22Q 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A2CK                    TCGA-EM-A2CN 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A2CP                    TCGA-EM-A2CQ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A2CT                    TCGA-EM-A2CU 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A2OV                    TCGA-EM-A2OX 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A2OY                    TCGA-EM-A2OZ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A2P0                    TCGA-EM-A2P1 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A2P2                    TCGA-EM-A3AJ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A3AK                    TCGA-EM-A3AL 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A3AN                    TCGA-EM-A3AO 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A3AQ                    TCGA-EM-A3AR 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A3FJ                    TCGA-EM-A3FK 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A3FM                    TCGA-EM-A3FN 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A3FO                    TCGA-EM-A3FP 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A3FQ                    TCGA-EM-A3FR 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A3O3                    TCGA-EM-A3O8 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A3O9                    TCGA-EM-A3OA 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A3OB                    TCGA-EM-A3ST 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A3SU                    TCGA-EM-A3SX 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A3SZ                    TCGA-EM-A4FF 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A4FM                    TCGA-EM-A4FN 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A4FO                    TCGA-EM-A4FQ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A4FR                    TCGA-EM-A4FV 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A4G1                    TCGA-ET-A25G 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A25I                    TCGA-ET-A25J 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A25K                    TCGA-ET-A25L 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A25M                    TCGA-ET-A25N 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A25O                    TCGA-ET-A25P 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A2MX                    TCGA-ET-A2MZ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A2N0                    TCGA-ET-A2N1 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A2N4                    TCGA-ET-A39K 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A39L                    TCGA-ET-A39O 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A39P                    TCGA-ET-A39R 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A39S                    TCGA-ET-A39T 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A3BO                    TCGA-ET-A3BP 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A3BQ                    TCGA-ET-A3BS 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A3BT                    TCGA-ET-A3BU 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A3BV                    TCGA-ET-A3BX 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A3DQ                    TCGA-ET-A3DR 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A3DS                    TCGA-ET-A3DT 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A3DU                    TCGA-ET-A3DV 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A3DW                    TCGA-ET-A40P 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A40Q                    TCGA-ET-A40R 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A40S                    TCGA-ET-A40T 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A4KN                    TCGA-FE-A22Z 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FE-A230                    TCGA-FE-A231 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FE-A232                    TCGA-FE-A233 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FE-A234                    TCGA-FE-A235 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FE-A236                    TCGA-FE-A237 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FE-A238                    TCGA-FE-A239 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FE-A23A                    TCGA-FE-A3PB 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FE-A3PC                    TCGA-FE-A3PD 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FK-A3S3                    TCGA-FK-A3SB 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FK-A3SE                    TCGA-FK-A3SG 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FK-A3SH                    TCGA-FK-A4UB 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FY-A2QD                    TCGA-FY-A3I4 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FY-A3NM                    TCGA-FY-A3NN 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FY-A3ON                    TCGA-FY-A3R6 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FY-A3R7                    TCGA-FY-A3R9 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FY-A3TY                    TCGA-FY-A3W9 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FY-A3YR                    TCGA-FY-A40K 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FY-A40L                    TCGA-FY-A40M 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FY-A40N                    TCGA-FY-A4B3 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FY-A4B4                    TCGA-GE-A2C6 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-H2-A26U                    TCGA-H2-A2K9 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-H2-A3RH                    TCGA-H2-A3RI 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-H2-A421                    TCGA-H2-A422 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-IM-A3EB                    TCGA-IM-A3ED 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-IM-A3U2                    TCGA-IM-A3U3 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-IM-A41Y                    TCGA-IM-A41Z 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-IM-A420                    TCGA-IM-A4EB 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-J8-A3NZ                    TCGA-J8-A3O0 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-J8-A3O1                    TCGA-J8-A3O2 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-J8-A3YD                    TCGA-J8-A3YE 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-J8-A3YF                    TCGA-J8-A3YG 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-J8-A3YH                    TCGA-J8-A42S 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-J8-A4HW                    TCGA-J8-A4HY 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-KS-A41F                    TCGA-KS-A41I 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-KS-A41J                    TCGA-KS-A41L 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-KS-A4I1                    TCGA-KS-A4I3 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-KS-A4I5                    TCGA-KS-A4I7 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-KS-A4I9                    TCGA-KS-A4IB 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-KS-A4IC                    TCGA-KS-A4ID 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-L6-A4EP                    TCGA-L6-A4EQ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-L6-A4EU                    TCGA-MK-A4N6 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-MK-A4N7                    TCGA-MK-A4N9 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-QD-A8IV 
"DEL PEAK  1(1Q24.2) WILD-TYPE" 
D63V14, binary
                               cls
clus                              0   1
  DEL PEAK  1(1Q24.2) MUTATED     1   2
  DEL PEAK  1(1Q24.2) WILD-TYPE 224 262
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(1Q24.2) MUTATED      1    2
  DEL PEAK  1(1Q24.2) WILD-TYPE  224  262
            clus
vv           DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE
  MULTIFOCAL                           1                           224
  UNIFOCAL                             2                           262
[1] 2 2
[1] FALSE
D63V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  1(1Q24.2) MUTATED                                  0     0
  DEL PEAK  1(1Q24.2) WILD-TYPE                                1    52
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1Q24.2) MUTATED                           0     2
  DEL PEAK  1(1Q24.2) WILD-TYPE                        27   326
D63V16, multiclass
[1] "Remove cluster labels:"      "DEL PEAK  1(1Q24.2) MUTATED"
clus
  DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE 
                            2                           406 
                   TCGA-4C-A93U                    TCGA-BJ-A0YZ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A0Z2                    TCGA-BJ-A0Z3 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A0Z5                    TCGA-BJ-A0Z9 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A0ZA                    TCGA-BJ-A0ZB 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A0ZC                    TCGA-BJ-A0ZE 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A0ZG                    TCGA-BJ-A0ZH 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A0ZJ                    TCGA-BJ-A18Y 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A18Z                    TCGA-BJ-A190 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A191                    TCGA-BJ-A192 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A28R                    TCGA-BJ-A28S 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A28T                    TCGA-BJ-A28V 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A28W                    TCGA-BJ-A28X 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A28Z                    TCGA-BJ-A290 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A291                    TCGA-BJ-A2N7 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A2N8                    TCGA-BJ-A2N9 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A2NA                    TCGA-BJ-A2P4 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A3EZ                    TCGA-BJ-A3F0 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A3PR                    TCGA-BJ-A3PT 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A3PU                    TCGA-BJ-A45C 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A45D                    TCGA-BJ-A45E 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A45F                    TCGA-BJ-A45G 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A45H                    TCGA-BJ-A45I 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A45J                    TCGA-BJ-A45K 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A4O8                    TCGA-BJ-A4O9 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-CE-A13K                    TCGA-CE-A27D 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-CE-A3MD                    TCGA-CE-A3ME 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-CE-A481                    TCGA-CE-A482 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-CE-A483                    TCGA-CE-A484 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-CE-A485                    TCGA-DE-A0XZ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DE-A0Y2                    TCGA-DE-A0Y3 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DE-A2OL                    TCGA-DE-A3KN 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DE-A4M8                    TCGA-DE-A4M9 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DE-A4MA                    TCGA-DE-A4MB 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DE-A4MC                    TCGA-DE-A4MD 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DE-A69J                    TCGA-DE-A69K 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DE-A7U5                    TCGA-DJ-A13L 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A13M                    TCGA-DJ-A13O 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A13P                    TCGA-DJ-A13R 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A13S                    TCGA-DJ-A13T 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A13U                    TCGA-DJ-A13W 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A1QD                    TCGA-DJ-A1QE 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A1QF                    TCGA-DJ-A1QG 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A1QH                    TCGA-DJ-A1QI 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A1QM                    TCGA-DJ-A1QO 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A1QQ                    TCGA-DJ-A2PN 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A2PO                    TCGA-DJ-A2PQ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A2PR                    TCGA-DJ-A2PS 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A2PT                    TCGA-DJ-A2PU 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A2PV                    TCGA-DJ-A2PW 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A2PX                    TCGA-DJ-A2PY 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A2PZ                    TCGA-DJ-A2Q0 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A2Q1                    TCGA-DJ-A2Q2 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A2Q3                    TCGA-DJ-A2Q4 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A2Q5                    TCGA-DJ-A2Q6 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A2Q7                    TCGA-DJ-A2Q9 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A2QA                    TCGA-DJ-A2QB 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3UK                    TCGA-DJ-A3UM 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3UN                    TCGA-DJ-A3UO 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3UQ                    TCGA-DJ-A3UR 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3US                    TCGA-DJ-A3UT 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3UU                    TCGA-DJ-A3UW 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3UX                    TCGA-DJ-A3UY 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3UZ                    TCGA-DJ-A3V2 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3V3                    TCGA-DJ-A3V4 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3V5                    TCGA-DJ-A3V7 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3V8                    TCGA-DJ-A3V9 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3VD                    TCGA-DJ-A3VE 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3VF                    TCGA-DJ-A3VG 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3VI                    TCGA-DJ-A3VJ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3VK                    TCGA-DJ-A3VL 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3VM                    TCGA-DJ-A4UL 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A4UP                    TCGA-DJ-A4UQ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A4UR                    TCGA-DJ-A4UT 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A4UW                    TCGA-DJ-A4V0 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A4V4                    TCGA-DJ-A4V5 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DO-A1JZ                    TCGA-DO-A1K0 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DO-A2HM                    TCGA-E3-A3DY 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E3-A3DZ                    TCGA-E3-A3E0 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E3-A3E1                    TCGA-E3-A3E2 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E3-A3E3                    TCGA-E3-A3E5 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E8-A242                    TCGA-E8-A2EA 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E8-A3X7                    TCGA-E8-A413 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E8-A414                    TCGA-E8-A415 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E8-A416                    TCGA-E8-A417 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E8-A418                    TCGA-E8-A419 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E8-A432                    TCGA-E8-A433 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E8-A434                    TCGA-E8-A436 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E8-A437                    TCGA-E8-A438 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E8-A44K                    TCGA-E8-A44M 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3CL                    TCGA-EL-A3CM 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3CN                    TCGA-EL-A3CO 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3CP                    TCGA-EL-A3CR 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3CS                    TCGA-EL-A3CT 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3CU                    TCGA-EL-A3CV 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3CW                    TCGA-EL-A3CX 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3CY                    TCGA-EL-A3CZ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3D0                    TCGA-EL-A3D1 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3D4                    TCGA-EL-A3D5 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3D6                    TCGA-EL-A3GO 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3GP                    TCGA-EL-A3GQ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3GR                    TCGA-EL-A3GS 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3GU                    TCGA-EL-A3GV 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3GW                    TCGA-EL-A3GX 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3GY                    TCGA-EL-A3GZ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3H1                    TCGA-EL-A3H2 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3H3                    TCGA-EL-A3H4 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3H5                    TCGA-EL-A3H7 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3H8                    TCGA-EL-A3MW 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3MX                    TCGA-EL-A3MY 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3MZ                    TCGA-EL-A3N2 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3N3                    TCGA-EL-A3T0 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3T1                    TCGA-EL-A3T2 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3T3                    TCGA-EL-A3T6 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3T7                    TCGA-EL-A3T8 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3T9                    TCGA-EL-A3TA 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3TB                    TCGA-EL-A3ZG 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3ZH                    TCGA-EL-A3ZK 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3ZL                    TCGA-EL-A3ZN 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3ZO                    TCGA-EL-A3ZP 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3ZQ                    TCGA-EL-A3ZR 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3ZS                    TCGA-EL-A3ZT 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A4JV                    TCGA-EL-A4JW 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A4JX                    TCGA-EL-A4JZ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A4K0                    TCGA-EL-A4K1 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A4K2                    TCGA-EL-A4K4 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A4K6                    TCGA-EL-A4K7 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A4K9                    TCGA-EL-A4KD 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A4KG                    TCGA-EL-A4KH 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A4KI                    TCGA-EM-A22M 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A22O                    TCGA-EM-A2OV 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A3AI                    TCGA-ET-A25G 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A25I                    TCGA-ET-A25J 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A25K                    TCGA-ET-A25L 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A25M                    TCGA-ET-A25N 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A25O                    TCGA-ET-A25P 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A25R                    TCGA-ET-A2MX 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A2MY                    TCGA-ET-A2MZ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A2N0                    TCGA-ET-A2N1 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A2N3                    TCGA-ET-A2N4 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A2N5                    TCGA-ET-A39I 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A39J                    TCGA-ET-A39K 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A39M                    TCGA-ET-A39O 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A39P                    TCGA-ET-A39R 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A39S                    TCGA-ET-A39T 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A3BN                    TCGA-ET-A3BO 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A3BP                    TCGA-ET-A3BQ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A3BS                    TCGA-ET-A3BT 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A3BU                    TCGA-ET-A3BV 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A3BW                    TCGA-ET-A3BX 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A3DO                    TCGA-ET-A3DP 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A3DQ                    TCGA-ET-A3DR 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A3DS                    TCGA-ET-A3DT 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A3DU                    TCGA-ET-A3DV 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A3DW                    TCGA-ET-A40P 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A40Q                    TCGA-ET-A40R 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A40S                    TCGA-ET-A40T 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A4KN                    TCGA-ET-A4KQ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FE-A22Z                    TCGA-FE-A230 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FE-A231                    TCGA-FE-A232 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FE-A233                    TCGA-FE-A234 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FE-A235                    TCGA-FE-A236 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FE-A237                    TCGA-FE-A238 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FE-A239                    TCGA-FE-A23A 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FE-A3PA                    TCGA-FE-A3PB 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FE-A3PC                    TCGA-FE-A3PD 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FK-A3S3                    TCGA-FK-A3SB 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FK-A3SD                    TCGA-FK-A3SE 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FK-A3SG                    TCGA-FK-A3SH 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FK-A4UB                    TCGA-FY-A2QD 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FY-A3BL                    TCGA-FY-A3I4 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FY-A3NM                    TCGA-FY-A3ON 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FY-A3R6                    TCGA-FY-A3R7 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FY-A3R8                    TCGA-FY-A3R9 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FY-A3RA                    TCGA-FY-A3W9 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FY-A3WA                    TCGA-FY-A3YR 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FY-A40K                    TCGA-FY-A40L 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FY-A40M                    TCGA-FY-A40N 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FY-A4B0                    TCGA-FY-A4B3 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FY-A4B4                    TCGA-FY-A76V 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-GE-A2C6                    TCGA-H2-A26U 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-H2-A2K9                    TCGA-H2-A3RH 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-H2-A3RI                    TCGA-H2-A421 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-H2-A422                    TCGA-IM-A3EB 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-IM-A3ED                    TCGA-IM-A3U2 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-IM-A3U3                    TCGA-IM-A41Y 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-IM-A41Z                    TCGA-IM-A420 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-IM-A4EB                    TCGA-J8-A3NZ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-J8-A3O0                    TCGA-J8-A3O1 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-J8-A3O2                    TCGA-J8-A3YD 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-J8-A3YE                    TCGA-J8-A3YF 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-J8-A3YG                    TCGA-J8-A3YH 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-J8-A42S                    TCGA-J8-A4HW 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-J8-A4HY                    TCGA-KS-A41F 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-KS-A41I                    TCGA-KS-A41J 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-KS-A41L                    TCGA-KS-A4I1 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-KS-A4I3                    TCGA-KS-A4I5 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-KS-A4I7                    TCGA-KS-A4I9 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-KS-A4IB                    TCGA-KS-A4IC 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-KS-A4ID                    TCGA-L6-A4EP 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-L6-A4EQ                    TCGA-L6-A4ET 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-L6-A4EU                    TCGA-MK-A4N6 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-MK-A4N7                    TCGA-MK-A4N9 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-MK-A84Z                    TCGA-QD-A8IV 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
D63V17, binary
                               cls
clus                              0   1
  DEL PEAK  1(1Q24.2) MUTATED     0   2
  DEL PEAK  1(1Q24.2) WILD-TYPE  38 357
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(1Q24.2) MUTATED      0    2
  DEL PEAK  1(1Q24.2) WILD-TYPE   38  357
                        clus
vv                       DEL PEAK  1(1Q24.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           2
                        clus
vv                       DEL PEAK  1(1Q24.2) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           357
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK  2(1Q42.13) MUTATION ANALYSIS
D64V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  2(1Q42.13) MUTATED     5   0
  DEL PEAK  2(1Q42.13) WILD-TYPE 476  16
  DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE 
                             5                            492 
  DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE 
                             0                             16 
$`DEL PEAK  2(1Q42.13) MUTATED`
TCGA-EL-A3CV TCGA-EL-A3CX TCGA-EM-A1YE TCGA-ET-A39N TCGA-FY-A3I5 
       37.94       106.62        54.08       123.32         7.82 

$`DEL PEAK  2(1Q42.13) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
       30.58        35.41        27.45        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74         6.77        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        36.33        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       35.87        40.96        36.99        20.22        30.61        42.54 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20        23.21        21.27        20.48        24.82        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ 
       21.01        18.97         7.76        35.67         3.12        36.43 
TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       24.76        17.23        27.62        30.87        21.34        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        80.52        63.19        52.44        39.95        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04         0.72 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
        0.26         3.02        25.45        30.61         0.16         0.23 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        33.50         0.39         0.39        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS 
       26.73       155.54        97.74       158.83         7.66        45.53 
TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CW TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       60.95       157.15        57.01         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       47.84        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       78.61        57.01        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       14.53        10.65        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
       17.88        13.18        23.51         6.05         2.99        12.30 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       48.46        13.15        22.16        40.34        19.73        32.32 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       33.96        17.59        17.46        17.29        14.60        22.52 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.06         7.33         0.49         9.24        13.91        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.86        29.95        29.85        13.51        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      107.41       108.46        84.89       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        98.20        28.24        50.40        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.79        87.62        77.82        75.42        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       62.83       166.62        24.72        43.99        46.26        44.38 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       40.21        37.48        33.17        31.40        73.74        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
      112.80        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        13.28 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10       116.09         1.25        20.42        17.82 
TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
        0.99        19.56        13.91        16.27        15.68        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08         0.30         0.76        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58        22.49        19.04         1.35        21.60         1.68 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46         2.99        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        18.51        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
       31.10         8.22        25.64        17.23        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
      113.85        26.70        43.69        18.64        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       84.72        35.28        33.24        33.40        40.37        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        9.50        36.10        32.45        30.21        23.93        12.89 

  DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE 
                          7.82                           0.16 
  DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE 
                        123.32                         169.32 
  DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE 
                        54.080                         30.595 
[1] "7.8 - 123.3 (54.1)" "0.2 - 169.3 (30.6)"
[1] "hr="     "9200000"
D64V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK  2(1Q42.13) MUTATED         3        1         1        0         0
  DEL PEAK  2(1Q42.13) WILD-TYPE     279       49       110        2        46
                                vv
clus                             STAGE IVC
  DEL PEAK  2(1Q42.13) MUTATED           0
  DEL PEAK  2(1Q42.13) WILD-TYPE         6
D64V3, multiclass
           clus
vv          DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE
  STAGE I                              3                            279
  STAGE II                             1                             49
  STAGE III                            1                            110
  STAGE IV                             0                              2
  STAGE IVA                            0                             46
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK  2(1Q42.13) MUTATED     0   2   3   0
  DEL PEAK  2(1Q42.13) WILD-TYPE 142 163 164  23
D64V4, multiclass
    clus
vv   DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE
  T1                            0                            142
  T2                            2                            163
  T3                            3                            164
  T4                            0                             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"
D64V5, binary
                                cls
clus                               0   1
  DEL PEAK  2(1Q42.13) MUTATED     3   1
  DEL PEAK  2(1Q42.13) WILD-TYPE 222 223
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1Q42.13) MUTATED      3    1
  DEL PEAK  2(1Q42.13) WILD-TYPE  222  223
   clus
vv  DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE
  0                            3                            222
  1                            1                            223
[1] 2 2
[1] FALSE
D64V6, binary
                                cls
clus                               0   1
  DEL PEAK  2(1Q42.13) MUTATED     2   0
  DEL PEAK  2(1Q42.13) WILD-TYPE 276   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1Q42.13) MUTATED      2    0
  DEL PEAK  2(1Q42.13) WILD-TYPE  276    9
   clus
vv  DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE
  0                            2                            276
  1                            0                              9
[1] 2 2
[1] FALSE
D64V7, binary
                                cls
clus                               0   1
  DEL PEAK  2(1Q42.13) MUTATED     4   1
  DEL PEAK  2(1Q42.13) WILD-TYPE 361 133
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1Q42.13) MUTATED      4    1
  DEL PEAK  2(1Q42.13) WILD-TYPE  361  133
        clus
vv       DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE
  FEMALE                            4                            361
  MALE                              1                            133
[1] 2 2
[1] FALSE
D64V8, binary
                                cls
clus                               0   1
  DEL PEAK  2(1Q42.13) MUTATED     1   3
  DEL PEAK  2(1Q42.13) WILD-TYPE 184 287
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1Q42.13) MUTATED      1    3
  DEL PEAK  2(1Q42.13) WILD-TYPE  184  287
     clus
vv    DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE
  NO                             1                            184
  YES                            3                            287
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK  2(1Q42.13) MUTATED                0
  DEL PEAK  2(1Q42.13) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK  2(1Q42.13) MUTATED                                               3
  DEL PEAK  2(1Q42.13) WILD-TYPE                                           352
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK  2(1Q42.13) MUTATED                                                                        2
  DEL PEAK  2(1Q42.13) WILD-TYPE                                                                     98
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK  2(1Q42.13) MUTATED                                                                     0
  DEL PEAK  2(1Q42.13) WILD-TYPE                                                                  36
D64V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK  2(1Q42.13) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       DEL PEAK  2(1Q42.13) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V10, binary
                                cls
clus                               0   1
  DEL PEAK  2(1Q42.13) MUTATED     4   0
  DEL PEAK  2(1Q42.13) WILD-TYPE 416  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1Q42.13) MUTATED      4    0
  DEL PEAK  2(1Q42.13) WILD-TYPE  416   17
     clus
vv    DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE
  NO                             4                            416
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK  2(1Q42.13) MUTATED              1                       0    4
  DEL PEAK  2(1Q42.13) WILD-TYPE          131                      18  326
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK  2(1Q42.13) MUTATED                     0
  DEL PEAK  2(1Q42.13) WILD-TYPE                   1
D64V11, multiclass
                         clus
vv                        DEL PEAK  2(1Q42.13) MUTATED
  MINIMAL (T3)                                       1
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               4
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK  2(1Q42.13) WILD-TYPE
  MINIMAL (T3)                                       131
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               326
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  2(1Q42.13) MUTATED     4   1   0   0
  DEL PEAK  2(1Q42.13) WILD-TYPE 379  50   4  30
D64V12, multiclass
    clus
vv   DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE
  R0                            4                            379
  R1                            1                             50
  R2                            0                              4
  RX                            0                             30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V13, continuous
D64V14, binary
                                cls
clus                               0   1
  DEL PEAK  2(1Q42.13) MUTATED     2   3
  DEL PEAK  2(1Q42.13) WILD-TYPE 223 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1Q42.13) MUTATED      2    3
  DEL PEAK  2(1Q42.13) WILD-TYPE  223  261
            clus
vv           DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE
  MULTIFOCAL                            2                            223
  UNIFOCAL                              3                            261
[1] 2 2
[1] FALSE
D64V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  2(1Q42.13) MUTATED                                  0     0
  DEL PEAK  2(1Q42.13) WILD-TYPE                                1    52
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1Q42.13) MUTATED                           0     4
  DEL PEAK  2(1Q42.13) WILD-TYPE                        27   324
D64V16, multiclass
                                  clus
vv                                 DEL PEAK  2(1Q42.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       4
                                  clus
vv                                 DEL PEAK  2(1Q42.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        52
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V17, binary
                                cls
clus                               0   1
  DEL PEAK  2(1Q42.13) MUTATED     2   2
  DEL PEAK  2(1Q42.13) WILD-TYPE  36 357
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1Q42.13) MUTATED      2    2
  DEL PEAK  2(1Q42.13) WILD-TYPE   36  357
                        clus
vv                       DEL PEAK  2(1Q42.13) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                            2
                        clus
vv                       DEL PEAK  2(1Q42.13) WILD-TYPE
  HISPANIC OR LATINO                                 36
  NOT HISPANIC OR LATINO                            357
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK  3(2P23.1) MUTATION ANALYSIS
D65V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2P23.1) MUTATED    12   0
  DEL PEAK  3(2P23.1) WILD-TYPE 469  16
  DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE 
                           12                           485 
  DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE 
                            0                            16 
$`DEL PEAK  3(2P23.1) MUTATED`
TCGA-BJ-A190 TCGA-DJ-A2Q0 TCGA-DJ-A3US TCGA-EM-A1YE TCGA-EM-A22N TCGA-EM-A2CO 
       20.58        34.36        32.81        54.08        10.65         6.05 
TCGA-EM-A2OY TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-EM-A4FR TCGA-ET-A3DS TCGA-FY-A3I5 
       32.32         9.24        13.51        21.53        66.84         7.82 

$`DEL PEAK  3(2P23.1) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        42.08        51.39        41.52         4.83        44.35 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
       42.15        21.04        35.54        32.45        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.08        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       34.85        28.96         8.78         8.42        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24        33.93        37.48        36.46        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        33.53        35.18        15.88        36.92        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3UT 
       32.42        31.46        16.41        19.56        36.33        36.33 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        59.57        11.34        35.87        40.96        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        42.54        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM 
       35.67         3.12        36.43        24.76        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       30.87        21.34        33.04        34.78        27.06        26.93 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       35.54         3.12        15.81        35.38        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        92.55        47.21        66.38        80.52        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 
       52.44        39.95        31.23        35.67        31.27        29.98 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 
       31.50        31.04         0.72         0.26         3.02        25.45 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       30.61         0.16         0.23        14.96         7.69        33.50 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
        0.39         0.39        31.66        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      158.83         7.66        45.53        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 
       57.01       106.62         4.18        79.50       139.86        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       69.57        57.11       108.36        64.87        49.51        50.24 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
      115.10        65.39       136.01        50.37        50.20       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       83.57       139.00       150.48       108.66        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       52.50        29.65       147.42       142.52       129.57        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      132.07        98.24        41.29       107.47         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM 
       82.82        89.56        78.97        51.78        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        65.49        61.22        60.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       34.39        30.51        53.36        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       43.59        24.30        27.06        23.90        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        48.49        18.05        19.79        19.46        78.61 
TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       57.01        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       44.19        41.29        14.24        47.57        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
       23.51         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       40.34        19.73        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        29.72        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA 
       15.02        14.50        15.06         7.33         0.49        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.66        38.86        29.95        29.85        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       60.49        24.46        13.68        81.93        81.70        77.56 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       70.42        56.58        60.20        63.39        65.29        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       63.45        88.41        58.75        37.25        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       83.34         2.66        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      108.46        84.89       123.32       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        98.20        28.24        50.40        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.79        87.62        77.82        75.42        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU 
      116.78        94.59        84.85        80.58        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      166.62        24.72        43.99        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        13.28         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM 
       48.10       116.09         1.25        20.42        17.82         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
        0.30         0.76        17.06        17.36        15.16         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
       22.49        19.04         1.35        21.60         1.68        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46         2.99        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        8.22        25.64        17.23        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
       26.70        43.69        18.64        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       36.10        32.45        30.21        23.93        12.89 

  DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE 
                         6.05                          0.16 
  DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE 
                        66.84                        169.32 
  DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE 
                       21.055                        30.610 
[1] "6.0 - 66.8 (21.1)"  "0.2 - 169.3 (30.6)"
[1] "hr="     "9100000"
D65V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK  3(2P23.1) MUTATED         6        5         1        0         0
  DEL PEAK  3(2P23.1) WILD-TYPE     276       45       110        2        46
                               vv
clus                            STAGE IVC
  DEL PEAK  3(2P23.1) MUTATED           0
  DEL PEAK  3(2P23.1) WILD-TYPE         6
D65V3, multiclass
           clus
vv          DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE
  STAGE I                             6                           276
  STAGE II                            5                            45
  STAGE III                           1                           110
  STAGE IV                            0                             2
  STAGE IVA                           0                            46
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  3(2P23.1) MUTATED     4   5   3   0
  DEL PEAK  3(2P23.1) WILD-TYPE 138 160 164  23
D65V4, multiclass
    clus
vv   DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE
  T1                           4                           138
  T2                           5                           160
  T3                           3                           164
  T4                           0                            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"
D65V5, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P23.1) MUTATED     9   1
  DEL PEAK  3(2P23.1) WILD-TYPE 216 223
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P23.1) MUTATED      9    1
  DEL PEAK  3(2P23.1) WILD-TYPE  216  223
   clus
vv  DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE
  0                           9                           216
  1                           1                           223
[1] 2 2
[1] FALSE
D65V6, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P23.1) MUTATED     2   0
  DEL PEAK  3(2P23.1) WILD-TYPE 276   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P23.1) MUTATED      2    0
  DEL PEAK  3(2P23.1) WILD-TYPE  276    9
   clus
vv  DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE
  0                           2                           276
  1                           0                             9
[1] 2 2
[1] FALSE
D65V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P23.1) MUTATED     8   4
  DEL PEAK  3(2P23.1) WILD-TYPE 357 130
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P23.1) MUTATED      8    4
  DEL PEAK  3(2P23.1) WILD-TYPE  357  130
        clus
vv       DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE
  FEMALE                           8                           357
  MALE                             4                           130
[1] 2 2
[1] FALSE
D65V8, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P23.1) MUTATED     4   7
  DEL PEAK  3(2P23.1) WILD-TYPE 181 283
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P23.1) MUTATED      4    7
  DEL PEAK  3(2P23.1) WILD-TYPE  181  283
     clus
vv    DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE
  NO                            4                           181
  YES                           7                           283
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  DEL PEAK  3(2P23.1) MUTATED                1
  DEL PEAK  3(2P23.1) WILD-TYPE              7
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK  3(2P23.1) MUTATED                                               4
  DEL PEAK  3(2P23.1) WILD-TYPE                                           351
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK  3(2P23.1) MUTATED                                                                        7
  DEL PEAK  3(2P23.1) WILD-TYPE                                                                     93
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK  3(2P23.1) MUTATED                                                                     0
  DEL PEAK  3(2P23.1) WILD-TYPE                                                                  36
D65V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK  3(2P23.1) MUTATED
  OTHER  SPECIFY                                                                                   1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           7
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       DEL PEAK  3(2P23.1) WILD-TYPE
  OTHER  SPECIFY                                                                                     7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            93
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V10, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P23.1) MUTATED    11   0
  DEL PEAK  3(2P23.1) WILD-TYPE 409  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P23.1) MUTATED     11    0
  DEL PEAK  3(2P23.1) WILD-TYPE  409   17
     clus
vv    DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE
  NO                           11                           409
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK  3(2P23.1) MUTATED              0                       0   12
  DEL PEAK  3(2P23.1) WILD-TYPE          132                      18  318
                               vv
clus                            VERY ADVANCED (T4B)
  DEL PEAK  3(2P23.1) MUTATED                     0
  DEL PEAK  3(2P23.1) WILD-TYPE                   1
D65V11, multiclass
                         clus
vv                        DEL PEAK  3(2P23.1) MUTATED
  MINIMAL (T3)                                      0
  MODERATE/ADVANCED (T4A)                           0
  NONE                                             12
  VERY ADVANCED (T4B)                               0
                         clus
vv                        DEL PEAK  3(2P23.1) WILD-TYPE
  MINIMAL (T3)                                      132
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              318
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  3(2P23.1) MUTATED    11   0   0   1
  DEL PEAK  3(2P23.1) WILD-TYPE 372  51   4  29
D65V12, multiclass
    clus
vv   DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE
  R0                          11                           372
  R1                           0                            51
  R2                           0                             4
  RX                           1                            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"
D65V13, continuous
D65V14, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P23.1) MUTATED     6   6
  DEL PEAK  3(2P23.1) WILD-TYPE 219 258
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P23.1) MUTATED      6    6
  DEL PEAK  3(2P23.1) WILD-TYPE  219  258
            clus
vv           DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE
  MULTIFOCAL                           6                           219
  UNIFOCAL                             6                           258
[1] 2 2
[1] FALSE
D65V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  3(2P23.1) MUTATED                                  0     0
  DEL PEAK  3(2P23.1) WILD-TYPE                                1    52
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(2P23.1) MUTATED                           0     5
  DEL PEAK  3(2P23.1) WILD-TYPE                        27   323
D65V16, multiclass
                                  clus
vv                                 DEL PEAK  3(2P23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      5
                                  clus
vv                                 DEL PEAK  3(2P23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       52
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      323
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V17, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P23.1) MUTATED     0   5
  DEL PEAK  3(2P23.1) WILD-TYPE  38 354
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P23.1) MUTATED      0    5
  DEL PEAK  3(2P23.1) WILD-TYPE   38  354
                        clus
vv                       DEL PEAK  3(2P23.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           5
                        clus
vv                       DEL PEAK  3(2P23.1) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           354
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK  4(2Q22.1) MUTATION ANALYSIS
D66V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(2Q22.1) MUTATED    10   0
  DEL PEAK  4(2Q22.1) WILD-TYPE 471  16
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           10                           487 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                            0                            16 
$`DEL PEAK  4(2Q22.1) MUTATED`
TCGA-BJ-A190 TCGA-DJ-A2Q0 TCGA-EM-A1YE TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY 
       20.58        34.36        54.08        10.65         6.05        32.32 
TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A39N TCGA-FY-A3I5 
        9.24        13.51       123.32         7.82 

$`DEL PEAK  4(2Q22.1) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        42.08        51.39        41.52         4.83        44.35 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
       42.15        21.04        35.54        32.45        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.08        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       34.85        28.96         8.78         8.42        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24        33.93        37.48        36.46        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        33.53        35.18        15.88        36.92        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       32.42        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        17.69        59.57        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        42.54        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL 
        7.76        35.67         3.12        36.43        24.76        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        21.34        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        52.44        39.95        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       47.84        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       78.61        57.01        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       14.53        44.19        41.29        14.24        47.57        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU 
       13.18        23.51         2.99        12.30        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        40.34        19.73        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       33.07        13.38         8.35        29.72        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        47.38        21.01        12.07        17.49        17.39 
TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 
       16.18        15.02        14.50        15.06         7.33         0.49 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ 
       13.91        38.66        38.86        29.95        29.85        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
      106.09       107.41       108.46        84.89       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       94.13        55.10        98.20        28.24        50.40        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
       76.64         5.79        87.62        77.82        75.42        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
       52.47       116.78        94.59        84.85        80.58        66.84 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       43.73        62.83       166.62        24.72        43.99        46.26 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
       44.38        40.21        37.48        33.17        31.40        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       71.44        31.59        79.69        24.69        68.22       117.40 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77       112.80        39.95        33.63        81.83       106.36 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD 
       85.15        85.68        78.77        71.08         4.11         1.05 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       13.28         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       17.82         0.99        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08         0.30         0.76        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       15.16         6.58        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83        31.10         8.22        25.64        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        23.93 
TCGA-QD-A8IV 
       12.89 

  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                         6.05                          0.16 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                       123.32                        169.32 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                       17.045                        30.610 
[1] "6.0 - 123.3 (17.0)" "0.2 - 169.3 (30.6)"
[1] "hr="     "9100000"
D66V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK  4(2Q22.1) MUTATED         4        5         1        0         0
  DEL PEAK  4(2Q22.1) WILD-TYPE     278       45       110        2        46
                               vv
clus                            STAGE IVC
  DEL PEAK  4(2Q22.1) MUTATED           0
  DEL PEAK  4(2Q22.1) WILD-TYPE         6
D66V3, multiclass
           clus
vv          DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  STAGE I                             4                           278
  STAGE II                            5                            45
  STAGE III                           1                           110
  STAGE IV                            0                             2
  STAGE IVA                           0                            46
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  4(2Q22.1) MUTATED     2   5   3   0
  DEL PEAK  4(2Q22.1) WILD-TYPE 140 160 164  23
D66V4, multiclass
    clus
vv   DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  T1                           2                           140
  T2                           5                           160
  T3                           3                           164
  T4                           0                            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"
D66V5, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED     7   0
  DEL PEAK  4(2Q22.1) WILD-TYPE 218 224
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      7    0
  DEL PEAK  4(2Q22.1) WILD-TYPE  218  224
   clus
vv  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  0                           7                           218
  1                           0                           224
[1] 2 2
[1] FALSE
D66V6, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED     1   0
  DEL PEAK  4(2Q22.1) WILD-TYPE 277   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      1    0
  DEL PEAK  4(2Q22.1) WILD-TYPE  277    9
   clus
vv  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  0                           1                           277
  1                           0                             9
[1] 2 2
[1] FALSE
D66V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED     7   3
  DEL PEAK  4(2Q22.1) WILD-TYPE 358 131
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      7    3
  DEL PEAK  4(2Q22.1) WILD-TYPE  358  131
        clus
vv       DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  FEMALE                           7                           358
  MALE                             3                           131
[1] 2 2
[1] FALSE
D66V8, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED     2   7
  DEL PEAK  4(2Q22.1) WILD-TYPE 183 283
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      2    7
  DEL PEAK  4(2Q22.1) WILD-TYPE  183  283
     clus
vv    DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  NO                            2                           183
  YES                           7                           283
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  DEL PEAK  4(2Q22.1) MUTATED                0
  DEL PEAK  4(2Q22.1) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK  4(2Q22.1) MUTATED                                               3
  DEL PEAK  4(2Q22.1) WILD-TYPE                                           352
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK  4(2Q22.1) MUTATED                                                                        7
  DEL PEAK  4(2Q22.1) WILD-TYPE                                                                     93
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK  4(2Q22.1) MUTATED                                                                     0
  DEL PEAK  4(2Q22.1) WILD-TYPE                                                                  36
D66V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK  4(2Q22.1) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           7
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       DEL PEAK  4(2Q22.1) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            93
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V10, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED     9   0
  DEL PEAK  4(2Q22.1) WILD-TYPE 411  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      9    0
  DEL PEAK  4(2Q22.1) WILD-TYPE  411   17
     clus
vv    DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  NO                            9                           411
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK  4(2Q22.1) MUTATED              0                       0   10
  DEL PEAK  4(2Q22.1) WILD-TYPE          132                      18  320
                               vv
clus                            VERY ADVANCED (T4B)
  DEL PEAK  4(2Q22.1) MUTATED                     0
  DEL PEAK  4(2Q22.1) WILD-TYPE                   1
D66V11, multiclass
                         clus
vv                        DEL PEAK  4(2Q22.1) MUTATED
  MINIMAL (T3)                                      0
  MODERATE/ADVANCED (T4A)                           0
  NONE                                             10
  VERY ADVANCED (T4B)                               0
                         clus
vv                        DEL PEAK  4(2Q22.1) WILD-TYPE
  MINIMAL (T3)                                      132
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              320
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  4(2Q22.1) MUTATED     9   0   0   1
  DEL PEAK  4(2Q22.1) WILD-TYPE 374  51   4  29
D66V12, multiclass
    clus
vv   DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  R0                           9                           374
  R1                           0                            51
  R2                           0                             4
  RX                           1                            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"
D66V13, continuous
D66V14, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED     5   5
  DEL PEAK  4(2Q22.1) WILD-TYPE 220 259
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      5    5
  DEL PEAK  4(2Q22.1) WILD-TYPE  220  259
            clus
vv           DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  MULTIFOCAL                           5                           220
  UNIFOCAL                             5                           259
[1] 2 2
[1] FALSE
D66V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  4(2Q22.1) MUTATED                                  0     0
  DEL PEAK  4(2Q22.1) WILD-TYPE                                1    52
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q22.1) MUTATED                           0     4
  DEL PEAK  4(2Q22.1) WILD-TYPE                        27   324
D66V16, multiclass
                                  clus
vv                                 DEL PEAK  4(2Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      4
                                  clus
vv                                 DEL PEAK  4(2Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       52
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V17, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED     0   4
  DEL PEAK  4(2Q22.1) WILD-TYPE  38 355
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      0    4
  DEL PEAK  4(2Q22.1) WILD-TYPE   38  355
                        clus
vv                       DEL PEAK  4(2Q22.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           4
                        clus
vv                       DEL PEAK  4(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           355
[1] 2 2
[1] FALSE

Clustering(67) Variable = DEL PEAK  5(2Q37.3) MUTATION ANALYSIS
D67V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(2Q37.3) MUTATED    12   1
  DEL PEAK  5(2Q37.3) WILD-TYPE 469  15
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           13                           484 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                            1                            15 
$`DEL PEAK  5(2Q37.3) MUTATED`
TCGA-BJ-A190 TCGA-BJ-A192 TCGA-DJ-A2Q0 TCGA-DJ-A2Q5 TCGA-EL-A3H2 TCGA-EM-A1YE 
       20.58        44.35        34.36        37.48        33.50        54.08 
TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A39N 
       10.65         6.05        32.32         9.24        13.51       123.32 
TCGA-FY-A3I5 
        7.82 

$`DEL PEAK  5(2Q37.3) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A28R 
       15.12        42.08        51.39        41.52         4.83        42.15 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04        35.54        32.45        11.31        30.97        11.08 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       30.21        22.88        18.38        16.57        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        7.99        10.88        21.01         3.45        23.84        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
       15.45        21.63        23.18        19.43        23.47        12.66 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
       12.43        12.66        35.84        21.63        50.17        37.64 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M 
       25.12        14.70        14.27         2.76         9.96        48.79 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       38.17       169.32        18.58         8.71        56.19        23.38 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       43.17        52.37         8.32        11.01       135.91        30.61 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       44.98        42.51        14.96        17.59         6.02        42.58 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
       47.41        17.56        10.09         7.82        30.58        35.41 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       27.45        26.20        38.83        33.96        31.99        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
       28.96         8.78         8.42        37.74         6.77        40.24 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
       33.93        36.46        35.11        39.09        35.90        33.53 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       35.18        15.88        36.92        31.04        32.42        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU 
       16.41        19.56        36.33        32.81        36.33        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       59.57        11.34        35.87        40.96        36.99        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        42.54        19.20        23.21        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       24.82        22.92        21.01        18.97         7.76        35.67 
TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        3.12        36.43        24.76        17.23        27.62        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       21.34        33.04        34.78        27.06        26.93        35.54 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        35.38        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       92.55        47.21        66.38        80.52        63.19        52.44 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       39.95        31.23        35.67        31.27        29.98        31.50 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 
       31.04         0.72         0.26         3.02        25.45        30.61 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
        0.16         0.23        14.96         7.69        33.50         0.39 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
        0.39        31.66        26.73       155.54        97.74       158.83 
TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
        7.66        45.53        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 
      106.62         4.18        79.50       139.86        98.53        69.57 
TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR 
       57.11       108.36        64.87        49.51        50.24       115.10 
TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY 
       65.39       136.01        50.37        50.20       147.75       101.13 
TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
      139.99        49.32        43.36        49.71        83.57       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 
      150.48       108.66        57.63        17.52        52.50        29.65 
TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
      147.42       142.52       129.57        32.48       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       41.29       107.47         5.72        66.90        82.82        89.56 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO 
       78.97        51.78        62.30        36.03        53.06        47.38 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       65.49        61.22        60.16         7.07        59.44        57.47 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       34.72        45.96        37.94        31.04        34.39        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       53.36        44.15        41.13        47.84        43.59        24.30 
TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       27.06        23.90        26.86        18.18        20.91        48.49 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I 
       18.05        19.79        19.46        78.61        57.01        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P 
       14.50        15.75        10.45        14.53        44.19        41.29 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP 
       14.24        47.57        17.88        13.18        23.51         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       33.96        17.59        17.46        17.29        14.60        22.52 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
       15.06         7.33         0.49        13.91        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       29.95        29.85        12.79        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        5.33        26.37        26.37        22.45        21.53        60.49 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       24.46        13.68        81.93        81.70        77.56        70.42 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       56.58        60.20        63.39        65.29        18.38        63.45 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       88.41        58.75        37.25        52.60        54.35        83.34 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89       100.57        95.34        94.13        55.10        98.20 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24        50.40        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       77.82        75.42        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       71.08         4.11         1.05        13.28         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON 
      116.09         1.25        20.42        17.82         0.99        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
       13.91        16.27        15.68        16.57        18.08         0.30 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
        0.76        17.06        17.36        15.16         6.58        22.49 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04         1.35        21.60         1.68        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46         2.99        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        18.51        16.90        21.83        31.10         8.22 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
       25.64        17.23        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW 
       27.85        24.69        22.29         5.75         2.47         2.60 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       43.69        18.64        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       33.24        33.40        40.37        21.83         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45        30.21        23.93        12.89 

  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                         6.05                          0.16 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                       123.32                        169.32 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                        32.32                         30.61 
[1] "6.0 - 123.3 (32.3)" "0.2 - 169.3 (30.6)"
[1] "hr=" "3.1"
D67V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK  5(2Q37.3) MUTATED         4        6         2        0         1
  DEL PEAK  5(2Q37.3) WILD-TYPE     278       44       109        2        45
                               vv
clus                            STAGE IVC
  DEL PEAK  5(2Q37.3) MUTATED           0
  DEL PEAK  5(2Q37.3) WILD-TYPE         6
D67V3, multiclass
           clus
vv          DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  STAGE I                             4                           278
  STAGE II                            6                            44
  STAGE III                           2                           109
  STAGE IV                            0                             2
  STAGE IVA                           1                            45
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  5(2Q37.3) MUTATED     2   7   4   0
  DEL PEAK  5(2Q37.3) WILD-TYPE 140 158 163  23
D67V4, multiclass
    clus
vv   DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  T1                           2                           140
  T2                           7                           158
  T3                           4                           163
  T4                           0                            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"
D67V5, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.3) MUTATED     8   1
  DEL PEAK  5(2Q37.3) WILD-TYPE 217 223
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED      8    1
  DEL PEAK  5(2Q37.3) WILD-TYPE  217  223
   clus
vv  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  0                           8                           217
  1                           1                           223
[1] 2 2
[1] FALSE
D67V6, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.3) MUTATED     3   0
  DEL PEAK  5(2Q37.3) WILD-TYPE 275   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED      3    0
  DEL PEAK  5(2Q37.3) WILD-TYPE  275    9
   clus
vv  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  0                           3                           275
  1                           0                             9
[1] 2 2
[1] FALSE
D67V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.3) MUTATED     8   5
  DEL PEAK  5(2Q37.3) WILD-TYPE 357 129
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED      8    5
  DEL PEAK  5(2Q37.3) WILD-TYPE  357  129
        clus
vv       DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  FEMALE                           8                           357
  MALE                             5                           129
[1] 2 2
[1] FALSE
D67V8, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.3) MUTATED     3   9
  DEL PEAK  5(2Q37.3) WILD-TYPE 182 281
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED      3    9
  DEL PEAK  5(2Q37.3) WILD-TYPE  182  281
     clus
vv    DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  NO                            3                           182
  YES                           9                           281
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  DEL PEAK  5(2Q37.3) MUTATED                0
  DEL PEAK  5(2Q37.3) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK  5(2Q37.3) MUTATED                                               6
  DEL PEAK  5(2Q37.3) WILD-TYPE                                           349
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK  5(2Q37.3) MUTATED                                                                        7
  DEL PEAK  5(2Q37.3) WILD-TYPE                                                                     93
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK  5(2Q37.3) MUTATED                                                                     0
  DEL PEAK  5(2Q37.3) WILD-TYPE                                                                  36
D67V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK  5(2Q37.3) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    6
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           7
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       DEL PEAK  5(2Q37.3) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    349
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            93
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V10, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.3) MUTATED    11   1
  DEL PEAK  5(2Q37.3) WILD-TYPE 409  16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED     11    1
  DEL PEAK  5(2Q37.3) WILD-TYPE  409   16
     clus
vv    DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  NO                           11                           409
  YES                           1                            16
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK  5(2Q37.3) MUTATED              1                       0   12
  DEL PEAK  5(2Q37.3) WILD-TYPE          131                      18  318
                               vv
clus                            VERY ADVANCED (T4B)
  DEL PEAK  5(2Q37.3) MUTATED                     0
  DEL PEAK  5(2Q37.3) WILD-TYPE                   1
D67V11, multiclass
                         clus
vv                        DEL PEAK  5(2Q37.3) MUTATED
  MINIMAL (T3)                                      1
  MODERATE/ADVANCED (T4A)                           0
  NONE                                             12
  VERY ADVANCED (T4B)                               0
                         clus
vv                        DEL PEAK  5(2Q37.3) WILD-TYPE
  MINIMAL (T3)                                      131
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              318
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  5(2Q37.3) MUTATED    11   0   0   2
  DEL PEAK  5(2Q37.3) WILD-TYPE 372  51   4  28
D67V12, multiclass
    clus
vv   DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  R0                          11                           372
  R1                           0                            51
  R2                           0                             4
  RX                           2                            28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V13, continuous
D67V14, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.3) MUTATED     5   8
  DEL PEAK  5(2Q37.3) WILD-TYPE 220 256
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED      5    8
  DEL PEAK  5(2Q37.3) WILD-TYPE  220  256
            clus
vv           DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  MULTIFOCAL                           5                           220
  UNIFOCAL                             8                           256
[1] 2 2
[1] FALSE
D67V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  5(2Q37.3) MUTATED                                  0     0
  DEL PEAK  5(2Q37.3) WILD-TYPE                                1    52
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(2Q37.3) MUTATED                           0     7
  DEL PEAK  5(2Q37.3) WILD-TYPE                        27   321
D67V16, multiclass
                                  clus
vv                                 DEL PEAK  5(2Q37.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      7
                                  clus
vv                                 DEL PEAK  5(2Q37.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       52
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      321
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V17, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.3) MUTATED     0   6
  DEL PEAK  5(2Q37.3) WILD-TYPE  38 353
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED      0    6
  DEL PEAK  5(2Q37.3) WILD-TYPE   38  353
                        clus
vv                       DEL PEAK  5(2Q37.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           6
                        clus
vv                       DEL PEAK  5(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           353
[1] 2 2
[1] FALSE

Clustering(68) Variable = DEL PEAK  7(4Q34.3) MUTATION ANALYSIS
D68V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(4Q34.3) MUTATED     5   0
  DEL PEAK  7(4Q34.3) WILD-TYPE 476  16
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                            5                           492 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                            0                            16 
$`DEL PEAK  7(4Q34.3) MUTATED`
TCGA-BJ-A190 TCGA-E8-A414 TCGA-EM-A1YE TCGA-ET-A39N TCGA-FE-A22Z 
       20.58        31.50        54.08       123.32        73.74 

$`DEL PEAK  7(4Q34.3) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        42.08        51.39        41.52         4.83        44.35 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
       42.15        21.04        35.54        32.45        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.08        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       31.27        29.98        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       47.84        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       78.61        57.01        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       14.53        10.65        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
       17.88        13.18        23.51         6.05         2.99        12.30 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       48.46        13.15        22.16        40.34        19.73        32.32 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       33.96        17.59        17.46        17.29        14.60        22.52 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.06         7.33         0.49         9.24        13.91        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.86        29.95        29.85        13.51        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      107.41       108.46        84.89       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        98.20        28.24        50.40        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.79        87.62        77.82        75.42        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       62.83       166.62        24.72        43.99        46.26        44.38 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A230 TCGA-FE-A231 
       40.21        37.48        33.17        31.40        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        13.28         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 
       48.10       116.09         1.25        20.42        17.82         7.82 
TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
        0.99        19.56        13.91        16.27        15.68        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       18.08         0.30         0.76        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58        22.49        19.04         1.35        21.60         1.68 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46         2.99        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        18.51        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
       31.10         8.22        25.64        17.23        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
      113.85        26.70        43.69        18.64        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       84.72        35.28        33.24        33.40        40.37        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        9.50        36.10        32.45        30.21        23.93        12.89 

  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                        20.58                          0.16 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                       123.32                        169.32 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                       54.080                        30.595 
[1] "20.6 - 123.3 (54.1)" "0.2 - 169.3 (30.6)" 
[1] "hr="     "9200000"
D68V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK  7(4Q34.3) MUTATED         1        2         1        0         1
  DEL PEAK  7(4Q34.3) WILD-TYPE     281       48       110        2        45
                               vv
clus                            STAGE IVC
  DEL PEAK  7(4Q34.3) MUTATED           0
  DEL PEAK  7(4Q34.3) WILD-TYPE         6
D68V3, multiclass
           clus
vv          DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  STAGE I                             1                           281
  STAGE II                            2                            48
  STAGE III                           1                           110
  STAGE IV                            0                             2
  STAGE IVA                           1                            45
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  7(4Q34.3) MUTATED     0   2   2   1
  DEL PEAK  7(4Q34.3) WILD-TYPE 142 163 165  22
D68V4, multiclass
    clus
vv   DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  T1                           0                           142
  T2                           2                           163
  T3                           2                           165
  T4                           1                            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"
D68V5, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q34.3) MUTATED     3   1
  DEL PEAK  7(4Q34.3) WILD-TYPE 222 223
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED      3    1
  DEL PEAK  7(4Q34.3) WILD-TYPE  222  223
   clus
vv  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  0                           3                           222
  1                           1                           223
[1] 2 2
[1] FALSE
D68V6, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q34.3) MUTATED     1   0
  DEL PEAK  7(4Q34.3) WILD-TYPE 277   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED      1    0
  DEL PEAK  7(4Q34.3) WILD-TYPE  277    9
   clus
vv  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  0                           1                           277
  1                           0                             9
[1] 2 2
[1] FALSE
D68V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q34.3) MUTATED     4   1
  DEL PEAK  7(4Q34.3) WILD-TYPE 361 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED      4    1
  DEL PEAK  7(4Q34.3) WILD-TYPE  361  133
        clus
vv       DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  FEMALE                           4                           361
  MALE                             1                           133
[1] 2 2
[1] FALSE
D68V8, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q34.3) MUTATED     2   3
  DEL PEAK  7(4Q34.3) WILD-TYPE 183 287
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED      2    3
  DEL PEAK  7(4Q34.3) WILD-TYPE  183  287
     clus
vv    DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  NO                            2                           183
  YES                           3                           287
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  DEL PEAK  7(4Q34.3) MUTATED                0
  DEL PEAK  7(4Q34.3) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK  7(4Q34.3) MUTATED                                               3
  DEL PEAK  7(4Q34.3) WILD-TYPE                                           352
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK  7(4Q34.3) MUTATED                                                                        2
  DEL PEAK  7(4Q34.3) WILD-TYPE                                                                     98
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK  7(4Q34.3) MUTATED                                                                     0
  DEL PEAK  7(4Q34.3) WILD-TYPE                                                                  36
D68V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK  7(4Q34.3) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       DEL PEAK  7(4Q34.3) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V10, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q34.3) MUTATED     5   0
  DEL PEAK  7(4Q34.3) WILD-TYPE 415  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED      5    0
  DEL PEAK  7(4Q34.3) WILD-TYPE  415   17
     clus
vv    DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  NO                            5                           415
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK  7(4Q34.3) MUTATED              0                       1    4
  DEL PEAK  7(4Q34.3) WILD-TYPE          132                      17  326
                               vv
clus                            VERY ADVANCED (T4B)
  DEL PEAK  7(4Q34.3) MUTATED                     0
  DEL PEAK  7(4Q34.3) WILD-TYPE                   1
D68V11, multiclass
                         clus
vv                        DEL PEAK  7(4Q34.3) MUTATED
  MINIMAL (T3)                                      0
  MODERATE/ADVANCED (T4A)                           1
  NONE                                              4
  VERY ADVANCED (T4B)                               0
                         clus
vv                        DEL PEAK  7(4Q34.3) WILD-TYPE
  MINIMAL (T3)                                      132
  MODERATE/ADVANCED (T4A)                            17
  NONE                                              326
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  7(4Q34.3) MUTATED     5   0   0   0
  DEL PEAK  7(4Q34.3) WILD-TYPE 378  51   4  30
D68V12, multiclass
    clus
vv   DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  R0                           5                           378
  R1                           0                            51
  R2                           0                             4
  RX                           0                            30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V13, continuous
D68V14, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q34.3) MUTATED     1   4
  DEL PEAK  7(4Q34.3) WILD-TYPE 224 260
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED      1    4
  DEL PEAK  7(4Q34.3) WILD-TYPE  224  260
            clus
vv           DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  MULTIFOCAL                           1                           224
  UNIFOCAL                             4                           260
[1] 2 2
[1] FALSE
D68V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  7(4Q34.3) MUTATED                                  0     1
  DEL PEAK  7(4Q34.3) WILD-TYPE                                1    51
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(4Q34.3) MUTATED                           0     3
  DEL PEAK  7(4Q34.3) WILD-TYPE                        27   325
D68V16, multiclass
                                  clus
vv                                 DEL PEAK  7(4Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      3
                                  clus
vv                                 DEL PEAK  7(4Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       51
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V17, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q34.3) MUTATED     0   4
  DEL PEAK  7(4Q34.3) WILD-TYPE  38 355
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED      0    4
  DEL PEAK  7(4Q34.3) WILD-TYPE   38  355
                        clus
vv                       DEL PEAK  7(4Q34.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           4
                        clus
vv                       DEL PEAK  7(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           355
[1] 2 2
[1] FALSE

Clustering(69) Variable = DEL PEAK  8(5P15.2) MUTATION ANALYSIS
D69V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(5P15.2) MUTATED     4   0
  DEL PEAK  8(5P15.2) WILD-TYPE 477  16
  DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE 
                            4                           493 
  DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE 
                            0                            16 
$`DEL PEAK  8(5P15.2) MUTATED`
TCGA-BJ-A4O9 TCGA-DE-A4MB TCGA-DJ-A3V2 TCGA-L6-A4EU 
       23.47        11.57        20.22         9.50 

$`DEL PEAK  8(5P15.2) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MC 
       37.64        15.85        18.54        18.84        30.12        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M 
       25.12        14.70        14.27         2.76         9.96        48.79 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       38.17       169.32        18.58         8.71        56.19        23.38 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       43.17        52.37         8.32        11.01       135.91        30.61 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       44.98        42.51        14.96        17.59         6.02        42.58 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
       47.41        17.56        10.09         7.82        30.58        35.41 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       27.45        26.20        38.83        33.96        31.99        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       28.96         8.78         8.42        34.36        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24        33.93        37.48        36.46        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        33.53        35.18        15.88        36.92        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       32.42        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        17.69        59.57        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        30.61        42.54        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM 
       35.67         3.12        36.43        24.76        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       30.87        21.34        33.04        34.78        27.06        26.93 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       35.54         3.12        15.81        35.38        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        92.55        47.21        66.38        80.52        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 
       52.44        39.95        31.23        35.67        31.27        29.98 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 
       31.50        31.04         0.72         0.26         3.02        25.45 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       30.61         0.16         0.23        14.96         7.69        33.50 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
        0.39         0.39        31.66        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      158.83         7.66        45.53        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 
       57.01       106.62         4.18        79.50       139.86        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       69.57        57.11       108.36        64.87        49.51        50.24 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
      115.10        65.39       136.01        50.37        50.20       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       83.57       139.00       150.48       108.66        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       52.50        29.65       147.42       142.52       129.57        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      132.07        98.24        41.29       107.47         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM 
       82.82        89.56        78.97        51.78        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        65.49        61.22        60.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       34.39        30.51        53.36        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       43.59        24.30        27.06        23.90        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        48.49        18.05        19.79        19.46        78.61 
TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       57.01        54.08        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       14.53        10.65        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
       17.88        13.18        23.51         6.05         2.99        12.30 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       48.46        13.15        22.16        40.34        19.73        32.32 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       33.96        17.59        17.46        17.29        14.60        22.52 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.06         7.33         0.49         9.24        13.91        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.86        29.95        29.85        13.51        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
      107.41       108.46        84.89       123.32       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       94.13        55.10        98.20        28.24        50.40        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
       76.64         5.79        87.62        77.82        75.42        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
       52.47       116.78        94.59        84.85        80.58        66.84 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       43.73        62.83       166.62        24.72        43.99        46.26 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
       44.38        40.21        37.48        33.17        31.40        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       71.44        31.59        79.69        24.69        68.22       117.40 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77       112.80        39.95        33.63        81.83       106.36 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD 
       85.15        85.68        78.77        71.08         4.11         1.05 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       13.28         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       17.82         7.82         0.99        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83        31.10         8.22        25.64        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       40.37        21.83        36.10        32.45        30.21        23.93 
TCGA-QD-A8IV 
       12.89 

  DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE 
                         9.50                          0.16 
  DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE 
                        23.47                        169.32 
  DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE 
                       15.895                        30.870 
[1] "9.5 - 23.5 (15.9)"  "0.2 - 169.3 (30.9)"
[1] "hr="     "1200000"
D69V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK  8(5P15.2) MUTATED         1        1         1        0         1
  DEL PEAK  8(5P15.2) WILD-TYPE     281       49       110        2        45
                               vv
clus                            STAGE IVC
  DEL PEAK  8(5P15.2) MUTATED           0
  DEL PEAK  8(5P15.2) WILD-TYPE         6
D69V3, multiclass
           clus
vv          DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE
  STAGE I                             1                           281
  STAGE II                            1                            49
  STAGE III                           1                           110
  STAGE IV                            0                             2
  STAGE IVA                           1                            45
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  8(5P15.2) MUTATED     0   2   2   0
  DEL PEAK  8(5P15.2) WILD-TYPE 142 163 165  23
D69V4, multiclass
    clus
vv   DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE
  T1                           0                           142
  T2                           2                           163
  T3                           2                           165
  T4                           0                            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"
D69V5, binary
                               cls
clus                              0   1
  DEL PEAK  8(5P15.2) MUTATED     1   3
  DEL PEAK  8(5P15.2) WILD-TYPE 224 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5P15.2) MUTATED      1    3
  DEL PEAK  8(5P15.2) WILD-TYPE  224  221
   clus
vv  DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE
  0                           1                           224
  1                           3                           221
[1] 2 2
[1] FALSE
D69V6, binary
                               cls
clus                              0   1
  DEL PEAK  8(5P15.2) MUTATED     4   0
  DEL PEAK  8(5P15.2) WILD-TYPE 274   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5P15.2) MUTATED      4    0
  DEL PEAK  8(5P15.2) WILD-TYPE  274    9
   clus
vv  DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE
  0                           4                           274
  1                           0                             9
[1] 2 2
[1] FALSE
D69V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(5P15.2) MUTATED     4   0
  DEL PEAK  8(5P15.2) WILD-TYPE 361 134
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5P15.2) MUTATED      4    0
  DEL PEAK  8(5P15.2) WILD-TYPE  361  134
        clus
vv       DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE
  FEMALE                           4                           361
  MALE                             0                           134
[1] 2 2
[1] FALSE
D69V8, binary
                               cls
clus                              0   1
  DEL PEAK  8(5P15.2) MUTATED     2   2
  DEL PEAK  8(5P15.2) WILD-TYPE 183 288
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5P15.2) MUTATED      2    2
  DEL PEAK  8(5P15.2) WILD-TYPE  183  288
     clus
vv    DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE
  NO                            2                           183
  YES                           2                           288
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  DEL PEAK  8(5P15.2) MUTATED                0
  DEL PEAK  8(5P15.2) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK  8(5P15.2) MUTATED                                               2
  DEL PEAK  8(5P15.2) WILD-TYPE                                           353
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK  8(5P15.2) MUTATED                                                                        1
  DEL PEAK  8(5P15.2) WILD-TYPE                                                                     99
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK  8(5P15.2) MUTATED                                                                     1
  DEL PEAK  8(5P15.2) WILD-TYPE                                                                  35
D69V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK  8(5P15.2) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              1
                                                                        clus
vv                                                                       DEL PEAK  8(5P15.2) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            99
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V10, binary
                               cls
clus                              0   1
  DEL PEAK  8(5P15.2) MUTATED     3   0
  DEL PEAK  8(5P15.2) WILD-TYPE 417  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5P15.2) MUTATED      3    0
  DEL PEAK  8(5P15.2) WILD-TYPE  417   17
     clus
vv    DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE
  NO                            3                           417
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK  8(5P15.2) MUTATED              2                       0    2
  DEL PEAK  8(5P15.2) WILD-TYPE          130                      18  328
                               vv
clus                            VERY ADVANCED (T4B)
  DEL PEAK  8(5P15.2) MUTATED                     0
  DEL PEAK  8(5P15.2) WILD-TYPE                   1
D69V11, multiclass
                         clus
vv                        DEL PEAK  8(5P15.2) MUTATED
  MINIMAL (T3)                                      2
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              2
  VERY ADVANCED (T4B)                               0
                         clus
vv                        DEL PEAK  8(5P15.2) WILD-TYPE
  MINIMAL (T3)                                      130
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              328
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  8(5P15.2) MUTATED     1   2   0   0
  DEL PEAK  8(5P15.2) WILD-TYPE 382  49   4  30
D69V12, multiclass
    clus
vv   DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE
  R0                           1                           382
  R1                           2                            49
  R2                           0                             4
  RX                           0                            30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V13, continuous
D69V14, binary
                               cls
clus                              0   1
  DEL PEAK  8(5P15.2) MUTATED     3   1
  DEL PEAK  8(5P15.2) WILD-TYPE 222 263
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5P15.2) MUTATED      3    1
  DEL PEAK  8(5P15.2) WILD-TYPE  222  263
            clus
vv           DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE
  MULTIFOCAL                           3                           222
  UNIFOCAL                             1                           263
[1] 2 2
[1] FALSE
D69V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  8(5P15.2) MUTATED                                  0     0
  DEL PEAK  8(5P15.2) WILD-TYPE                                1    52
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(5P15.2) MUTATED                           1     3
  DEL PEAK  8(5P15.2) WILD-TYPE                        26   325
D69V16, multiclass
                                  clus
vv                                 DEL PEAK  8(5P15.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                      3
                                  clus
vv                                 DEL PEAK  8(5P15.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       52
  BLACK OR AFRICAN AMERICAN                                   26
  WHITE                                                      325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V17, binary
                               cls
clus                              0   1
  DEL PEAK  8(5P15.2) MUTATED     1   3
  DEL PEAK  8(5P15.2) WILD-TYPE  37 356
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5P15.2) MUTATED      1    3
  DEL PEAK  8(5P15.2) WILD-TYPE   37  356
                        clus
vv                       DEL PEAK  8(5P15.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                           3
                        clus
vv                       DEL PEAK  8(5P15.2) WILD-TYPE
  HISPANIC OR LATINO                                37
  NOT HISPANIC OR LATINO                           356
[1] 2 2
[1] FALSE

Clustering(70) Variable = DEL PEAK 11(6Q22.31) MUTATION ANALYSIS
D70V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 11(6Q22.31) MUTATED     4   2
  DEL PEAK 11(6Q22.31) WILD-TYPE 477  14
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                             6                            491 
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                             2                             14 
$`DEL PEAK 11(6Q22.31) MUTATED`
TCGA-EL-A3H2 TCGA-EM-A1YE TCGA-ET-A39N TCGA-ET-A3BV TCGA-FE-A239 TCGA-FY-A3I5 
       33.50        54.08       123.32        75.42        33.63         7.82 

$`DEL PEAK 11(6Q22.31) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
       30.58        35.41        27.45        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74         6.77        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        36.33        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       35.87        40.96        36.99        20.22        30.61        42.54 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20        23.21        21.27        20.48        24.82        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ 
       21.01        18.97         7.76        35.67         3.12        36.43 
TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       24.76        17.23        27.62        30.87        21.34        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        80.52        63.19        52.44        39.95        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04         0.72 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
        0.26         3.02        25.45        30.61         0.16         0.23 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        33.50         0.39         0.39        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS 
       26.73       155.54        97.74       158.83         7.66        45.53 
TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY 
       60.95       157.15        37.94        57.01       106.62         4.18 
TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 
       79.50       139.86        98.53        69.57        57.11       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
       64.87        49.51        50.24       115.10        65.39       136.01 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        50.20       147.75       101.13       139.99        49.32 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       150.48       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        89.56        78.97        51.78 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        47.38        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       60.16         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        47.84        43.59        24.30        27.06        23.90 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.46        78.61        57.01        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       32.32        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       22.52        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33         0.49         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       65.29        18.38        63.45        88.41        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       52.60        54.35        83.34         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
      106.09       107.41       108.46        84.89       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       94.13        55.10        98.20        28.24        50.40        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX 
       76.64         5.79        87.62        77.82        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       62.83       166.62        24.72        43.99        46.26        44.38 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       40.21        37.48        33.17        31.40        73.74        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
      112.80        39.95        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        13.28         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM 
       48.10       116.09         1.25        20.42        17.82         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
        0.30         0.76        17.06        17.36        15.16         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
       22.49        19.04         1.35        21.60         1.68        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46         2.99        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        8.22        25.64        17.23        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
       26.70        43.69        18.64        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       36.10        32.45        30.21        23.93        12.89 

  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                          7.82                           0.16 
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                        123.32                         169.32 
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                        43.855                         30.580 
[1] "7.8 - 123.3 (43.9)" "0.2 - 169.3 (30.6)"
[1] "hr=" "7.2"
D70V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 11(6Q22.31) MUTATED         2        2         3        0         0
  DEL PEAK 11(6Q22.31) WILD-TYPE     280       48       108        2        46
                                vv
clus                             STAGE IVC
  DEL PEAK 11(6Q22.31) MUTATED           0
  DEL PEAK 11(6Q22.31) WILD-TYPE         6
D70V3, multiclass
           clus
vv          DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  STAGE I                              2                            280
  STAGE II                             2                             48
  STAGE III                            3                            108
  STAGE IV                             0                              2
  STAGE IVA                            0                             46
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 11(6Q22.31) MUTATED     1   3   3   0
  DEL PEAK 11(6Q22.31) WILD-TYPE 141 162 164  23
D70V4, multiclass
    clus
vv   DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  T1                            1                            141
  T2                            3                            162
  T3                            3                            164
  T4                            0                             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"
D70V5, binary
                                cls
clus                               0   1
  DEL PEAK 11(6Q22.31) MUTATED     4   1
  DEL PEAK 11(6Q22.31) WILD-TYPE 221 223
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(6Q22.31) MUTATED      4    1
  DEL PEAK 11(6Q22.31) WILD-TYPE  221  223
   clus
vv  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  0                            4                            221
  1                            1                            223
[1] 2 2
[1] FALSE
D70V6, binary
                                cls
clus                               0   1
  DEL PEAK 11(6Q22.31) MUTATED     0   0
  DEL PEAK 11(6Q22.31) WILD-TYPE 278   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(6Q22.31) MUTATED      0    0
  DEL PEAK 11(6Q22.31) WILD-TYPE  278    9
D70V7, binary
                                cls
clus                               0   1
  DEL PEAK 11(6Q22.31) MUTATED     4   3
  DEL PEAK 11(6Q22.31) WILD-TYPE 361 131
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(6Q22.31) MUTATED      4    3
  DEL PEAK 11(6Q22.31) WILD-TYPE  361  131
        clus
vv       DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  FEMALE                            4                            361
  MALE                              3                            131
[1] 2 2
[1] FALSE
D70V8, binary
                                cls
clus                               0   1
  DEL PEAK 11(6Q22.31) MUTATED     0   5
  DEL PEAK 11(6Q22.31) WILD-TYPE 185 285
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(6Q22.31) MUTATED      0    5
  DEL PEAK 11(6Q22.31) WILD-TYPE  185  285
     clus
vv    DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  NO                             0                            185
  YES                            5                            285
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 11(6Q22.31) MUTATED                0
  DEL PEAK 11(6Q22.31) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 11(6Q22.31) MUTATED                                               5
  DEL PEAK 11(6Q22.31) WILD-TYPE                                           350
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 11(6Q22.31) MUTATED                                                                        2
  DEL PEAK 11(6Q22.31) WILD-TYPE                                                                     98
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 11(6Q22.31) MUTATED                                                                     0
  DEL PEAK 11(6Q22.31) WILD-TYPE                                                                  36
D70V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 11(6Q22.31) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     5
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       DEL PEAK 11(6Q22.31) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V10, binary
                                cls
clus                               0   1
  DEL PEAK 11(6Q22.31) MUTATED     5   1
  DEL PEAK 11(6Q22.31) WILD-TYPE 415  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(6Q22.31) MUTATED      5    1
  DEL PEAK 11(6Q22.31) WILD-TYPE  415   16
     clus
vv    DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  NO                             5                            415
  YES                            1                             16
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 11(6Q22.31) MUTATED              0                       0    7
  DEL PEAK 11(6Q22.31) WILD-TYPE          132                      18  323
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 11(6Q22.31) MUTATED                     0
  DEL PEAK 11(6Q22.31) WILD-TYPE                   1
D70V11, multiclass
                         clus
vv                        DEL PEAK 11(6Q22.31) MUTATED
  MINIMAL (T3)                                       0
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               7
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK 11(6Q22.31) WILD-TYPE
  MINIMAL (T3)                                       132
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               323
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 11(6Q22.31) MUTATED     6   1   0   0
  DEL PEAK 11(6Q22.31) WILD-TYPE 377  50   4  30
D70V12, multiclass
    clus
vv   DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  R0                            6                            377
  R1                            1                             50
  R2                            0                              4
  RX                            0                             30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V13, continuous
D70V14, binary
                                cls
clus                               0   1
  DEL PEAK 11(6Q22.31) MUTATED     2   5
  DEL PEAK 11(6Q22.31) WILD-TYPE 223 259
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(6Q22.31) MUTATED      2    5
  DEL PEAK 11(6Q22.31) WILD-TYPE  223  259
            clus
vv           DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  MULTIFOCAL                            2                            223
  UNIFOCAL                              5                            259
[1] 2 2
[1] FALSE
D70V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 11(6Q22.31) MUTATED                                  0     0
  DEL PEAK 11(6Q22.31) WILD-TYPE                                1    52
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(6Q22.31) MUTATED                           0     6
  DEL PEAK 11(6Q22.31) WILD-TYPE                        27   322
D70V16, multiclass
                                  clus
vv                                 DEL PEAK 11(6Q22.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       6
                                  clus
vv                                 DEL PEAK 11(6Q22.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        52
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       322
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V17, binary
                                cls
clus                               0   1
  DEL PEAK 11(6Q22.31) MUTATED     0   6
  DEL PEAK 11(6Q22.31) WILD-TYPE  38 353
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(6Q22.31) MUTATED      0    6
  DEL PEAK 11(6Q22.31) WILD-TYPE   38  353
                        clus
vv                       DEL PEAK 11(6Q22.31) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            6
                        clus
vv                       DEL PEAK 11(6Q22.31) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            353
[1] 2 2
[1] FALSE

Clustering(71) Variable = DEL PEAK 13(7Q34) MUTATION ANALYSIS
D71V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 13(7Q34) MUTATED     4   0
  DEL PEAK 13(7Q34) WILD-TYPE 477  16
  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE 
                          4                         493 
  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE 
                          0                          16 
$`DEL PEAK 13(7Q34) MUTATED`
TCGA-DJ-A2Q8 TCGA-DJ-A3VM TCGA-ET-A2MX TCGA-FY-A40N 
       39.09        27.62        88.41        19.04 

$`DEL PEAK 13(7Q34) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
       30.58        35.41        27.45        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74         6.77        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       35.11        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       17.23        30.87        21.34        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        52.44        39.95        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       47.84        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       78.61        57.01        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       32.32        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       22.52        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33         0.49         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
       38.66        38.86        29.95        29.85        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       84.59        29.33        21.34         5.33        26.37        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       22.45        21.53        60.49        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       81.70        77.56        70.42        56.58        60.20        63.39 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       65.29        18.38        63.45        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
      107.41       108.46        84.89       123.32       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       94.13        55.10        98.20        28.24        50.40        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
       76.64         5.79        87.62        77.82        75.42        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
       52.47       116.78        94.59        84.85        80.58        66.84 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       43.73        62.83       166.62        24.72        43.99        46.26 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
       44.38        40.21        37.48        33.17        31.40        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       71.44        31.59        79.69        24.69        68.22       117.40 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77       112.80        39.95        33.63        81.83       106.36 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD 
       85.15        85.68        78.77        71.08         4.11         1.05 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       13.28         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       17.82         7.82         0.99        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A4B3 TCGA-FY-A4B4 
       17.36        15.16         6.58        22.49         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83        31.10         8.22        25.64        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        23.93 
TCGA-QD-A8IV 
       12.89 

  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE 
                      19.04                        0.16 
  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE 
                      88.41                      169.32 
  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE 
                     33.355                      30.610 
[1] "19.0 - 88.4 (33.4)" "0.2 - 169.3 (30.6)"
[1] "hr="     "3300000"
D71V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 13(7Q34) MUTATED         3        1         0        0         0
  DEL PEAK 13(7Q34) WILD-TYPE     279       49       111        2        46
                             vv
clus                          STAGE IVC
  DEL PEAK 13(7Q34) MUTATED           0
  DEL PEAK 13(7Q34) WILD-TYPE         6
D71V3, multiclass
           clus
vv          DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  STAGE I                           3                         279
  STAGE II                          1                          49
  STAGE III                         0                         111
  STAGE IV                          0                           2
  STAGE IVA                         0                          46
  STAGE IVC                         0                           6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK 13(7Q34) MUTATED     2   2   0   0
  DEL PEAK 13(7Q34) WILD-TYPE 140 163 167  23
D71V4, multiclass
    clus
vv   DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  T1                         2                         140
  T2                         2                         163
  T3                         0                         167
  T4                         0                          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"
D71V5, binary
                             cls
clus                            0   1
  DEL PEAK 13(7Q34) MUTATED     3   1
  DEL PEAK 13(7Q34) WILD-TYPE 222 223
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED      3    1
  DEL PEAK 13(7Q34) WILD-TYPE  222  223
   clus
vv  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  0                         3                         222
  1                         1                         223
[1] 2 2
[1] FALSE
D71V6, binary
                             cls
clus                            0   1
  DEL PEAK 13(7Q34) MUTATED     2   0
  DEL PEAK 13(7Q34) WILD-TYPE 276   9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED      2    0
  DEL PEAK 13(7Q34) WILD-TYPE  276    9
   clus
vv  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  0                         2                         276
  1                         0                           9
[1] 2 2
[1] FALSE
D71V7, binary
                             cls
clus                            0   1
  DEL PEAK 13(7Q34) MUTATED     3   1
  DEL PEAK 13(7Q34) WILD-TYPE 362 133
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED      3    1
  DEL PEAK 13(7Q34) WILD-TYPE  362  133
        clus
vv       DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  FEMALE                         3                         362
  MALE                           1                         133
[1] 2 2
[1] FALSE
D71V8, binary
                             cls
clus                            0   1
  DEL PEAK 13(7Q34) MUTATED     2   2
  DEL PEAK 13(7Q34) WILD-TYPE 183 288
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED      2    2
  DEL PEAK 13(7Q34) WILD-TYPE  183  288
     clus
vv    DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  NO                          2                         183
  YES                         2                         288
[1] 2 2
[1] FALSE
                             vv
clus                          OTHER  SPECIFY
  DEL PEAK 13(7Q34) MUTATED                0
  DEL PEAK 13(7Q34) WILD-TYPE              8
                             vv
clus                          THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 13(7Q34) MUTATED                                               1
  DEL PEAK 13(7Q34) WILD-TYPE                                           354
                             vv
clus                          THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 13(7Q34) MUTATED                                                                        2
  DEL PEAK 13(7Q34) WILD-TYPE                                                                     98
                             vv
clus                          THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 13(7Q34) MUTATED                                                                     1
  DEL PEAK 13(7Q34) WILD-TYPE                                                                  35
D71V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 13(7Q34) MUTATED
  OTHER  SPECIFY                                                                                 0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  1
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                         2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                            1
                                                                        clus
vv                                                                       DEL PEAK 13(7Q34) WILD-TYPE
  OTHER  SPECIFY                                                                                   8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  354
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                             35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V10, binary
                             cls
clus                            0   1
  DEL PEAK 13(7Q34) MUTATED     3   0
  DEL PEAK 13(7Q34) WILD-TYPE 417  17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED      3    0
  DEL PEAK 13(7Q34) WILD-TYPE  417   17
     clus
vv    DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  NO                          3                         417
  YES                         0                          17
[1] 2 2
[1] FALSE
                             vv
clus                          MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 13(7Q34) MUTATED              0                       0    4
  DEL PEAK 13(7Q34) WILD-TYPE          132                      18  326
                             vv
clus                          VERY ADVANCED (T4B)
  DEL PEAK 13(7Q34) MUTATED                     0
  DEL PEAK 13(7Q34) WILD-TYPE                   1
D71V11, multiclass
                         clus
vv                        DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  MINIMAL (T3)                                    0                         132
  MODERATE/ADVANCED (T4A)                         0                          18
  NONE                                            4                         326
  VERY ADVANCED (T4B)                             0                           1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 13(7Q34) MUTATED     4   0   0   0
  DEL PEAK 13(7Q34) WILD-TYPE 379  51   4  30
D71V12, multiclass
    clus
vv   DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  R0                         4                         379
  R1                         0                          51
  R2                         0                           4
  RX                         0                          30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V13, continuous
D71V14, binary
                             cls
clus                            0   1
  DEL PEAK 13(7Q34) MUTATED     1   3
  DEL PEAK 13(7Q34) WILD-TYPE 224 261
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED      1    3
  DEL PEAK 13(7Q34) WILD-TYPE  224  261
            clus
vv           DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  MULTIFOCAL                         1                         224
  UNIFOCAL                           3                         261
[1] 2 2
[1] FALSE
D71V15, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(7Q34) MUTATED                                  0     0
  DEL PEAK 13(7Q34) WILD-TYPE                                1    52
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(7Q34) MUTATED                           0     3
  DEL PEAK 13(7Q34) WILD-TYPE                        27   325
D71V16, multiclass
                                  clus
vv                                 DEL PEAK 13(7Q34) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                0
  WHITE                                                    3
                                  clus
vv                                 DEL PEAK 13(7Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     52
  BLACK OR AFRICAN AMERICAN                                 27
  WHITE                                                    325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V17, binary
                             cls
clus                            0   1
  DEL PEAK 13(7Q34) MUTATED     0   4
  DEL PEAK 13(7Q34) WILD-TYPE  38 355
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED      0    4
  DEL PEAK 13(7Q34) WILD-TYPE   38  355
                        clus
vv                       DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  HISPANIC OR LATINO                             0                          38
  NOT HISPANIC OR LATINO                         4                         355
[1] 2 2
[1] FALSE

Clustering(72) Variable = DEL PEAK 14(8P23.2) MUTATION ANALYSIS
D72V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(8P23.2) MUTATED     4   0
  DEL PEAK 14(8P23.2) WILD-TYPE 477  16
  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE 
                            4                           493 
  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE 
                            0                            16 
$`DEL PEAK 14(8P23.2) MUTATED`
TCGA-BJ-A190 TCGA-DJ-A2Q0 TCGA-EM-A3O9 TCGA-EM-A3SY 
       20.58        34.36         9.24        13.51 

$`DEL PEAK 14(8P23.2) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        42.08        51.39        41.52         4.83        44.35 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
       42.15        21.04        35.54        32.45        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.08        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       34.85        28.96         8.78         8.42        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24        33.93        37.48        36.46        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        33.53        35.18        15.88        36.92        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       32.42        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        17.69        59.57        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        42.54        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL 
        7.76        35.67         3.12        36.43        24.76        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        21.34        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        52.44        39.95        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       47.84        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       78.61        57.01        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       32.32        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       22.52        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB 
       14.50        15.06         7.33         0.49        13.91        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       38.86        29.95        29.85        12.79        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
       21.34         5.33        26.37        26.37        22.45        21.53 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       60.49        24.46        13.68        81.93        81.70        77.56 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       70.42        56.58        60.20        63.39        65.29        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       63.45        88.41        58.75        37.25        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       83.34         2.66        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      108.46        84.89       123.32       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        98.20        28.24        50.40        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.79        87.62        77.82        75.42        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       62.83       166.62        24.72        43.99        46.26        44.38 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       40.21        37.48        33.17        31.40        73.74        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
      112.80        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        13.28 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10       116.09         1.25        20.42        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        7.82         0.99        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08         0.30         0.76        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       15.16         6.58        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83        31.10         8.22        25.64        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        23.93 
TCGA-QD-A8IV 
       12.89 

  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE 
                         9.24                          0.16 
  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE 
                        34.36                        169.32 
  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE 
                       17.045                        30.610 
[1] "9.2 - 34.4 (17.0)"  "0.2 - 169.3 (30.6)"
[1] "hr="     "1200000"
D72V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 14(8P23.2) MUTATED         2        2         0        0         0
  DEL PEAK 14(8P23.2) WILD-TYPE     280       48       111        2        46
                               vv
clus                            STAGE IVC
  DEL PEAK 14(8P23.2) MUTATED           0
  DEL PEAK 14(8P23.2) WILD-TYPE         6
D72V3, multiclass
           clus
vv          DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
  STAGE I                             2                           280
  STAGE II                            2                            48
  STAGE III                           0                           111
  STAGE IV                            0                             2
  STAGE IVA                           0                            46
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 14(8P23.2) MUTATED     1   2   1   0
  DEL PEAK 14(8P23.2) WILD-TYPE 141 163 166  23
D72V4, multiclass
    clus
vv   DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
  T1                           1                           141
  T2                           2                           163
  T3                           1                           166
  T4                           0                            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"
D72V5, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.2) MUTATED     3   0
  DEL PEAK 14(8P23.2) WILD-TYPE 222 224
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.2) MUTATED      3    0
  DEL PEAK 14(8P23.2) WILD-TYPE  222  224
   clus
vv  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
  0                           3                           222
  1                           0                           224
[1] 2 2
[1] FALSE
D72V6, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.2) MUTATED     1   0
  DEL PEAK 14(8P23.2) WILD-TYPE 277   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.2) MUTATED      1    0
  DEL PEAK 14(8P23.2) WILD-TYPE  277    9
   clus
vv  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
  0                           1                           277
  1                           0                             9
[1] 2 2
[1] FALSE
D72V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.2) MUTATED     1   3
  DEL PEAK 14(8P23.2) WILD-TYPE 364 131
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.2) MUTATED      1    3
  DEL PEAK 14(8P23.2) WILD-TYPE  364  131
        clus
vv       DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
  FEMALE                           1                           364
  MALE                             3                           131
[1] 2 2
[1] FALSE
D72V8, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.2) MUTATED     2   2
  DEL PEAK 14(8P23.2) WILD-TYPE 183 288
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.2) MUTATED      2    2
  DEL PEAK 14(8P23.2) WILD-TYPE  183  288
     clus
vv    DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
  NO                            2                           183
  YES                           2                           288
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  DEL PEAK 14(8P23.2) MUTATED                0
  DEL PEAK 14(8P23.2) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 14(8P23.2) MUTATED                                               2
  DEL PEAK 14(8P23.2) WILD-TYPE                                           353
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 14(8P23.2) MUTATED                                                                        2
  DEL PEAK 14(8P23.2) WILD-TYPE                                                                     98
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 14(8P23.2) MUTATED                                                                     0
  DEL PEAK 14(8P23.2) WILD-TYPE                                                                  36
D72V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 14(8P23.2) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       DEL PEAK 14(8P23.2) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V10, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.2) MUTATED     4   0
  DEL PEAK 14(8P23.2) WILD-TYPE 416  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.2) MUTATED      4    0
  DEL PEAK 14(8P23.2) WILD-TYPE  416   17
     clus
vv    DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
  NO                            4                           416
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 14(8P23.2) MUTATED              0                       0    4
  DEL PEAK 14(8P23.2) WILD-TYPE          132                      18  326
                               vv
clus                            VERY ADVANCED (T4B)
  DEL PEAK 14(8P23.2) MUTATED                     0
  DEL PEAK 14(8P23.2) WILD-TYPE                   1
D72V11, multiclass
                         clus
vv                        DEL PEAK 14(8P23.2) MUTATED
  MINIMAL (T3)                                      0
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              4
  VERY ADVANCED (T4B)                               0
                         clus
vv                        DEL PEAK 14(8P23.2) WILD-TYPE
  MINIMAL (T3)                                      132
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              326
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 14(8P23.2) MUTATED     4   0   0   0
  DEL PEAK 14(8P23.2) WILD-TYPE 379  51   4  30
D72V12, multiclass
    clus
vv   DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
  R0                           4                           379
  R1                           0                            51
  R2                           0                             4
  RX                           0                            30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V13, continuous
D72V14, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.2) MUTATED     2   2
  DEL PEAK 14(8P23.2) WILD-TYPE 223 262
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.2) MUTATED      2    2
  DEL PEAK 14(8P23.2) WILD-TYPE  223  262
            clus
vv           DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
  MULTIFOCAL                           2                           223
  UNIFOCAL                             2                           262
[1] 2 2
[1] FALSE
D72V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 14(8P23.2) MUTATED                                  0     0
  DEL PEAK 14(8P23.2) WILD-TYPE                                1    52
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(8P23.2) MUTATED                           0     2
  DEL PEAK 14(8P23.2) WILD-TYPE                        27   326
D72V16, multiclass
[1] "Remove cluster labels:"      "DEL PEAK 14(8P23.2) MUTATED"
clus
  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE 
                            2                           406 
                   TCGA-4C-A93U                    TCGA-BJ-A0YZ 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A0Z2                    TCGA-BJ-A0Z3 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A0Z5                    TCGA-BJ-A0Z9 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A0ZA                    TCGA-BJ-A0ZB 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A0ZC                    TCGA-BJ-A0ZE 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A0ZG                    TCGA-BJ-A0ZH 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A0ZJ                    TCGA-BJ-A18Y 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A18Z                    TCGA-BJ-A191 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A192                    TCGA-BJ-A28R 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A28S                    TCGA-BJ-A28T 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A28V                    TCGA-BJ-A28W 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A28X                    TCGA-BJ-A28Z 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A290                    TCGA-BJ-A291 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A2N7                    TCGA-BJ-A2N8 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A2N9                    TCGA-BJ-A2NA 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A2P4                    TCGA-BJ-A3EZ 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A3F0                    TCGA-BJ-A3PR 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A3PT                    TCGA-BJ-A3PU 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A45C                    TCGA-BJ-A45D 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A45E                    TCGA-BJ-A45F 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A45G                    TCGA-BJ-A45H 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A45I                    TCGA-BJ-A45J 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A45K                    TCGA-BJ-A4O8 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A4O9                    TCGA-CE-A13K 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-CE-A27D                    TCGA-CE-A3MD 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-CE-A3ME                    TCGA-CE-A481 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-CE-A482                    TCGA-CE-A483 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-CE-A484                    TCGA-CE-A485 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DE-A0XZ                    TCGA-DE-A0Y2 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DE-A0Y3                    TCGA-DE-A2OL 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DE-A3KN                    TCGA-DE-A4M8 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DE-A4M9                    TCGA-DE-A4MA 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DE-A4MB                    TCGA-DE-A4MC 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DE-A4MD                    TCGA-DE-A69J 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DE-A69K                    TCGA-DE-A7U5 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A13L                    TCGA-DJ-A13M 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A13O                    TCGA-DJ-A13P 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A13R                    TCGA-DJ-A13S 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A13T                    TCGA-DJ-A13U 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A13W                    TCGA-DJ-A1QD 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A1QE                    TCGA-DJ-A1QF 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A1QG                    TCGA-DJ-A1QH 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A1QI                    TCGA-DJ-A1QM 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A1QO                    TCGA-DJ-A1QQ 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2PN                    TCGA-DJ-A2PO 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2PQ                    TCGA-DJ-A2PR 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2PS                    TCGA-DJ-A2PT 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2PU                    TCGA-DJ-A2PV 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2PW                    TCGA-DJ-A2PX 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2PY                    TCGA-DJ-A2PZ 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2Q1                    TCGA-DJ-A2Q2 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2Q3                    TCGA-DJ-A2Q4 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2Q5                    TCGA-DJ-A2Q6 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2Q7                    TCGA-DJ-A2Q9 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2QA                    TCGA-DJ-A2QB 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3UK                    TCGA-DJ-A3UM 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3UN                    TCGA-DJ-A3UO 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3UQ                    TCGA-DJ-A3UR 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3US                    TCGA-DJ-A3UT 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3UU                    TCGA-DJ-A3UW 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3UX                    TCGA-DJ-A3UY 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3UZ                    TCGA-DJ-A3V2 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3V3                    TCGA-DJ-A3V4 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3V5                    TCGA-DJ-A3V7 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3V8                    TCGA-DJ-A3V9 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3VD                    TCGA-DJ-A3VE 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3VF                    TCGA-DJ-A3VG 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3VI                    TCGA-DJ-A3VJ 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3VK                    TCGA-DJ-A3VL 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3VM                    TCGA-DJ-A4UL 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A4UP                    TCGA-DJ-A4UQ 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A4UR                    TCGA-DJ-A4UT 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A4UW                    TCGA-DJ-A4V0 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A4V4                    TCGA-DJ-A4V5 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DO-A1JZ                    TCGA-DO-A1K0 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DO-A2HM                    TCGA-E3-A3DY 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-E3-A3DZ                    TCGA-E3-A3E0 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-E3-A3E1                    TCGA-E3-A3E2 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-E3-A3E3                    TCGA-E3-A3E5 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-E8-A242                    TCGA-E8-A2EA 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-E8-A3X7                    TCGA-E8-A413 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-E8-A414                    TCGA-E8-A415 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-E8-A416                    TCGA-E8-A417 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-E8-A418                    TCGA-E8-A419 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-E8-A432                    TCGA-E8-A433 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-E8-A434                    TCGA-E8-A436 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-E8-A437                    TCGA-E8-A438 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-E8-A44K                    TCGA-E8-A44M 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3CL                    TCGA-EL-A3CM 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3CN                    TCGA-EL-A3CO 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3CP                    TCGA-EL-A3CR 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3CS                    TCGA-EL-A3CT 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3CU                    TCGA-EL-A3CV 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3CW                    TCGA-EL-A3CX 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3CY                    TCGA-EL-A3CZ 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3D0                    TCGA-EL-A3D1 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3D4                    TCGA-EL-A3D5 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3D6                    TCGA-EL-A3GO 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3GP                    TCGA-EL-A3GQ 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3GR                    TCGA-EL-A3GS 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3GU                    TCGA-EL-A3GV 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3GW                    TCGA-EL-A3GX 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3GY                    TCGA-EL-A3GZ 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3H1                    TCGA-EL-A3H2 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3H3                    TCGA-EL-A3H4 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3H5                    TCGA-EL-A3H7 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3H8                    TCGA-EL-A3MW 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3MX                    TCGA-EL-A3MY 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3MZ                    TCGA-EL-A3N2 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3N3                    TCGA-EL-A3T0 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3T1                    TCGA-EL-A3T2 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3T3                    TCGA-EL-A3T6 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3T7                    TCGA-EL-A3T8 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3T9                    TCGA-EL-A3TA 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3TB                    TCGA-EL-A3ZG 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3ZH                    TCGA-EL-A3ZK 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3ZL                    TCGA-EL-A3ZN 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3ZO                    TCGA-EL-A3ZP 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3ZQ                    TCGA-EL-A3ZR 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3ZS                    TCGA-EL-A3ZT 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A4JV                    TCGA-EL-A4JW 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A4JX                    TCGA-EL-A4JZ 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A4K0                    TCGA-EL-A4K1 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A4K2                    TCGA-EL-A4K4 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A4K6                    TCGA-EL-A4K7 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A4K9                    TCGA-EL-A4KD 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A4KG                    TCGA-EL-A4KH 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A4KI                    TCGA-EM-A22M 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EM-A22O                    TCGA-EM-A2OV 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EM-A3AI                    TCGA-ET-A25G 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A25I                    TCGA-ET-A25J 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A25K                    TCGA-ET-A25L 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A25M                    TCGA-ET-A25N 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A25O                    TCGA-ET-A25P 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A25R                    TCGA-ET-A2MX 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A2MY                    TCGA-ET-A2MZ 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A2N0                    TCGA-ET-A2N1 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A2N3                    TCGA-ET-A2N4 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A2N5                    TCGA-ET-A39I 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A39J                    TCGA-ET-A39K 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A39M                    TCGA-ET-A39N 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A39O                    TCGA-ET-A39P 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A39R                    TCGA-ET-A39S 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A39T                    TCGA-ET-A3BN 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A3BO                    TCGA-ET-A3BP 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A3BQ                    TCGA-ET-A3BS 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A3BT                    TCGA-ET-A3BU 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A3BV                    TCGA-ET-A3BW 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A3BX                    TCGA-ET-A3DO 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A3DP                    TCGA-ET-A3DQ 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A3DR                    TCGA-ET-A3DS 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A3DT                    TCGA-ET-A3DU 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A3DV                    TCGA-ET-A3DW 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A40P                    TCGA-ET-A40Q 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A40R                    TCGA-ET-A40S 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A40T                    TCGA-ET-A4KN 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A4KQ                    TCGA-FE-A22Z 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FE-A230                    TCGA-FE-A231 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FE-A232                    TCGA-FE-A233 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FE-A234                    TCGA-FE-A235 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FE-A236                    TCGA-FE-A237 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FE-A238                    TCGA-FE-A239 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FE-A23A                    TCGA-FE-A3PA 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FE-A3PB                    TCGA-FE-A3PC 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FE-A3PD                    TCGA-FK-A3S3 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FK-A3SB                    TCGA-FK-A3SD 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FK-A3SE                    TCGA-FK-A3SG 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FK-A3SH                    TCGA-FK-A4UB 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FY-A2QD                    TCGA-FY-A3BL 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FY-A3I4                    TCGA-FY-A3I5 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FY-A3NM                    TCGA-FY-A3ON 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FY-A3R6                    TCGA-FY-A3R7 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FY-A3R8                    TCGA-FY-A3R9 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FY-A3RA                    TCGA-FY-A3W9 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FY-A3WA                    TCGA-FY-A3YR 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FY-A40K                    TCGA-FY-A40L 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FY-A40M                    TCGA-FY-A40N 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FY-A4B0                    TCGA-FY-A4B3 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FY-A4B4                    TCGA-FY-A76V 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-GE-A2C6                    TCGA-H2-A26U 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-H2-A2K9                    TCGA-H2-A3RH 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-H2-A3RI                    TCGA-H2-A421 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-H2-A422                    TCGA-IM-A3EB 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-IM-A3ED                    TCGA-IM-A3U2 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-IM-A3U3                    TCGA-IM-A41Y 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-IM-A41Z                    TCGA-IM-A420 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-IM-A4EB                    TCGA-J8-A3NZ 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-J8-A3O0                    TCGA-J8-A3O1 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-J8-A3O2                    TCGA-J8-A3YD 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-J8-A3YE                    TCGA-J8-A3YF 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-J8-A3YG                    TCGA-J8-A3YH 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-J8-A42S                    TCGA-J8-A4HW 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-J8-A4HY                    TCGA-KS-A41F 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-KS-A41I                    TCGA-KS-A41J 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-KS-A41L                    TCGA-KS-A4I1 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-KS-A4I3                    TCGA-KS-A4I5 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-KS-A4I7                    TCGA-KS-A4I9 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-KS-A4IB                    TCGA-KS-A4IC 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-KS-A4ID                    TCGA-L6-A4EP 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-L6-A4EQ                    TCGA-L6-A4ET 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-L6-A4EU                    TCGA-MK-A4N6 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-MK-A4N7                    TCGA-MK-A4N9 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-MK-A84Z                    TCGA-QD-A8IV 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
D72V17, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.2) MUTATED     0   2
  DEL PEAK 14(8P23.2) WILD-TYPE  38 357
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.2) MUTATED      0    2
  DEL PEAK 14(8P23.2) WILD-TYPE   38  357
                        clus
vv                       DEL PEAK 14(8P23.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           2
                        clus
vv                       DEL PEAK 14(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           357
[1] 2 2
[1] FALSE

Clustering(73) Variable = DEL PEAK 15(8P22) MUTATION ANALYSIS
D73V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 15(8P22) MUTATED     4   0
  DEL PEAK 15(8P22) WILD-TYPE 477  16
  DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE 
                          4                         493 
  DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE 
                          0                          16 
$`DEL PEAK 15(8P22) MUTATED`
TCGA-BJ-A190 TCGA-DJ-A2Q0 TCGA-EM-A3O9 TCGA-EM-A3SY 
       20.58        34.36         9.24        13.51 

$`DEL PEAK 15(8P22) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        42.08        51.39        41.52         4.83        44.35 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
       42.15        21.04        35.54        32.45        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.08        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       34.85        28.96         8.78         8.42        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24        33.93        37.48        36.46        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        33.53        35.18        15.88        36.92        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       32.42        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        17.69        59.57        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        42.54        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL 
        7.76        35.67         3.12        36.43        24.76        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        21.34        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        52.44        39.95        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       47.84        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       78.61        57.01        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       32.32        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       22.52        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB 
       14.50        15.06         7.33         0.49        13.91        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       38.86        29.95        29.85        12.79        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
       21.34         5.33        26.37        26.37        22.45        21.53 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       60.49        24.46        13.68        81.93        81.70        77.56 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       70.42        56.58        60.20        63.39        65.29        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       63.45        88.41        58.75        37.25        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       83.34         2.66        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      108.46        84.89       123.32       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        98.20        28.24        50.40        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.79        87.62        77.82        75.42        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       62.83       166.62        24.72        43.99        46.26        44.38 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       40.21        37.48        33.17        31.40        73.74        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
      112.80        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        13.28 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10       116.09         1.25        20.42        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        7.82         0.99        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08         0.30         0.76        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       15.16         6.58        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83        31.10         8.22        25.64        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        23.93 
TCGA-QD-A8IV 
       12.89 

  DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE 
                       9.24                        0.16 
  DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE 
                      34.36                      169.32 
  DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE 
                     17.045                      30.610 
[1] "9.2 - 34.4 (17.0)"  "0.2 - 169.3 (30.6)"
[1] "hr="     "1200000"
D73V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 15(8P22) MUTATED         2        2         0        0         0
  DEL PEAK 15(8P22) WILD-TYPE     280       48       111        2        46
                             vv
clus                          STAGE IVC
  DEL PEAK 15(8P22) MUTATED           0
  DEL PEAK 15(8P22) WILD-TYPE         6
D73V3, multiclass
           clus
vv          DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE
  STAGE I                           2                         280
  STAGE II                          2                          48
  STAGE III                         0                         111
  STAGE IV                          0                           2
  STAGE IVA                         0                          46
  STAGE IVC                         0                           6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK 15(8P22) MUTATED     1   2   1   0
  DEL PEAK 15(8P22) WILD-TYPE 141 163 166  23
D73V4, multiclass
    clus
vv   DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE
  T1                         1                         141
  T2                         2                         163
  T3                         1                         166
  T4                         0                          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"
D73V5, binary
                             cls
clus                            0   1
  DEL PEAK 15(8P22) MUTATED     3   0
  DEL PEAK 15(8P22) WILD-TYPE 222 224
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(8P22) MUTATED      3    0
  DEL PEAK 15(8P22) WILD-TYPE  222  224
   clus
vv  DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE
  0                         3                         222
  1                         0                         224
[1] 2 2
[1] FALSE
D73V6, binary
                             cls
clus                            0   1
  DEL PEAK 15(8P22) MUTATED     1   0
  DEL PEAK 15(8P22) WILD-TYPE 277   9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(8P22) MUTATED      1    0
  DEL PEAK 15(8P22) WILD-TYPE  277    9
   clus
vv  DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE
  0                         1                         277
  1                         0                           9
[1] 2 2
[1] FALSE
D73V7, binary
                             cls
clus                            0   1
  DEL PEAK 15(8P22) MUTATED     1   3
  DEL PEAK 15(8P22) WILD-TYPE 364 131
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(8P22) MUTATED      1    3
  DEL PEAK 15(8P22) WILD-TYPE  364  131
        clus
vv       DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE
  FEMALE                         1                         364
  MALE                           3                         131
[1] 2 2
[1] FALSE
D73V8, binary
                             cls
clus                            0   1
  DEL PEAK 15(8P22) MUTATED     2   2
  DEL PEAK 15(8P22) WILD-TYPE 183 288
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(8P22) MUTATED      2    2
  DEL PEAK 15(8P22) WILD-TYPE  183  288
     clus
vv    DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE
  NO                          2                         183
  YES                         2                         288
[1] 2 2
[1] FALSE
                             vv
clus                          OTHER  SPECIFY
  DEL PEAK 15(8P22) MUTATED                0
  DEL PEAK 15(8P22) WILD-TYPE              8
                             vv
clus                          THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 15(8P22) MUTATED                                               2
  DEL PEAK 15(8P22) WILD-TYPE                                           353
                             vv
clus                          THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 15(8P22) MUTATED                                                                        2
  DEL PEAK 15(8P22) WILD-TYPE                                                                     98
                             vv
clus                          THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 15(8P22) MUTATED                                                                     0
  DEL PEAK 15(8P22) WILD-TYPE                                                                  36
D73V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 15(8P22) MUTATED
  OTHER  SPECIFY                                                                                 0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                         2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                            0
                                                                        clus
vv                                                                       DEL PEAK 15(8P22) WILD-TYPE
  OTHER  SPECIFY                                                                                   8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                             36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V10, binary
                             cls
clus                            0   1
  DEL PEAK 15(8P22) MUTATED     4   0
  DEL PEAK 15(8P22) WILD-TYPE 416  17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(8P22) MUTATED      4    0
  DEL PEAK 15(8P22) WILD-TYPE  416   17
     clus
vv    DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE
  NO                          4                         416
  YES                         0                          17
[1] 2 2
[1] FALSE
                             vv
clus                          MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 15(8P22) MUTATED              0                       0    4
  DEL PEAK 15(8P22) WILD-TYPE          132                      18  326
                             vv
clus                          VERY ADVANCED (T4B)
  DEL PEAK 15(8P22) MUTATED                     0
  DEL PEAK 15(8P22) WILD-TYPE                   1
D73V11, multiclass
                         clus
vv                        DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE
  MINIMAL (T3)                                    0                         132
  MODERATE/ADVANCED (T4A)                         0                          18
  NONE                                            4                         326
  VERY ADVANCED (T4B)                             0                           1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 15(8P22) MUTATED     4   0   0   0
  DEL PEAK 15(8P22) WILD-TYPE 379  51   4  30
D73V12, multiclass
    clus
vv   DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE
  R0                         4                         379
  R1                         0                          51
  R2                         0                           4
  RX                         0                          30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V13, continuous
D73V14, binary
                             cls
clus                            0   1
  DEL PEAK 15(8P22) MUTATED     2   2
  DEL PEAK 15(8P22) WILD-TYPE 223 262
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(8P22) MUTATED      2    2
  DEL PEAK 15(8P22) WILD-TYPE  223  262
            clus
vv           DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE
  MULTIFOCAL                         2                         223
  UNIFOCAL                           2                         262
[1] 2 2
[1] FALSE
D73V15, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(8P22) MUTATED                                  0     0
  DEL PEAK 15(8P22) WILD-TYPE                                1    52
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(8P22) MUTATED                           0     2
  DEL PEAK 15(8P22) WILD-TYPE                        27   326
D73V16, multiclass
[1] "Remove cluster labels:"    "DEL PEAK 15(8P22) MUTATED"
clus
  DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE 
                          2                         406 
                 TCGA-4C-A93U                  TCGA-BJ-A0YZ 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A0Z2                  TCGA-BJ-A0Z3 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A0Z5                  TCGA-BJ-A0Z9 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A0ZA                  TCGA-BJ-A0ZB 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A0ZC                  TCGA-BJ-A0ZE 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A0ZG                  TCGA-BJ-A0ZH 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A0ZJ                  TCGA-BJ-A18Y 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A18Z                  TCGA-BJ-A191 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A192                  TCGA-BJ-A28R 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A28S                  TCGA-BJ-A28T 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A28V                  TCGA-BJ-A28W 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A28X                  TCGA-BJ-A28Z 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A290                  TCGA-BJ-A291 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A2N7                  TCGA-BJ-A2N8 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A2N9                  TCGA-BJ-A2NA 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A2P4                  TCGA-BJ-A3EZ 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A3F0                  TCGA-BJ-A3PR 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A3PT                  TCGA-BJ-A3PU 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A45C                  TCGA-BJ-A45D 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A45E                  TCGA-BJ-A45F 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A45G                  TCGA-BJ-A45H 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A45I                  TCGA-BJ-A45J 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A45K                  TCGA-BJ-A4O8 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A4O9                  TCGA-CE-A13K 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-CE-A27D                  TCGA-CE-A3MD 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-CE-A3ME                  TCGA-CE-A481 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-CE-A482                  TCGA-CE-A483 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-CE-A484                  TCGA-CE-A485 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DE-A0XZ                  TCGA-DE-A0Y2 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DE-A0Y3                  TCGA-DE-A2OL 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DE-A3KN                  TCGA-DE-A4M8 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DE-A4M9                  TCGA-DE-A4MA 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DE-A4MB                  TCGA-DE-A4MC 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DE-A4MD                  TCGA-DE-A69J 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DE-A69K                  TCGA-DE-A7U5 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A13L                  TCGA-DJ-A13M 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A13O                  TCGA-DJ-A13P 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A13R                  TCGA-DJ-A13S 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A13T                  TCGA-DJ-A13U 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A13W                  TCGA-DJ-A1QD 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A1QE                  TCGA-DJ-A1QF 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A1QG                  TCGA-DJ-A1QH 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A1QI                  TCGA-DJ-A1QM 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A1QO                  TCGA-DJ-A1QQ 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A2PN                  TCGA-DJ-A2PO 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A2PQ                  TCGA-DJ-A2PR 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A2PS                  TCGA-DJ-A2PT 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A2PU                  TCGA-DJ-A2PV 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A2PW                  TCGA-DJ-A2PX 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A2PY                  TCGA-DJ-A2PZ 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A2Q1                  TCGA-DJ-A2Q2 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A2Q3                  TCGA-DJ-A2Q4 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A2Q5                  TCGA-DJ-A2Q6 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A2Q7                  TCGA-DJ-A2Q9 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A2QA                  TCGA-DJ-A2QB 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A3UK                  TCGA-DJ-A3UM 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A3UN                  TCGA-DJ-A3UO 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A3UQ                  TCGA-DJ-A3UR 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A3US                  TCGA-DJ-A3UT 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A3UU                  TCGA-DJ-A3UW 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A3UX                  TCGA-DJ-A3UY 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A3UZ                  TCGA-DJ-A3V2 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A3V3                  TCGA-DJ-A3V4 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A3V5                  TCGA-DJ-A3V7 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A3V8                  TCGA-DJ-A3V9 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A3VD                  TCGA-DJ-A3VE 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A3VF                  TCGA-DJ-A3VG 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A3VI                  TCGA-DJ-A3VJ 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A3VK                  TCGA-DJ-A3VL 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A3VM                  TCGA-DJ-A4UL 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A4UP                  TCGA-DJ-A4UQ 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A4UR                  TCGA-DJ-A4UT 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A4UW                  TCGA-DJ-A4V0 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A4V4                  TCGA-DJ-A4V5 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DO-A1JZ                  TCGA-DO-A1K0 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DO-A2HM                  TCGA-E3-A3DY 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-E3-A3DZ                  TCGA-E3-A3E0 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-E3-A3E1                  TCGA-E3-A3E2 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-E3-A3E3                  TCGA-E3-A3E5 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-E8-A242                  TCGA-E8-A2EA 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-E8-A3X7                  TCGA-E8-A413 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-E8-A414                  TCGA-E8-A415 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-E8-A416                  TCGA-E8-A417 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-E8-A418                  TCGA-E8-A419 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-E8-A432                  TCGA-E8-A433 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-E8-A434                  TCGA-E8-A436 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-E8-A437                  TCGA-E8-A438 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-E8-A44K                  TCGA-E8-A44M 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3CL                  TCGA-EL-A3CM 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3CN                  TCGA-EL-A3CO 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3CP                  TCGA-EL-A3CR 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3CS                  TCGA-EL-A3CT 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3CU                  TCGA-EL-A3CV 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3CW                  TCGA-EL-A3CX 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3CY                  TCGA-EL-A3CZ 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3D0                  TCGA-EL-A3D1 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3D4                  TCGA-EL-A3D5 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3D6                  TCGA-EL-A3GO 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3GP                  TCGA-EL-A3GQ 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3GR                  TCGA-EL-A3GS 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3GU                  TCGA-EL-A3GV 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3GW                  TCGA-EL-A3GX 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3GY                  TCGA-EL-A3GZ 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3H1                  TCGA-EL-A3H2 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3H3                  TCGA-EL-A3H4 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3H5                  TCGA-EL-A3H7 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3H8                  TCGA-EL-A3MW 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3MX                  TCGA-EL-A3MY 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3MZ                  TCGA-EL-A3N2 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3N3                  TCGA-EL-A3T0 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3T1                  TCGA-EL-A3T2 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3T3                  TCGA-EL-A3T6 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3T7                  TCGA-EL-A3T8 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3T9                  TCGA-EL-A3TA 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3TB                  TCGA-EL-A3ZG 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3ZH                  TCGA-EL-A3ZK 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3ZL                  TCGA-EL-A3ZN 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3ZO                  TCGA-EL-A3ZP 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3ZQ                  TCGA-EL-A3ZR 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3ZS                  TCGA-EL-A3ZT 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A4JV                  TCGA-EL-A4JW 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A4JX                  TCGA-EL-A4JZ 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A4K0                  TCGA-EL-A4K1 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A4K2                  TCGA-EL-A4K4 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A4K6                  TCGA-EL-A4K7 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A4K9                  TCGA-EL-A4KD 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A4KG                  TCGA-EL-A4KH 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A4KI                  TCGA-EM-A22M 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EM-A22O                  TCGA-EM-A2OV 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EM-A3AI                  TCGA-ET-A25G 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A25I                  TCGA-ET-A25J 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A25K                  TCGA-ET-A25L 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A25M                  TCGA-ET-A25N 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A25O                  TCGA-ET-A25P 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A25R                  TCGA-ET-A2MX 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A2MY                  TCGA-ET-A2MZ 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A2N0                  TCGA-ET-A2N1 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A2N3                  TCGA-ET-A2N4 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A2N5                  TCGA-ET-A39I 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A39J                  TCGA-ET-A39K 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A39M                  TCGA-ET-A39N 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A39O                  TCGA-ET-A39P 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A39R                  TCGA-ET-A39S 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A39T                  TCGA-ET-A3BN 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A3BO                  TCGA-ET-A3BP 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A3BQ                  TCGA-ET-A3BS 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A3BT                  TCGA-ET-A3BU 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A3BV                  TCGA-ET-A3BW 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A3BX                  TCGA-ET-A3DO 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A3DP                  TCGA-ET-A3DQ 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A3DR                  TCGA-ET-A3DS 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A3DT                  TCGA-ET-A3DU 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A3DV                  TCGA-ET-A3DW 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A40P                  TCGA-ET-A40Q 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A40R                  TCGA-ET-A40S 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A40T                  TCGA-ET-A4KN 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A4KQ                  TCGA-FE-A22Z 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FE-A230                  TCGA-FE-A231 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FE-A232                  TCGA-FE-A233 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FE-A234                  TCGA-FE-A235 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FE-A236                  TCGA-FE-A237 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FE-A238                  TCGA-FE-A239 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FE-A23A                  TCGA-FE-A3PA 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FE-A3PB                  TCGA-FE-A3PC 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FE-A3PD                  TCGA-FK-A3S3 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FK-A3SB                  TCGA-FK-A3SD 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FK-A3SE                  TCGA-FK-A3SG 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FK-A3SH                  TCGA-FK-A4UB 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FY-A2QD                  TCGA-FY-A3BL 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FY-A3I4                  TCGA-FY-A3I5 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FY-A3NM                  TCGA-FY-A3ON 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FY-A3R6                  TCGA-FY-A3R7 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FY-A3R8                  TCGA-FY-A3R9 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FY-A3RA                  TCGA-FY-A3W9 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FY-A3WA                  TCGA-FY-A3YR 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FY-A40K                  TCGA-FY-A40L 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FY-A40M                  TCGA-FY-A40N 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FY-A4B0                  TCGA-FY-A4B3 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FY-A4B4                  TCGA-FY-A76V 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-GE-A2C6                  TCGA-H2-A26U 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-H2-A2K9                  TCGA-H2-A3RH 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-H2-A3RI                  TCGA-H2-A421 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-H2-A422                  TCGA-IM-A3EB 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-IM-A3ED                  TCGA-IM-A3U2 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-IM-A3U3                  TCGA-IM-A41Y 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-IM-A41Z                  TCGA-IM-A420 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-IM-A4EB                  TCGA-J8-A3NZ 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-J8-A3O0                  TCGA-J8-A3O1 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-J8-A3O2                  TCGA-J8-A3YD 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-J8-A3YE                  TCGA-J8-A3YF 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-J8-A3YG                  TCGA-J8-A3YH 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-J8-A42S                  TCGA-J8-A4HW 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-J8-A4HY                  TCGA-KS-A41F 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-KS-A41I                  TCGA-KS-A41J 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-KS-A41L                  TCGA-KS-A4I1 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-KS-A4I3                  TCGA-KS-A4I5 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-KS-A4I7                  TCGA-KS-A4I9 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-KS-A4IB                  TCGA-KS-A4IC 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-KS-A4ID                  TCGA-L6-A4EP 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-L6-A4EQ                  TCGA-L6-A4ET 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-L6-A4EU                  TCGA-MK-A4N6 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-MK-A4N7                  TCGA-MK-A4N9 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-MK-A84Z                  TCGA-QD-A8IV 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
D73V17, binary
                             cls
clus                            0   1
  DEL PEAK 15(8P22) MUTATED     0   2
  DEL PEAK 15(8P22) WILD-TYPE  38 357
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(8P22) MUTATED      0    2
  DEL PEAK 15(8P22) WILD-TYPE   38  357
                        clus
vv                       DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE
  HISPANIC OR LATINO                             0                          38
  NOT HISPANIC OR LATINO                         2                         357
[1] 2 2
[1] FALSE

Clustering(74) Variable = DEL PEAK 16(8P12) MUTATION ANALYSIS
D74V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 16(8P12) MUTATED     4   0
  DEL PEAK 16(8P12) WILD-TYPE 477  16
  DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE 
                          4                         493 
  DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE 
                          0                          16 
$`DEL PEAK 16(8P12) MUTATED`
TCGA-BJ-A190 TCGA-DJ-A2Q0 TCGA-EM-A3O9 TCGA-EM-A3SY 
       20.58        34.36         9.24        13.51 

$`DEL PEAK 16(8P12) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        42.08        51.39        41.52         4.83        44.35 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
       42.15        21.04        35.54        32.45        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.08        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       34.85        28.96         8.78         8.42        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24        33.93        37.48        36.46        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        33.53        35.18        15.88        36.92        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       32.42        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        17.69        59.57        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        42.54        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL 
        7.76        35.67         3.12        36.43        24.76        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        21.34        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        52.44        39.95        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       47.84        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       78.61        57.01        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       32.32        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       22.52        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB 
       14.50        15.06         7.33         0.49        13.91        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       38.86        29.95        29.85        12.79        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
       21.34         5.33        26.37        26.37        22.45        21.53 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       60.49        24.46        13.68        81.93        81.70        77.56 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       70.42        56.58        60.20        63.39        65.29        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       63.45        88.41        58.75        37.25        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       83.34         2.66        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      108.46        84.89       123.32       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        98.20        28.24        50.40        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.79        87.62        77.82        75.42        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       62.83       166.62        24.72        43.99        46.26        44.38 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       40.21        37.48        33.17        31.40        73.74        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
      112.80        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        13.28 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10       116.09         1.25        20.42        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        7.82         0.99        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08         0.30         0.76        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       15.16         6.58        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83        31.10         8.22        25.64        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        23.93 
TCGA-QD-A8IV 
       12.89 

  DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE 
                       9.24                        0.16 
  DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE 
                      34.36                      169.32 
  DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE 
                     17.045                      30.610 
[1] "9.2 - 34.4 (17.0)"  "0.2 - 169.3 (30.6)"
[1] "hr="     "1200000"
D74V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 16(8P12) MUTATED         2        2         0        0         0
  DEL PEAK 16(8P12) WILD-TYPE     280       48       111        2        46
                             vv
clus                          STAGE IVC
  DEL PEAK 16(8P12) MUTATED           0
  DEL PEAK 16(8P12) WILD-TYPE         6
D74V3, multiclass
           clus
vv          DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE
  STAGE I                           2                         280
  STAGE II                          2                          48
  STAGE III                         0                         111
  STAGE IV                          0                           2
  STAGE IVA                         0                          46
  STAGE IVC                         0                           6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK 16(8P12) MUTATED     1   2   1   0
  DEL PEAK 16(8P12) WILD-TYPE 141 163 166  23
D74V4, multiclass
    clus
vv   DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE
  T1                         1                         141
  T2                         2                         163
  T3                         1                         166
  T4                         0                          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"
D74V5, binary
                             cls
clus                            0   1
  DEL PEAK 16(8P12) MUTATED     3   0
  DEL PEAK 16(8P12) WILD-TYPE 222 224
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(8P12) MUTATED      3    0
  DEL PEAK 16(8P12) WILD-TYPE  222  224
   clus
vv  DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE
  0                         3                         222
  1                         0                         224
[1] 2 2
[1] FALSE
D74V6, binary
                             cls
clus                            0   1
  DEL PEAK 16(8P12) MUTATED     1   0
  DEL PEAK 16(8P12) WILD-TYPE 277   9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(8P12) MUTATED      1    0
  DEL PEAK 16(8P12) WILD-TYPE  277    9
   clus
vv  DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE
  0                         1                         277
  1                         0                           9
[1] 2 2
[1] FALSE
D74V7, binary
                             cls
clus                            0   1
  DEL PEAK 16(8P12) MUTATED     1   3
  DEL PEAK 16(8P12) WILD-TYPE 364 131
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(8P12) MUTATED      1    3
  DEL PEAK 16(8P12) WILD-TYPE  364  131
        clus
vv       DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE
  FEMALE                         1                         364
  MALE                           3                         131
[1] 2 2
[1] FALSE
D74V8, binary
                             cls
clus                            0   1
  DEL PEAK 16(8P12) MUTATED     2   2
  DEL PEAK 16(8P12) WILD-TYPE 183 288
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(8P12) MUTATED      2    2
  DEL PEAK 16(8P12) WILD-TYPE  183  288
     clus
vv    DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE
  NO                          2                         183
  YES                         2                         288
[1] 2 2
[1] FALSE
                             vv
clus                          OTHER  SPECIFY
  DEL PEAK 16(8P12) MUTATED                0
  DEL PEAK 16(8P12) WILD-TYPE              8
                             vv
clus                          THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 16(8P12) MUTATED                                               2
  DEL PEAK 16(8P12) WILD-TYPE                                           353
                             vv
clus                          THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 16(8P12) MUTATED                                                                        2
  DEL PEAK 16(8P12) WILD-TYPE                                                                     98
                             vv
clus                          THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 16(8P12) MUTATED                                                                     0
  DEL PEAK 16(8P12) WILD-TYPE                                                                  36
D74V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 16(8P12) MUTATED
  OTHER  SPECIFY                                                                                 0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                         2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                            0
                                                                        clus
vv                                                                       DEL PEAK 16(8P12) WILD-TYPE
  OTHER  SPECIFY                                                                                   8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                             36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V10, binary
                             cls
clus                            0   1
  DEL PEAK 16(8P12) MUTATED     4   0
  DEL PEAK 16(8P12) WILD-TYPE 416  17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(8P12) MUTATED      4    0
  DEL PEAK 16(8P12) WILD-TYPE  416   17
     clus
vv    DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE
  NO                          4                         416
  YES                         0                          17
[1] 2 2
[1] FALSE
                             vv
clus                          MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 16(8P12) MUTATED              0                       0    4
  DEL PEAK 16(8P12) WILD-TYPE          132                      18  326
                             vv
clus                          VERY ADVANCED (T4B)
  DEL PEAK 16(8P12) MUTATED                     0
  DEL PEAK 16(8P12) WILD-TYPE                   1
D74V11, multiclass
                         clus
vv                        DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE
  MINIMAL (T3)                                    0                         132
  MODERATE/ADVANCED (T4A)                         0                          18
  NONE                                            4                         326
  VERY ADVANCED (T4B)                             0                           1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 16(8P12) MUTATED     4   0   0   0
  DEL PEAK 16(8P12) WILD-TYPE 379  51   4  30
D74V12, multiclass
    clus
vv   DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE
  R0                         4                         379
  R1                         0                          51
  R2                         0                           4
  RX                         0                          30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V13, continuous
D74V14, binary
                             cls
clus                            0   1
  DEL PEAK 16(8P12) MUTATED     2   2
  DEL PEAK 16(8P12) WILD-TYPE 223 262
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(8P12) MUTATED      2    2
  DEL PEAK 16(8P12) WILD-TYPE  223  262
            clus
vv           DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE
  MULTIFOCAL                         2                         223
  UNIFOCAL                           2                         262
[1] 2 2
[1] FALSE
D74V15, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(8P12) MUTATED                                  0     0
  DEL PEAK 16(8P12) WILD-TYPE                                1    52
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(8P12) MUTATED                           0     2
  DEL PEAK 16(8P12) WILD-TYPE                        27   326
D74V16, multiclass
[1] "Remove cluster labels:"    "DEL PEAK 16(8P12) MUTATED"
clus
  DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE 
                          2                         406 
                 TCGA-4C-A93U                  TCGA-BJ-A0YZ 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A0Z2                  TCGA-BJ-A0Z3 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A0Z5                  TCGA-BJ-A0Z9 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A0ZA                  TCGA-BJ-A0ZB 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A0ZC                  TCGA-BJ-A0ZE 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A0ZG                  TCGA-BJ-A0ZH 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A0ZJ                  TCGA-BJ-A18Y 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A18Z                  TCGA-BJ-A191 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A192                  TCGA-BJ-A28R 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A28S                  TCGA-BJ-A28T 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A28V                  TCGA-BJ-A28W 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A28X                  TCGA-BJ-A28Z 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A290                  TCGA-BJ-A291 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A2N7                  TCGA-BJ-A2N8 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A2N9                  TCGA-BJ-A2NA 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A2P4                  TCGA-BJ-A3EZ 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A3F0                  TCGA-BJ-A3PR 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A3PT                  TCGA-BJ-A3PU 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A45C                  TCGA-BJ-A45D 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A45E                  TCGA-BJ-A45F 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A45G                  TCGA-BJ-A45H 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A45I                  TCGA-BJ-A45J 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A45K                  TCGA-BJ-A4O8 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A4O9                  TCGA-CE-A13K 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-CE-A27D                  TCGA-CE-A3MD 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-CE-A3ME                  TCGA-CE-A481 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-CE-A482                  TCGA-CE-A483 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-CE-A484                  TCGA-CE-A485 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DE-A0XZ                  TCGA-DE-A0Y2 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DE-A0Y3                  TCGA-DE-A2OL 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DE-A3KN                  TCGA-DE-A4M8 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DE-A4M9                  TCGA-DE-A4MA 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DE-A4MB                  TCGA-DE-A4MC 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DE-A4MD                  TCGA-DE-A69J 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DE-A69K                  TCGA-DE-A7U5 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A13L                  TCGA-DJ-A13M 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A13O                  TCGA-DJ-A13P 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A13R                  TCGA-DJ-A13S 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A13T                  TCGA-DJ-A13U 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A13W                  TCGA-DJ-A1QD 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A1QE                  TCGA-DJ-A1QF 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A1QG                  TCGA-DJ-A1QH 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A1QI                  TCGA-DJ-A1QM 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A1QO                  TCGA-DJ-A1QQ 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A2PN                  TCGA-DJ-A2PO 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A2PQ                  TCGA-DJ-A2PR 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A2PS                  TCGA-DJ-A2PT 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A2PU                  TCGA-DJ-A2PV 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A2PW                  TCGA-DJ-A2PX 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A2PY                  TCGA-DJ-A2PZ 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A2Q1                  TCGA-DJ-A2Q2 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A2Q3                  TCGA-DJ-A2Q4 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A2Q5                  TCGA-DJ-A2Q6 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A2Q7                  TCGA-DJ-A2Q9 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A2QA                  TCGA-DJ-A2QB 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A3UK                  TCGA-DJ-A3UM 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A3UN                  TCGA-DJ-A3UO 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A3UQ                  TCGA-DJ-A3UR 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A3US                  TCGA-DJ-A3UT 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A3UU                  TCGA-DJ-A3UW 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A3UX                  TCGA-DJ-A3UY 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A3UZ                  TCGA-DJ-A3V2 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A3V3                  TCGA-DJ-A3V4 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A3V5                  TCGA-DJ-A3V7 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A3V8                  TCGA-DJ-A3V9 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A3VD                  TCGA-DJ-A3VE 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A3VF                  TCGA-DJ-A3VG 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A3VI                  TCGA-DJ-A3VJ 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A3VK                  TCGA-DJ-A3VL 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A3VM                  TCGA-DJ-A4UL 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A4UP                  TCGA-DJ-A4UQ 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A4UR                  TCGA-DJ-A4UT 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A4UW                  TCGA-DJ-A4V0 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A4V4                  TCGA-DJ-A4V5 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DO-A1JZ                  TCGA-DO-A1K0 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DO-A2HM                  TCGA-E3-A3DY 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-E3-A3DZ                  TCGA-E3-A3E0 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-E3-A3E1                  TCGA-E3-A3E2 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-E3-A3E3                  TCGA-E3-A3E5 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-E8-A242                  TCGA-E8-A2EA 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-E8-A3X7                  TCGA-E8-A413 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-E8-A414                  TCGA-E8-A415 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-E8-A416                  TCGA-E8-A417 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-E8-A418                  TCGA-E8-A419 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-E8-A432                  TCGA-E8-A433 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-E8-A434                  TCGA-E8-A436 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-E8-A437                  TCGA-E8-A438 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-E8-A44K                  TCGA-E8-A44M 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3CL                  TCGA-EL-A3CM 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3CN                  TCGA-EL-A3CO 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3CP                  TCGA-EL-A3CR 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3CS                  TCGA-EL-A3CT 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3CU                  TCGA-EL-A3CV 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3CW                  TCGA-EL-A3CX 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3CY                  TCGA-EL-A3CZ 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3D0                  TCGA-EL-A3D1 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3D4                  TCGA-EL-A3D5 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3D6                  TCGA-EL-A3GO 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3GP                  TCGA-EL-A3GQ 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3GR                  TCGA-EL-A3GS 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3GU                  TCGA-EL-A3GV 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3GW                  TCGA-EL-A3GX 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3GY                  TCGA-EL-A3GZ 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3H1                  TCGA-EL-A3H2 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3H3                  TCGA-EL-A3H4 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3H5                  TCGA-EL-A3H7 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3H8                  TCGA-EL-A3MW 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3MX                  TCGA-EL-A3MY 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3MZ                  TCGA-EL-A3N2 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3N3                  TCGA-EL-A3T0 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3T1                  TCGA-EL-A3T2 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3T3                  TCGA-EL-A3T6 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3T7                  TCGA-EL-A3T8 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3T9                  TCGA-EL-A3TA 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3TB                  TCGA-EL-A3ZG 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3ZH                  TCGA-EL-A3ZK 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3ZL                  TCGA-EL-A3ZN 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3ZO                  TCGA-EL-A3ZP 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3ZQ                  TCGA-EL-A3ZR 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3ZS                  TCGA-EL-A3ZT 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A4JV                  TCGA-EL-A4JW 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A4JX                  TCGA-EL-A4JZ 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A4K0                  TCGA-EL-A4K1 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A4K2                  TCGA-EL-A4K4 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A4K6                  TCGA-EL-A4K7 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A4K9                  TCGA-EL-A4KD 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A4KG                  TCGA-EL-A4KH 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A4KI                  TCGA-EM-A22M 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EM-A22O                  TCGA-EM-A2OV 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EM-A3AI                  TCGA-ET-A25G 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A25I                  TCGA-ET-A25J 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A25K                  TCGA-ET-A25L 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A25M                  TCGA-ET-A25N 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A25O                  TCGA-ET-A25P 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A25R                  TCGA-ET-A2MX 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A2MY                  TCGA-ET-A2MZ 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A2N0                  TCGA-ET-A2N1 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A2N3                  TCGA-ET-A2N4 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A2N5                  TCGA-ET-A39I 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A39J                  TCGA-ET-A39K 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A39M                  TCGA-ET-A39N 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A39O                  TCGA-ET-A39P 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A39R                  TCGA-ET-A39S 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A39T                  TCGA-ET-A3BN 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A3BO                  TCGA-ET-A3BP 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A3BQ                  TCGA-ET-A3BS 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A3BT                  TCGA-ET-A3BU 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A3BV                  TCGA-ET-A3BW 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A3BX                  TCGA-ET-A3DO 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A3DP                  TCGA-ET-A3DQ 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A3DR                  TCGA-ET-A3DS 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A3DT                  TCGA-ET-A3DU 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A3DV                  TCGA-ET-A3DW 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A40P                  TCGA-ET-A40Q 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A40R                  TCGA-ET-A40S 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A40T                  TCGA-ET-A4KN 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A4KQ                  TCGA-FE-A22Z 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FE-A230                  TCGA-FE-A231 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FE-A232                  TCGA-FE-A233 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FE-A234                  TCGA-FE-A235 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FE-A236                  TCGA-FE-A237 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FE-A238                  TCGA-FE-A239 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FE-A23A                  TCGA-FE-A3PA 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FE-A3PB                  TCGA-FE-A3PC 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FE-A3PD                  TCGA-FK-A3S3 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FK-A3SB                  TCGA-FK-A3SD 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FK-A3SE                  TCGA-FK-A3SG 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FK-A3SH                  TCGA-FK-A4UB 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FY-A2QD                  TCGA-FY-A3BL 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FY-A3I4                  TCGA-FY-A3I5 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FY-A3NM                  TCGA-FY-A3ON 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FY-A3R6                  TCGA-FY-A3R7 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FY-A3R8                  TCGA-FY-A3R9 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FY-A3RA                  TCGA-FY-A3W9 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FY-A3WA                  TCGA-FY-A3YR 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FY-A40K                  TCGA-FY-A40L 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FY-A40M                  TCGA-FY-A40N 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FY-A4B0                  TCGA-FY-A4B3 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FY-A4B4                  TCGA-FY-A76V 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-GE-A2C6                  TCGA-H2-A26U 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-H2-A2K9                  TCGA-H2-A3RH 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-H2-A3RI                  TCGA-H2-A421 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-H2-A422                  TCGA-IM-A3EB 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-IM-A3ED                  TCGA-IM-A3U2 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-IM-A3U3                  TCGA-IM-A41Y 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-IM-A41Z                  TCGA-IM-A420 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-IM-A4EB                  TCGA-J8-A3NZ 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-J8-A3O0                  TCGA-J8-A3O1 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-J8-A3O2                  TCGA-J8-A3YD 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-J8-A3YE                  TCGA-J8-A3YF 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-J8-A3YG                  TCGA-J8-A3YH 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-J8-A42S                  TCGA-J8-A4HW 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-J8-A4HY                  TCGA-KS-A41F 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-KS-A41I                  TCGA-KS-A41J 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-KS-A41L                  TCGA-KS-A4I1 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-KS-A4I3                  TCGA-KS-A4I5 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-KS-A4I7                  TCGA-KS-A4I9 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-KS-A4IB                  TCGA-KS-A4IC 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-KS-A4ID                  TCGA-L6-A4EP 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-L6-A4EQ                  TCGA-L6-A4ET 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-L6-A4EU                  TCGA-MK-A4N6 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-MK-A4N7                  TCGA-MK-A4N9 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-MK-A84Z                  TCGA-QD-A8IV 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
D74V17, binary
                             cls
clus                            0   1
  DEL PEAK 16(8P12) MUTATED     0   2
  DEL PEAK 16(8P12) WILD-TYPE  38 357
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(8P12) MUTATED      0    2
  DEL PEAK 16(8P12) WILD-TYPE   38  357
                        clus
vv                       DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE
  HISPANIC OR LATINO                             0                          38
  NOT HISPANIC OR LATINO                         2                         357
[1] 2 2
[1] FALSE

Clustering(75) Variable = DEL PEAK 17(8Q24.22) MUTATION ANALYSIS
D75V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 17(8Q24.22) MUTATED     7   0
  DEL PEAK 17(8Q24.22) WILD-TYPE 474  16
  DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE 
                             7                            490 
  DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE 
                             0                             16 
$`DEL PEAK 17(8Q24.22) MUTATED`
TCGA-BJ-A190 TCGA-BJ-A192 TCGA-DJ-A1QL TCGA-DJ-A2Q0 TCGA-EM-A2P2 TCGA-EM-A3O9 
       20.58        44.35        17.59        34.36        17.29         9.24 
TCGA-EM-A3SY 
       13.51 

$`DEL PEAK 17(8Q24.22) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A28R 
       15.12        42.08        51.39        41.52         4.83        42.15 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04        35.54        32.45        11.31        30.97        11.08 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       30.21        22.88        18.38        16.57        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        7.99        10.88        21.01         3.45        23.84        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
       15.45        21.63        23.18        19.43        23.47        12.66 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
       12.43        12.66        35.84        21.63        50.17        37.64 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M 
       25.12        14.70        14.27         2.76         9.96        48.79 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       38.17       169.32        18.58         8.71        56.19        23.38 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       43.17        52.37         8.32        11.01       135.91        30.61 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
       44.98        42.51        14.96         6.02        42.58        47.41 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
       17.56        10.09         7.82        30.58        35.41        27.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
       26.20        38.83        33.96        31.99        34.85        28.96 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.78         8.42        37.74         6.77        40.24        33.93 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
       37.48        36.46        35.11        39.09        35.90        33.53 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       35.18        15.88        36.92        31.04        32.42        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU 
       16.41        19.56        36.33        32.81        36.33        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       59.57        11.34        35.87        40.96        36.99        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        42.54        19.20        23.21        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       24.82        22.92        21.01        18.97         7.76        35.67 
TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        3.12        36.43        24.76        17.23        27.62        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       21.34        33.04        34.78        27.06        26.93        35.54 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        35.38        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       92.55        47.21        66.38        80.52        63.19        52.44 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       39.95        31.23        35.67        31.27        29.98        31.50 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 
       31.04         0.72         0.26         3.02        25.45        30.61 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
        0.16         0.23        14.96         7.69        33.50         0.39 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
        0.39        31.66        26.73       155.54        97.74       158.83 
TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
        7.66        45.53        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 
      106.62         4.18        79.50       139.86        98.53        69.57 
TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR 
       57.11       108.36        64.87        49.51        50.24       115.10 
TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY 
       65.39       136.01        50.37        50.20       147.75       101.13 
TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 
      139.99        49.32        33.50        43.36        49.71        83.57 
TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ 
      139.00       150.48       108.66        57.63        17.52        52.50 
TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       29.65       147.42       142.52       129.57        32.48       132.07 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
       98.24        41.29       107.47         5.72        66.90        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN 
       89.56        78.97        51.78        62.30        36.03        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        65.49        61.22        60.16         7.07        59.44 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       57.47        34.72        45.96        37.94        31.04        34.39 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        53.36        44.15        41.13        47.84        43.59 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       24.30        27.06        23.90        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
       48.49        18.05        19.79        19.46        78.61        57.01 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       54.08        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.65        44.19        41.29        14.24        47.57        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       13.18        23.51         6.05         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        40.34        19.73        32.32        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.59        17.46        14.60        22.52        30.94        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR 
       14.14        33.07        13.38         8.35        29.72        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        47.38        21.01        12.07        17.49 
TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 
       17.39        16.18        15.02        14.50        15.06         7.33 
TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
        0.49        13.91        38.66        38.86        29.95        29.85 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        84.59        29.33        21.34         5.33        26.37 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
       26.37        22.45        21.53        60.49        24.46        13.68 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       81.93        81.70        77.56        70.42        56.58        60.20 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       63.39        65.29        18.38        63.45        88.41        58.75 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       37.25        52.60        54.35        83.34         2.66        80.88 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
       33.24       106.09       107.41       108.46        84.89       123.32 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
      100.57        95.34        94.13        55.10        98.20        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
       50.40        79.10        76.64         5.79        87.62        77.82 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       75.42        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       117.40        66.77       112.80        39.95        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.11         1.05        13.28         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON 
        1.25        20.42        17.82         7.82         0.99        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
       13.91        16.27        15.68        16.57        18.08         0.30 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
        0.76        17.06        17.36        15.16         6.58        22.49 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04         1.35        21.60         1.68        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46         2.99        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        18.51        16.90        21.83        31.10         8.22 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
       25.64        17.23        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW 
       27.85        24.69        22.29         5.75         2.47         2.60 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       43.69        18.64        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       33.24        33.40        40.37        21.83         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45        30.21        23.93        12.89 

  DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE 
                          9.24                           0.16 
  DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE 
                         44.35                         169.32 
  DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE 
                         17.59                          30.74 
[1] "9.2 - 44.4 (17.6)"  "0.2 - 169.3 (30.7)"
[1] "hr="     "3300000"
D75V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 17(8Q24.22) MUTATED         2        3         2        0         0
  DEL PEAK 17(8Q24.22) WILD-TYPE     280       47       109        2        46
                                vv
clus                             STAGE IVC
  DEL PEAK 17(8Q24.22) MUTATED           0
  DEL PEAK 17(8Q24.22) WILD-TYPE         6
D75V3, multiclass
           clus
vv          DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE
  STAGE I                              2                            280
  STAGE II                             3                             47
  STAGE III                            2                            109
  STAGE IV                             0                              2
  STAGE IVA                            0                             46
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 17(8Q24.22) MUTATED     1   3   3   0
  DEL PEAK 17(8Q24.22) WILD-TYPE 141 162 164  23
D75V4, multiclass
    clus
vv   DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE
  T1                            1                            141
  T2                            3                            162
  T3                            3                            164
  T4                            0                             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"
D75V5, binary
                                cls
clus                               0   1
  DEL PEAK 17(8Q24.22) MUTATED     5   0
  DEL PEAK 17(8Q24.22) WILD-TYPE 220 224
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(8Q24.22) MUTATED      5    0
  DEL PEAK 17(8Q24.22) WILD-TYPE  220  224
   clus
vv  DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE
  0                            5                            220
  1                            0                            224
[1] 2 2
[1] FALSE
D75V6, binary
                                cls
clus                               0   1
  DEL PEAK 17(8Q24.22) MUTATED     3   0
  DEL PEAK 17(8Q24.22) WILD-TYPE 275   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(8Q24.22) MUTATED      3    0
  DEL PEAK 17(8Q24.22) WILD-TYPE  275    9
   clus
vv  DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE
  0                            3                            275
  1                            0                              9
[1] 2 2
[1] FALSE
D75V7, binary
                                cls
clus                               0   1
  DEL PEAK 17(8Q24.22) MUTATED     2   5
  DEL PEAK 17(8Q24.22) WILD-TYPE 363 129
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(8Q24.22) MUTATED      2    5
  DEL PEAK 17(8Q24.22) WILD-TYPE  363  129
        clus
vv       DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE
  FEMALE                            2                            363
  MALE                              5                            129
[1] 2 2
[1] FALSE
D75V8, binary
                                cls
clus                               0   1
  DEL PEAK 17(8Q24.22) MUTATED     4   3
  DEL PEAK 17(8Q24.22) WILD-TYPE 181 287
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(8Q24.22) MUTATED      4    3
  DEL PEAK 17(8Q24.22) WILD-TYPE  181  287
     clus
vv    DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE
  NO                             4                            181
  YES                            3                            287
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 17(8Q24.22) MUTATED                0
  DEL PEAK 17(8Q24.22) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 17(8Q24.22) MUTATED                                               3
  DEL PEAK 17(8Q24.22) WILD-TYPE                                           352
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 17(8Q24.22) MUTATED                                                                        4
  DEL PEAK 17(8Q24.22) WILD-TYPE                                                                     96
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 17(8Q24.22) MUTATED                                                                     0
  DEL PEAK 17(8Q24.22) WILD-TYPE                                                                  36
D75V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 17(8Q24.22) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            4
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       DEL PEAK 17(8Q24.22) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V10, binary
                                cls
clus                               0   1
  DEL PEAK 17(8Q24.22) MUTATED     7   0
  DEL PEAK 17(8Q24.22) WILD-TYPE 413  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(8Q24.22) MUTATED      7    0
  DEL PEAK 17(8Q24.22) WILD-TYPE  413   17
     clus
vv    DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE
  NO                             7                            413
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 17(8Q24.22) MUTATED              1                       0    6
  DEL PEAK 17(8Q24.22) WILD-TYPE          131                      18  324
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 17(8Q24.22) MUTATED                     0
  DEL PEAK 17(8Q24.22) WILD-TYPE                   1
D75V11, multiclass
                         clus
vv                        DEL PEAK 17(8Q24.22) MUTATED
  MINIMAL (T3)                                       1
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               6
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK 17(8Q24.22) WILD-TYPE
  MINIMAL (T3)                                       131
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               324
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 17(8Q24.22) MUTATED     6   0   0   1
  DEL PEAK 17(8Q24.22) WILD-TYPE 377  51   4  29
D75V12, multiclass
    clus
vv   DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE
  R0                            6                            377
  R1                            0                             51
  R2                            0                              4
  RX                            1                             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"
D75V13, continuous
D75V14, binary
                                cls
clus                               0   1
  DEL PEAK 17(8Q24.22) MUTATED     3   4
  DEL PEAK 17(8Q24.22) WILD-TYPE 222 260
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(8Q24.22) MUTATED      3    4
  DEL PEAK 17(8Q24.22) WILD-TYPE  222  260
            clus
vv           DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE
  MULTIFOCAL                            3                            222
  UNIFOCAL                              4                            260
[1] 2 2
[1] FALSE
D75V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(8Q24.22) MUTATED                                  0     0
  DEL PEAK 17(8Q24.22) WILD-TYPE                                1    52
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(8Q24.22) MUTATED                           0     3
  DEL PEAK 17(8Q24.22) WILD-TYPE                        27   325
D75V16, multiclass
                                  clus
vv                                 DEL PEAK 17(8Q24.22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       3
                                  clus
vv                                 DEL PEAK 17(8Q24.22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        52
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V17, binary
                                cls
clus                               0   1
  DEL PEAK 17(8Q24.22) MUTATED     0   3
  DEL PEAK 17(8Q24.22) WILD-TYPE  38 356
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(8Q24.22) MUTATED      0    3
  DEL PEAK 17(8Q24.22) WILD-TYPE   38  356
                        clus
vv                       DEL PEAK 17(8Q24.22) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            3
                        clus
vv                       DEL PEAK 17(8Q24.22) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            356
[1] 2 2
[1] FALSE

Clustering(76) Variable = DEL PEAK 18(9P21.3) MUTATION ANALYSIS
D76V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 18(9P21.3) MUTATED    17   2
  DEL PEAK 18(9P21.3) WILD-TYPE 464  14
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                           19                           478 
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                            2                            14 
$`DEL PEAK 18(9P21.3) MUTATED`
TCGA-BJ-A2N8 TCGA-DJ-A2Q0 TCGA-DO-A2HM TCGA-E8-A432 TCGA-EL-A3GP TCGA-EL-A3MX 
       16.57        34.36         2.33        30.61        49.51        57.63 
TCGA-EL-A3T9 TCGA-EL-A3ZK TCGA-EL-A3ZO TCGA-EL-A4K6 TCGA-EL-A4KI TCGA-EM-A1YE 
        5.72        51.78        47.38        44.15        23.90        54.08 
TCGA-EM-A2OY TCGA-EM-A3O3 TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A39N TCGA-FY-A3W9 
       32.32        14.50         9.24        13.51       123.32         0.76 
TCGA-FY-A40M 
       22.49 

$`DEL PEAK 18(9P21.3) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N9 
       30.97        11.08        30.21        22.88        18.38        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       34.85        28.96         8.78         8.42        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24        33.93        37.48        36.46        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        33.53        35.18        15.88        36.92        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       32.42        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        17.69        59.57        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        42.54        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL 
        7.76        35.67         3.12        36.43        24.76        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        21.34        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
       21.53        92.55        47.21        66.38        80.52        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 
       52.44        39.95        31.23        35.67        31.27        29.98 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 
       31.50        31.04         0.72         0.26         3.02        25.45 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
        0.16         0.23        14.96         7.69        33.50         0.39 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
        0.39        31.66        26.73       155.54        97.74       158.83 
TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
        7.66        45.53        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 
      106.62         4.18        79.50       139.86        98.53        69.57 
TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS 
       57.11       108.36        64.87        50.24       115.10        65.39 
TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
      136.01        50.37        50.20       147.75       101.13       139.99 
TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
       49.32        33.50        43.36        49.71        83.57       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 
      150.48       108.66        17.52        52.50        29.65       147.42 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZL 
      107.47        66.90        82.82        89.56        78.97        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       36.03        53.06        65.49        61.22        60.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       34.39        30.51        53.36        41.13        47.84        43.59 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       24.30        27.06        26.86        18.18        20.91        48.49 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I 
       18.05        19.79        19.46        78.61        57.01        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O 
       14.50        15.75        10.45        14.53        10.65        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        6.05         2.99        12.30        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       40.34        19.73        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        29.72        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.02        15.06         7.33         0.49        13.91        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       38.86        29.95        29.85        12.79        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
       21.34         5.33        26.37        26.37        22.45        21.53 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       60.49        24.46        13.68        81.93        81.70        77.56 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       70.42        56.58        60.20        63.39        65.29        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       63.45        88.41        58.75        37.25        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       83.34         2.66        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
      108.46        84.89       100.57        95.34        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       98.20        28.24        50.40        79.10        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       87.62        77.82        75.42        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       94.59        84.85        80.58        66.84        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      166.62        24.72        43.99        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        13.28         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 
       48.10       116.09         1.25        20.42        17.82         7.82 
TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
        0.99        19.56        13.91        16.27        15.68        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
       18.08         0.30        17.06        17.36        15.16         6.58 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04         1.35        21.60         1.68        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46         2.99        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        18.51        16.90        21.83        31.10         8.22 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
       25.64        17.23        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW 
       27.85        24.69        22.29         5.75         2.47         2.60 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       43.69        18.64        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       33.24        33.40        40.37        21.83         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45        30.21        23.93        12.89 

  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                         0.76                          0.16 
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                       123.32                        169.32 
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                        30.61                         30.61 
[1] "0.8 - 123.3 (30.6)" "0.2 - 169.3 (30.6)"
[1] "hr=" "4.4"
D76V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 18(9P21.3) MUTATED         7        5         4        2         1
  DEL PEAK 18(9P21.3) WILD-TYPE     275       45       107        0        45
                               vv
clus                            STAGE IVC
  DEL PEAK 18(9P21.3) MUTATED           1
  DEL PEAK 18(9P21.3) WILD-TYPE         5
D76V3, multiclass
           clus
vv          DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  STAGE I                             7                           275
  STAGE II                            5                            45
  STAGE III                           4                           107
  STAGE IV                            2                             0
  STAGE IVA                           1                            45
  STAGE IVC                           1                             5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 18(9P21.3) MUTATED     5   7   5   3
  DEL PEAK 18(9P21.3) WILD-TYPE 137 158 162  20
D76V4, multiclass
    clus
vv   DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  T1                           5                           137
  T2                           7                           158
  T3                           5                           162
  T4                           3                            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"
D76V5, binary
                               cls
clus                              0   1
  DEL PEAK 18(9P21.3) MUTATED     9   8
  DEL PEAK 18(9P21.3) WILD-TYPE 216 216
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(9P21.3) MUTATED      9    8
  DEL PEAK 18(9P21.3) WILD-TYPE  216  216
   clus
vv  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  0                           9                           216
  1                           8                           216
[1] 2 2
[1] FALSE
D76V6, binary
                               cls
clus                              0   1
  DEL PEAK 18(9P21.3) MUTATED     6   1
  DEL PEAK 18(9P21.3) WILD-TYPE 272   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(9P21.3) MUTATED      6    1
  DEL PEAK 18(9P21.3) WILD-TYPE  272    8
   clus
vv  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  0                           6                           272
  1                           1                             8
[1] 2 2
[1] FALSE
D76V7, binary
                               cls
clus                              0   1
  DEL PEAK 18(9P21.3) MUTATED    13   7
  DEL PEAK 18(9P21.3) WILD-TYPE 352 127
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(9P21.3) MUTATED     13    7
  DEL PEAK 18(9P21.3) WILD-TYPE  352  127
        clus
vv       DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  FEMALE                          13                           352
  MALE                             7                           127
[1] 2 2
[1] FALSE
D76V8, binary
                               cls
clus                              0   1
  DEL PEAK 18(9P21.3) MUTATED     5  11
  DEL PEAK 18(9P21.3) WILD-TYPE 180 279
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(9P21.3) MUTATED      5   11
  DEL PEAK 18(9P21.3) WILD-TYPE  180  279
     clus
vv    DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  NO                            5                           180
  YES                          11                           279
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  DEL PEAK 18(9P21.3) MUTATED                0
  DEL PEAK 18(9P21.3) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 18(9P21.3) MUTATED                                              15
  DEL PEAK 18(9P21.3) WILD-TYPE                                           340
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 18(9P21.3) MUTATED                                                                        5
  DEL PEAK 18(9P21.3) WILD-TYPE                                                                     95
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 18(9P21.3) MUTATED                                                                     0
  DEL PEAK 18(9P21.3) WILD-TYPE                                                                  36
D76V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 18(9P21.3) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   15
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           5
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       DEL PEAK 18(9P21.3) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    340
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            95
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V10, binary
                               cls
clus                              0   1
  DEL PEAK 18(9P21.3) MUTATED    19   0
  DEL PEAK 18(9P21.3) WILD-TYPE 401  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(9P21.3) MUTATED     19    0
  DEL PEAK 18(9P21.3) WILD-TYPE  401   17
     clus
vv    DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  NO                           19                           401
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 18(9P21.3) MUTATED              4                       0   14
  DEL PEAK 18(9P21.3) WILD-TYPE          128                      18  316
                               vv
clus                            VERY ADVANCED (T4B)
  DEL PEAK 18(9P21.3) MUTATED                     1
  DEL PEAK 18(9P21.3) WILD-TYPE                   0
D76V11, multiclass
                         clus
vv                        DEL PEAK 18(9P21.3) MUTATED
  MINIMAL (T3)                                      4
  MODERATE/ADVANCED (T4A)                           0
  NONE                                             14
  VERY ADVANCED (T4B)                               1
                         clus
vv                        DEL PEAK 18(9P21.3) WILD-TYPE
  MINIMAL (T3)                                      128
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              316
  VERY ADVANCED (T4B)                                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 18(9P21.3) MUTATED    14   3   0   2
  DEL PEAK 18(9P21.3) WILD-TYPE 369  48   4  28
D76V12, multiclass
    clus
vv   DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  R0                          14                           369
  R1                           3                            48
  R2                           0                             4
  RX                           2                            28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V13, continuous
D76V14, binary
                               cls
clus                              0   1
  DEL PEAK 18(9P21.3) MUTATED     6  14
  DEL PEAK 18(9P21.3) WILD-TYPE 219 250
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(9P21.3) MUTATED      6   14
  DEL PEAK 18(9P21.3) WILD-TYPE  219  250
            clus
vv           DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  MULTIFOCAL                           6                           219
  UNIFOCAL                            14                           250
[1] 2 2
[1] FALSE
D76V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(9P21.3) MUTATED                                  0     1
  DEL PEAK 18(9P21.3) WILD-TYPE                                1    51
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(9P21.3) MUTATED                           1    13
  DEL PEAK 18(9P21.3) WILD-TYPE                        26   315
D76V16, multiclass
                                  clus
vv                                 DEL PEAK 18(9P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     13
                                  clus
vv                                 DEL PEAK 18(9P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       51
  BLACK OR AFRICAN AMERICAN                                   26
  WHITE                                                      315
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V17, binary
                               cls
clus                              0   1
  DEL PEAK 18(9P21.3) MUTATED     0  15
  DEL PEAK 18(9P21.3) WILD-TYPE  38 344
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(9P21.3) MUTATED      0   15
  DEL PEAK 18(9P21.3) WILD-TYPE   38  344
                        clus
vv                       DEL PEAK 18(9P21.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          15
                        clus
vv                       DEL PEAK 18(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           344
[1] 2 2
[1] FALSE

Clustering(77) Variable = DEL PEAK 19(9Q22.33) MUTATION ANALYSIS
D77V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 19(9Q22.33) MUTATED    24   2
  DEL PEAK 19(9Q22.33) WILD-TYPE 457  14
  DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE 
                            26                            471 
  DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE 
                             2                             14 
$`DEL PEAK 19(9Q22.33) MUTATED`
TCGA-4C-A93U TCGA-BJ-A2N8 TCGA-CE-A484 TCGA-DE-A4MB TCGA-DJ-A13L TCGA-DJ-A2Q0 
        4.24        16.57        12.43        11.57         9.96        34.36 
TCGA-DO-A2HM TCGA-E8-A432 TCGA-EL-A3GP TCGA-EL-A3MX TCGA-EL-A3T9 TCGA-EL-A3ZK 
        2.33        30.61        49.51        57.63         5.72        51.78 
TCGA-EL-A3ZO TCGA-EL-A4K6 TCGA-EL-A4KI TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A2OY 
       47.38        44.15        23.90        19.46        54.08        32.32 
TCGA-EM-A3O3 TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A39N TCGA-FE-A231 TCGA-FK-A3SG 
       14.50         9.24        13.51       123.32        31.59         0.92 
TCGA-FY-A40M TCGA-IM-A3U2 
       22.49        18.51 

$`DEL PEAK 19(9Q22.33) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        49.78        16.34        14.73        41.33 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73        25.48        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       42.08        51.39        41.52        20.58         4.83        44.35 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
       42.15        21.04        35.54        32.45        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       11.08        30.21        22.88        18.38        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        7.99        10.88        21.01         3.45        23.84        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
       15.45        21.63        23.18        19.43        23.47        12.66 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.66        35.84        21.63        50.17        37.64        15.85 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.54        18.84        30.12        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       14.27         2.76        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        23.38        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       11.01       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT 
        7.82        30.58        35.41        27.45        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74         6.77        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        36.33        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       35.87        40.96        36.99        20.22        30.61        42.54 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20        23.21        21.27        20.48        24.82        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ 
       21.01        18.97         7.76        35.67         3.12        36.43 
TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       24.76        17.23        27.62        30.87        21.34        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       35.38        54.90        21.53        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        25.45         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GQ 
       98.53        69.57        57.11       108.36        64.87        50.24 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
      115.10        65.39       136.01        50.37        50.20       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MY TCGA-EL-A3MZ 
       83.57       139.00       150.48       108.66        17.52        52.50 
TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       29.65       147.42       142.52       129.57        32.48       132.07 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       98.24        41.29       107.47        66.90        82.82        89.56 
TCGA-EL-A3ZH TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       78.97        62.30        36.03        53.06        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       60.16         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K7 
       37.94        31.04        34.39        30.51        53.36        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT 
       47.84        43.59        24.30        27.06        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YC TCGA-EM-A1YD 
       20.91        48.49        18.05        19.79        78.61        57.01 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N 
       14.73        14.50        15.75        10.45        14.53        10.65 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       44.19        41.29        14.24        47.57        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         6.05         2.99        12.30        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        40.34        19.73        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       33.07        13.38         8.35        29.72        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        47.38        21.01        12.07        17.49        17.39 
TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA 
       16.18        15.02        15.06         7.33         0.49        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.66        38.86        29.95        29.85        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      107.41       108.46        84.89       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        98.20        28.24        50.40        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.79        87.62        77.82        75.42        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       62.83       166.62        24.72        43.99        46.26        44.38 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       40.21        37.48        33.17        31.40        73.74        71.44 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SH 
       78.77        71.08         4.11         1.05        13.28        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
      116.09         1.25        20.42        17.82         7.82         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
        0.30         0.76        17.06        17.36        15.16         6.58 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04         1.35        21.60         1.68        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46         2.99        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       47.41        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       17.23        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY 
       24.69        22.29         5.75         2.47         2.60         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.40        40.37        21.83         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       30.21        23.93        12.89 

  DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE 
                          0.92                           0.16 
  DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE 
                        123.32                         169.32 
  DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE 
                        20.975                         30.940 
[1] "0.9 - 123.3 (21.0)" "0.2 - 169.3 (30.9)"
[1] "hr=" "4"  
D77V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 19(9Q22.33) MUTATED        10        5         4        2         5
  DEL PEAK 19(9Q22.33) WILD-TYPE     272       45       107        0        41
                                vv
clus                             STAGE IVC
  DEL PEAK 19(9Q22.33) MUTATED           1
  DEL PEAK 19(9Q22.33) WILD-TYPE         5
D77V3, multiclass
           clus
vv          DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE
  STAGE I                             10                            272
  STAGE II                             5                             45
  STAGE III                            4                            107
  STAGE IV                             2                              0
  STAGE IVA                            5                             41
  STAGE IVC                            1                              5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 19(9Q22.33) MUTATED     6   9   8   4
  DEL PEAK 19(9Q22.33) WILD-TYPE 136 156 159  19
D77V4, multiclass
    clus
vv   DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE
  T1                            6                            136
  T2                            9                            156
  T3                            8                            159
  T4                            4                             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"
D77V5, binary
                                cls
clus                               0   1
  DEL PEAK 19(9Q22.33) MUTATED     9  14
  DEL PEAK 19(9Q22.33) WILD-TYPE 216 210
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(9Q22.33) MUTATED      9   14
  DEL PEAK 19(9Q22.33) WILD-TYPE  216  210
   clus
vv  DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE
  0                            9                            216
  1                           14                            210
[1] 2 2
[1] FALSE
D77V6, binary
                                cls
clus                               0   1
  DEL PEAK 19(9Q22.33) MUTATED    10   1
  DEL PEAK 19(9Q22.33) WILD-TYPE 268   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(9Q22.33) MUTATED     10    1
  DEL PEAK 19(9Q22.33) WILD-TYPE  268    8
   clus
vv  DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE
  0                           10                            268
  1                            1                              8
[1] 2 2
[1] FALSE
D77V7, binary
                                cls
clus                               0   1
  DEL PEAK 19(9Q22.33) MUTATED    18   9
  DEL PEAK 19(9Q22.33) WILD-TYPE 347 125
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(9Q22.33) MUTATED     18    9
  DEL PEAK 19(9Q22.33) WILD-TYPE  347  125
        clus
vv       DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE
  FEMALE                           18                            347
  MALE                              9                            125
[1] 2 2
[1] FALSE
D77V8, binary
                                cls
clus                               0   1
  DEL PEAK 19(9Q22.33) MUTATED    10  13
  DEL PEAK 19(9Q22.33) WILD-TYPE 175 277
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(9Q22.33) MUTATED     10   13
  DEL PEAK 19(9Q22.33) WILD-TYPE  175  277
     clus
vv    DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE
  NO                            10                            175
  YES                           13                            277
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 19(9Q22.33) MUTATED                0
  DEL PEAK 19(9Q22.33) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 19(9Q22.33) MUTATED                                              20
  DEL PEAK 19(9Q22.33) WILD-TYPE                                           335
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 19(9Q22.33) MUTATED                                                                        5
  DEL PEAK 19(9Q22.33) WILD-TYPE                                                                     95
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 19(9Q22.33) MUTATED                                                                     2
  DEL PEAK 19(9Q22.33) WILD-TYPE                                                                  34
D77V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 19(9Q22.33) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    20
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            5
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               2
                                                                        clus
vv                                                                       DEL PEAK 19(9Q22.33) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     335
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             95
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                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"
D77V10, binary
                                cls
clus                               0   1
  DEL PEAK 19(9Q22.33) MUTATED    25   1
  DEL PEAK 19(9Q22.33) WILD-TYPE 395  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(9Q22.33) MUTATED     25    1
  DEL PEAK 19(9Q22.33) WILD-TYPE  395   16
     clus
vv    DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE
  NO                            25                            395
  YES                            1                             16
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 19(9Q22.33) MUTATED              6                       1   18
  DEL PEAK 19(9Q22.33) WILD-TYPE          126                      17  312
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 19(9Q22.33) MUTATED                     1
  DEL PEAK 19(9Q22.33) WILD-TYPE                   0
D77V11, multiclass
                         clus
vv                        DEL PEAK 19(9Q22.33) MUTATED
  MINIMAL (T3)                                       6
  MODERATE/ADVANCED (T4A)                            1
  NONE                                              18
  VERY ADVANCED (T4B)                                1
                         clus
vv                        DEL PEAK 19(9Q22.33) WILD-TYPE
  MINIMAL (T3)                                       126
  MODERATE/ADVANCED (T4A)                             17
  NONE                                               312
  VERY ADVANCED (T4B)                                  0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 19(9Q22.33) MUTATED    21   3   0   2
  DEL PEAK 19(9Q22.33) WILD-TYPE 362  48   4  28
D77V12, multiclass
    clus
vv   DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE
  R0                           21                            362
  R1                            3                             48
  R2                            0                              4
  RX                            2                             28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V13, continuous
D77V14, binary
                                cls
clus                               0   1
  DEL PEAK 19(9Q22.33) MUTATED    11  16
  DEL PEAK 19(9Q22.33) WILD-TYPE 214 248
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(9Q22.33) MUTATED     11   16
  DEL PEAK 19(9Q22.33) WILD-TYPE  214  248
            clus
vv           DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE
  MULTIFOCAL                           11                            214
  UNIFOCAL                             16                            248
[1] 2 2
[1] FALSE
D77V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 19(9Q22.33) MUTATED                                  0     2
  DEL PEAK 19(9Q22.33) WILD-TYPE                                1    50
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(9Q22.33) MUTATED                           2    17
  DEL PEAK 19(9Q22.33) WILD-TYPE                        25   311
D77V16, multiclass
                                  clus
vv                                 DEL PEAK 19(9Q22.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      17
                                  clus
vv                                 DEL PEAK 19(9Q22.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        50
  BLACK OR AFRICAN AMERICAN                                    25
  WHITE                                                       311
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V17, binary
                                cls
clus                               0   1
  DEL PEAK 19(9Q22.33) MUTATED     2  19
  DEL PEAK 19(9Q22.33) WILD-TYPE  36 340
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(9Q22.33) MUTATED      2   19
  DEL PEAK 19(9Q22.33) WILD-TYPE   36  340
                        clus
vv                       DEL PEAK 19(9Q22.33) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           19
                        clus
vv                       DEL PEAK 19(9Q22.33) WILD-TYPE
  HISPANIC OR LATINO                                 36
  NOT HISPANIC OR LATINO                            340
[1] 2 2
[1] FALSE

Clustering(78) Variable = DEL PEAK 20(10P12.31) MUTATION ANALYSIS
D78V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 20(10P12.31) MUTATED     7   0
  DEL PEAK 20(10P12.31) WILD-TYPE 474  16
  DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE 
                              7                             490 
  DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE 
                              0                              16 
$`DEL PEAK 20(10P12.31) MUTATED`
TCGA-BJ-A190 TCGA-E8-A432 TCGA-EL-A4KI TCGA-EM-A3O9 TCGA-ET-A39N TCGA-ET-A3DS 
       20.58        30.61        23.90         9.24       123.32        66.84 
TCGA-FY-A3I5 
        7.82 

$`DEL PEAK 20(10P12.31) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        42.08        51.39        41.52         4.83        44.35 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
       42.15        21.04        35.54        32.45        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.08        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        25.45         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT 
       47.84        43.59        24.30        27.06        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        48.49        18.05        19.79        19.46        78.61 
TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       57.01        54.08        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       14.53        10.65        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
       17.88        13.18        23.51         6.05         2.99        12.30 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       48.46        13.15        22.16        40.34        19.73        32.32 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       33.96        17.59        17.46        17.29        14.60        22.52 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
       15.06         7.33         0.49        13.91        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       29.95        29.85        13.51        12.79        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
       21.34         5.33        26.37        26.37        22.45        21.53 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       60.49        24.46        13.68        81.93        81.70        77.56 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       70.42        56.58        60.20        63.39        65.29        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       63.45        88.41        58.75        37.25        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       83.34         2.66        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
      108.46        84.89       100.57        95.34        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       98.20        28.24        50.40        79.10        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       87.62        77.82        75.42        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       94.59        84.85        80.58        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       71.08         4.11         1.05        13.28         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON 
      116.09         1.25        20.42        17.82         0.99        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
       13.91        16.27        15.68        16.57        18.08         0.30 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
        0.76        17.06        17.36        15.16         6.58        22.49 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04         1.35        21.60         1.68        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46         2.99        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        18.51        16.90        21.83        31.10         8.22 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
       25.64        17.23        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW 
       27.85        24.69        22.29         5.75         2.47         2.60 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       43.69        18.64        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       33.24        33.40        40.37        21.83         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45        30.21        23.93        12.89 

  DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE 
                           7.82                            0.16 
  DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE 
                         123.32                          169.32 
  DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE 
                          23.90                           30.74 
[1] "7.8 - 123.3 (23.9)" "0.2 - 169.3 (30.7)"
[1] "hr="     "9100000"
D78V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 20(10P12.31) MUTATED         3        2         2        0         0
  DEL PEAK 20(10P12.31) WILD-TYPE     279       48       109        2        46
                                 vv
clus                              STAGE IVC
  DEL PEAK 20(10P12.31) MUTATED           0
  DEL PEAK 20(10P12.31) WILD-TYPE         6
D78V3, multiclass
           clus
vv          DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE
  STAGE I                               3                             279
  STAGE II                              2                              48
  STAGE III                             2                             109
  STAGE IV                              0                               2
  STAGE IVA                             0                              46
  STAGE IVC                             0                               6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 20(10P12.31) MUTATED     1   2   4   0
  DEL PEAK 20(10P12.31) WILD-TYPE 141 163 163  23
D78V4, multiclass
    clus
vv   DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE
  T1                             1                             141
  T2                             2                             163
  T3                             4                             163
  T4                             0                              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"
D78V5, binary
                                 cls
clus                                0   1
  DEL PEAK 20(10P12.31) MUTATED     6   0
  DEL PEAK 20(10P12.31) WILD-TYPE 219 224
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(10P12.31) MUTATED      6    0
  DEL PEAK 20(10P12.31) WILD-TYPE  219  224
   clus
vv  DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE
  0                             6                             219
  1                             0                             224
[1] 2 2
[1] FALSE
D78V6, binary
                                 cls
clus                                0   1
  DEL PEAK 20(10P12.31) MUTATED     1   0
  DEL PEAK 20(10P12.31) WILD-TYPE 277   9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(10P12.31) MUTATED      1    0
  DEL PEAK 20(10P12.31) WILD-TYPE  277    9
   clus
vv  DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE
  0                             1                             277
  1                             0                               9
[1] 2 2
[1] FALSE
D78V7, binary
                                 cls
clus                                0   1
  DEL PEAK 20(10P12.31) MUTATED     4   3
  DEL PEAK 20(10P12.31) WILD-TYPE 361 131
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(10P12.31) MUTATED      4    3
  DEL PEAK 20(10P12.31) WILD-TYPE  361  131
        clus
vv       DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE
  FEMALE                             4                             361
  MALE                               3                             131
[1] 2 2
[1] FALSE
D78V8, binary
                                 cls
clus                                0   1
  DEL PEAK 20(10P12.31) MUTATED     2   4
  DEL PEAK 20(10P12.31) WILD-TYPE 183 286
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(10P12.31) MUTATED      2    4
  DEL PEAK 20(10P12.31) WILD-TYPE  183  286
     clus
vv    DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE
  NO                              2                             183
  YES                             4                             286
[1] 2 2
[1] FALSE
                                 vv
clus                              OTHER  SPECIFY
  DEL PEAK 20(10P12.31) MUTATED                0
  DEL PEAK 20(10P12.31) WILD-TYPE              8
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 20(10P12.31) MUTATED                                               5
  DEL PEAK 20(10P12.31) WILD-TYPE                                           350
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 20(10P12.31) MUTATED                                                                        2
  DEL PEAK 20(10P12.31) WILD-TYPE                                                                     98
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 20(10P12.31) MUTATED                                                                     0
  DEL PEAK 20(10P12.31) WILD-TYPE                                                                  36
D78V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 20(10P12.31) MUTATED
  OTHER  SPECIFY                                                                                     0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      5
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                0
                                                                        clus
vv                                                                       DEL PEAK 20(10P12.31) WILD-TYPE
  OTHER  SPECIFY                                                                                       8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                              98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V10, binary
                                 cls
clus                                0   1
  DEL PEAK 20(10P12.31) MUTATED     6   0
  DEL PEAK 20(10P12.31) WILD-TYPE 414  17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(10P12.31) MUTATED      6    0
  DEL PEAK 20(10P12.31) WILD-TYPE  414   17
     clus
vv    DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE
  NO                              6                             414
  YES                             0                              17
[1] 2 2
[1] FALSE
                                 vv
clus                              MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 20(10P12.31) MUTATED              1                       0    6
  DEL PEAK 20(10P12.31) WILD-TYPE          131                      18  324
                                 vv
clus                              VERY ADVANCED (T4B)
  DEL PEAK 20(10P12.31) MUTATED                     0
  DEL PEAK 20(10P12.31) WILD-TYPE                   1
D78V11, multiclass
                         clus
vv                        DEL PEAK 20(10P12.31) MUTATED
  MINIMAL (T3)                                        1
  MODERATE/ADVANCED (T4A)                             0
  NONE                                                6
  VERY ADVANCED (T4B)                                 0
                         clus
vv                        DEL PEAK 20(10P12.31) WILD-TYPE
  MINIMAL (T3)                                        131
  MODERATE/ADVANCED (T4A)                              18
  NONE                                                324
  VERY ADVANCED (T4B)                                   1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 20(10P12.31) MUTATED     7   0   0   0
  DEL PEAK 20(10P12.31) WILD-TYPE 376  51   4  30
D78V12, multiclass
    clus
vv   DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE
  R0                             7                             376
  R1                             0                              51
  R2                             0                               4
  RX                             0                              30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V13, continuous
D78V14, binary
                                 cls
clus                                0   1
  DEL PEAK 20(10P12.31) MUTATED     4   3
  DEL PEAK 20(10P12.31) WILD-TYPE 221 261
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(10P12.31) MUTATED      4    3
  DEL PEAK 20(10P12.31) WILD-TYPE  221  261
            clus
vv           DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE
  MULTIFOCAL                             4                             221
  UNIFOCAL                               3                             261
[1] 2 2
[1] FALSE
D78V15, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(10P12.31) MUTATED                                  0     1
  DEL PEAK 20(10P12.31) WILD-TYPE                                1    51
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(10P12.31) MUTATED                           0     5
  DEL PEAK 20(10P12.31) WILD-TYPE                        27   323
D78V16, multiclass
                                  clus
vv                                 DEL PEAK 20(10P12.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                    0
  WHITE                                                        5
                                  clus
vv                                 DEL PEAK 20(10P12.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         51
  BLACK OR AFRICAN AMERICAN                                     27
  WHITE                                                        323
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V17, binary
                                 cls
clus                                0   1
  DEL PEAK 20(10P12.31) MUTATED     0   6
  DEL PEAK 20(10P12.31) WILD-TYPE  38 353
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(10P12.31) MUTATED      0    6
  DEL PEAK 20(10P12.31) WILD-TYPE   38  353
                        clus
vv                       DEL PEAK 20(10P12.31) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                             6
                        clus
vv                       DEL PEAK 20(10P12.31) WILD-TYPE
  HISPANIC OR LATINO                                  38
  NOT HISPANIC OR LATINO                             353
[1] 2 2
[1] FALSE

Clustering(79) Variable = DEL PEAK 21(10Q21.2) MUTATION ANALYSIS
D79V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 21(10Q21.2) MUTATED    12   0
  DEL PEAK 21(10Q21.2) WILD-TYPE 469  16
  DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE 
                            12                            485 
  DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE 
                             0                             16 
$`DEL PEAK 21(10Q21.2) MUTATED`
TCGA-BJ-A0ZC TCGA-BJ-A190 TCGA-BJ-A28Z TCGA-DE-A3KN TCGA-DO-A1JZ TCGA-E8-A432 
       11.57        20.58        11.08        15.85        54.90        30.61 
TCGA-EL-A3ZS TCGA-EL-A4KI TCGA-EM-A3O9 TCGA-ET-A39N TCGA-ET-A3DQ TCGA-FY-A3I5 
        7.07        23.90         9.24       123.32        84.85         7.82 

$`DEL PEAK 21(10Q21.2) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       41.33        18.87         4.01        16.73        25.48        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       42.08        51.39        41.52         4.83        44.35        42.15 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A290 
       21.04        35.54        32.45        11.31        30.97        30.21 
TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 
       22.88        18.38        16.57        20.48        18.97         7.04 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.01        13.94        36.39        23.31        18.64         7.99 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
       10.88        21.01         3.45        23.84        28.44        15.45 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
       21.63        23.18        19.43        23.47        12.66        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A4M8 
       12.66        35.84        21.63        50.17        37.64        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.27         2.76         9.96        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        23.38        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        11.01       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS 
       10.09         7.82        30.58        35.41        27.45        26.20 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY 
       38.83        33.96        31.99        34.85        28.96         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.42        34.36        37.74         6.77        40.24        33.93 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
       37.48        36.46        35.11        39.09        35.90        33.53 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       35.18        15.88        36.92        31.04        32.42        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU 
       16.41        19.56        36.33        32.81        36.33        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       59.57        11.34        35.87        40.96        36.99        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        42.54        19.20        23.21        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       24.82        22.92        21.01        18.97         7.76        35.67 
TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        3.12        36.43        24.76        17.23        27.62        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       21.34        33.04        34.78        27.06        26.93        35.54 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
        3.12        15.81        35.38        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       47.21        66.38        80.52        63.19        52.44        39.95 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
       31.23        35.67        31.27        29.98        31.50        31.04 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A434 
        0.72         0.26         3.02        25.45         0.16         0.23 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        33.50         0.39         0.39        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS 
       26.73       155.54        97.74       158.83         7.66        45.53 
TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY 
       60.95       157.15        37.94        57.01       106.62         4.18 
TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 
       79.50       139.86        98.53        69.57        57.11       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
       64.87        49.51        50.24       115.10        65.39       136.01 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        50.20       147.75       101.13       139.99        49.32 
TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 
       33.50        43.36        49.71        83.57       139.00       150.48 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 
      108.66        57.63        17.52        52.50        29.65       147.42 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        47.38        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       61.22        60.16        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS 
       41.13        47.84        43.59        24.30        27.06        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       78.61        57.01        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       32.32        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       22.52        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB 
       14.50        15.06         7.33         0.49        13.91        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.86        29.95        29.85        13.51        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      107.41       108.46        84.89       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        98.20        28.24        50.40        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.79        87.62        77.82        75.42        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
      116.78        94.59        80.58        66.84        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      166.62        24.72        43.99        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        13.28         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM 
       48.10       116.09         1.25        20.42        17.82         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
        0.30         0.76        17.06        17.36        15.16         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
       22.49        19.04         1.35        21.60         1.68        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46         2.99        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        8.22        25.64        17.23        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
       26.70        43.69        18.64        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       36.10        32.45        30.21        23.93        12.89 

  DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE 
                          7.07                           0.16 
  DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE 
                        123.32                         169.32 
  DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE 
                        18.215                         30.940 
[1] "7.1 - 123.3 (18.2)" "0.2 - 169.3 (30.9)"
[1] "hr="     "9200000"
D79V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 21(10Q21.2) MUTATED         6        2         3        0         1
  DEL PEAK 21(10Q21.2) WILD-TYPE     276       48       108        2        45
                                vv
clus                             STAGE IVC
  DEL PEAK 21(10Q21.2) MUTATED           0
  DEL PEAK 21(10Q21.2) WILD-TYPE         6
D79V3, multiclass
           clus
vv          DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE
  STAGE I                              6                            276
  STAGE II                             2                             48
  STAGE III                            3                            108
  STAGE IV                             0                              2
  STAGE IVA                            1                             45
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 21(10Q21.2) MUTATED     3   3   6   0
  DEL PEAK 21(10Q21.2) WILD-TYPE 139 162 161  23
D79V4, multiclass
    clus
vv   DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE
  T1                            3                            139
  T2                            3                            162
  T3                            6                            161
  T4                            0                             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"
D79V5, binary
                                cls
clus                               0   1
  DEL PEAK 21(10Q21.2) MUTATED     7   3
  DEL PEAK 21(10Q21.2) WILD-TYPE 218 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10Q21.2) MUTATED      7    3
  DEL PEAK 21(10Q21.2) WILD-TYPE  218  221
   clus
vv  DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE
  0                            7                            218
  1                            3                            221
[1] 2 2
[1] FALSE
D79V6, binary
                                cls
clus                               0   1
  DEL PEAK 21(10Q21.2) MUTATED     5   0
  DEL PEAK 21(10Q21.2) WILD-TYPE 273   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10Q21.2) MUTATED      5    0
  DEL PEAK 21(10Q21.2) WILD-TYPE  273    9
   clus
vv  DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE
  0                            5                            273
  1                            0                              9
[1] 2 2
[1] FALSE
D79V7, binary
                                cls
clus                               0   1
  DEL PEAK 21(10Q21.2) MUTATED     8   4
  DEL PEAK 21(10Q21.2) WILD-TYPE 357 130
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10Q21.2) MUTATED      8    4
  DEL PEAK 21(10Q21.2) WILD-TYPE  357  130
        clus
vv       DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE
  FEMALE                            8                            357
  MALE                              4                            130
[1] 2 2
[1] FALSE
D79V8, binary
                                cls
clus                               0   1
  DEL PEAK 21(10Q21.2) MUTATED     3   8
  DEL PEAK 21(10Q21.2) WILD-TYPE 182 282
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10Q21.2) MUTATED      3    8
  DEL PEAK 21(10Q21.2) WILD-TYPE  182  282
     clus
vv    DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE
  NO                             3                            182
  YES                            8                            282
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 21(10Q21.2) MUTATED                0
  DEL PEAK 21(10Q21.2) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 21(10Q21.2) MUTATED                                               8
  DEL PEAK 21(10Q21.2) WILD-TYPE                                           347
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 21(10Q21.2) MUTATED                                                                        4
  DEL PEAK 21(10Q21.2) WILD-TYPE                                                                     96
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 21(10Q21.2) MUTATED                                                                     0
  DEL PEAK 21(10Q21.2) WILD-TYPE                                                                  36
D79V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 21(10Q21.2) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     8
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            4
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       DEL PEAK 21(10Q21.2) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     347
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V10, binary
                                cls
clus                               0   1
  DEL PEAK 21(10Q21.2) MUTATED    10   0
  DEL PEAK 21(10Q21.2) WILD-TYPE 410  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10Q21.2) MUTATED     10    0
  DEL PEAK 21(10Q21.2) WILD-TYPE  410   17
     clus
vv    DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE
  NO                            10                            410
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 21(10Q21.2) MUTATED              3                       0    9
  DEL PEAK 21(10Q21.2) WILD-TYPE          129                      18  321
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 21(10Q21.2) MUTATED                     0
  DEL PEAK 21(10Q21.2) WILD-TYPE                   1
D79V11, multiclass
                         clus
vv                        DEL PEAK 21(10Q21.2) MUTATED
  MINIMAL (T3)                                       3
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               9
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK 21(10Q21.2) WILD-TYPE
  MINIMAL (T3)                                       129
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               321
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 21(10Q21.2) MUTATED    10   1   0   0
  DEL PEAK 21(10Q21.2) WILD-TYPE 373  50   4  30
D79V12, multiclass
    clus
vv   DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE
  R0                           10                            373
  R1                            1                             50
  R2                            0                              4
  RX                            0                             30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V13, continuous
D79V14, binary
                                cls
clus                               0   1
  DEL PEAK 21(10Q21.2) MUTATED     6   5
  DEL PEAK 21(10Q21.2) WILD-TYPE 219 259
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10Q21.2) MUTATED      6    5
  DEL PEAK 21(10Q21.2) WILD-TYPE  219  259
            clus
vv           DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE
  MULTIFOCAL                            6                            219
  UNIFOCAL                              5                            259
[1] 2 2
[1] FALSE
D79V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 21(10Q21.2) MUTATED                                  0     1
  DEL PEAK 21(10Q21.2) WILD-TYPE                                1    51
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(10Q21.2) MUTATED                           1     9
  DEL PEAK 21(10Q21.2) WILD-TYPE                        26   319
D79V16, multiclass
                                  clus
vv                                 DEL PEAK 21(10Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                       9
                                  clus
vv                                 DEL PEAK 21(10Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        51
  BLACK OR AFRICAN AMERICAN                                    26
  WHITE                                                       319
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V17, binary
                                cls
clus                               0   1
  DEL PEAK 21(10Q21.2) MUTATED     0  11
  DEL PEAK 21(10Q21.2) WILD-TYPE  38 348
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10Q21.2) MUTATED      0   11
  DEL PEAK 21(10Q21.2) WILD-TYPE   38  348
                        clus
vv                       DEL PEAK 21(10Q21.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           11
                        clus
vv                       DEL PEAK 21(10Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            348
[1] 2 2
[1] FALSE

Clustering(80) Variable = DEL PEAK 22(10Q23.31) MUTATION ANALYSIS
D80V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 22(10Q23.31) MUTATED    12   0
  DEL PEAK 22(10Q23.31) WILD-TYPE 469  16
  DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE 
                             12                             485 
  DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE 
                              0                              16 
$`DEL PEAK 22(10Q23.31) MUTATED`
TCGA-BJ-A0Z0 TCGA-BJ-A0ZC TCGA-BJ-A190 TCGA-DE-A3KN TCGA-E8-A432 TCGA-EL-A4KI 
       13.78        11.57        20.58        15.85        30.61        23.90 
TCGA-EM-A1YE TCGA-EM-A3O6 TCGA-EM-A3O9 TCGA-ET-A39N TCGA-ET-A3DQ TCGA-FY-A3I5 
       54.08        15.06         9.24       123.32        84.85         7.82 

$`DEL PEAK 22(10Q23.31) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
        4.24        24.79        49.78        16.34        14.73        41.33 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ 
       18.87         4.01        16.73        25.48        15.12        42.08 
TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S 
       51.39        41.52         4.83        44.35        42.15        21.04 
TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 
       35.54        32.45        11.31        30.97        11.08        30.21 
TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 
       22.88        18.38        16.57        20.48        18.97         7.04 
TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C 
       16.01        13.94        36.39        23.31        18.64         7.99 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
       10.88        21.01         3.45        23.84        28.44        15.45 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
       21.63        23.18        19.43        23.47        12.66        12.30 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
       12.79        12.46        11.38        10.68        15.02        12.43 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A4M8 
       12.66        35.84        21.63        50.17        37.64        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.27         2.76         9.96        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        23.38        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        11.01       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS 
       10.09         7.82        30.58        35.41        27.45        26.20 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY 
       38.83        33.96        31.99        34.85        28.96         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.42        34.36        37.74         6.77        40.24        33.93 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
       37.48        36.46        35.11        39.09        35.90        33.53 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       35.18        15.88        36.92        31.04        32.42        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU 
       16.41        19.56        36.33        32.81        36.33        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       59.57        11.34        35.87        40.96        36.99        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        42.54        19.20        23.21        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       24.82        22.92        21.01        18.97         7.76        35.67 
TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        3.12        36.43        24.76        17.23        27.62        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       21.34        33.04        34.78        27.06        26.93        35.54 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        35.38        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       92.55        47.21        66.38        80.52        63.19        52.44 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       39.95        31.23        35.67        31.27        29.98        31.50 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 
       31.04         0.72         0.26         3.02        25.45         0.16 
TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M 
        0.23        14.96         7.69        33.50         0.39         0.39 
TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR 
       31.66        26.73       155.54        97.74       158.83         7.66 
TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX 
       45.53        60.95       157.15        37.94        57.01       106.62 
TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 
        4.18        79.50       139.86        98.53        69.57        57.11 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS 
      108.36        64.87        49.51        50.24       115.10        65.39 
TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
      136.01        50.37        50.20       147.75       101.13       139.99 
TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
       49.32        33.50        43.36        49.71        83.57       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 
      150.48       108.66        57.63        17.52        52.50        29.65 
TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
      147.42       142.52       129.57        32.48       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       41.29       107.47         5.72        66.90        82.82        89.56 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO 
       78.97        51.78        62.30        36.03        53.06        47.38 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       65.49        61.22        60.16         7.07        59.44        57.47 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       34.72        45.96        37.94        31.04        34.39        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       53.36        44.15        41.13        47.84        43.59        24.30 
TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       27.06        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J 
       19.79        19.46        78.61        57.01        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P 
       15.75        10.45        14.53        10.65        44.19        41.29 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        47.57        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        2.99        12.30        48.46        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        32.32        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        29.72        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       47.38        21.01        12.07        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.02        14.50         7.33         0.49        13.91        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.86        29.95        29.85        13.51        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      107.41       108.46        84.89       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        98.20        28.24        50.40        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.79        87.62        77.82        75.42        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
      116.78        94.59        80.58        66.84        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      166.62        24.72        43.99        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        13.28         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM 
       48.10       116.09         1.25        20.42        17.82         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
        0.30         0.76        17.06        17.36        15.16         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
       22.49        19.04         1.35        21.60         1.68        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46         2.99        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        8.22        25.64        17.23        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
       26.70        43.69        18.64        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       36.10        32.45        30.21        23.93        12.89 

  DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE 
                           7.82                            0.16 
  DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE 
                         123.32                          169.32 
  DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE 
                         18.215                          30.940 
[1] "7.8 - 123.3 (18.2)" "0.2 - 169.3 (30.9)"
[1] "hr="     "9200000"
D80V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 22(10Q23.31) MUTATED         4        5         2        0         1
  DEL PEAK 22(10Q23.31) WILD-TYPE     278       45       109        2        45
                                 vv
clus                              STAGE IVC
  DEL PEAK 22(10Q23.31) MUTATED           0
  DEL PEAK 22(10Q23.31) WILD-TYPE         6
D80V3, multiclass
           clus
vv          DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE
  STAGE I                               4                             278
  STAGE II                              5                              45
  STAGE III                             2                             109
  STAGE IV                              0                               2
  STAGE IVA                             1                              45
  STAGE IVC                             0                               6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 22(10Q23.31) MUTATED     2   5   5   0
  DEL PEAK 22(10Q23.31) WILD-TYPE 140 160 162  23
D80V4, multiclass
    clus
vv   DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE
  T1                             2                             140
  T2                             5                             160
  T3                             5                             162
  T4                             0                              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"
D80V5, binary
                                 cls
clus                                0   1
  DEL PEAK 22(10Q23.31) MUTATED     9   1
  DEL PEAK 22(10Q23.31) WILD-TYPE 216 223
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(10Q23.31) MUTATED      9    1
  DEL PEAK 22(10Q23.31) WILD-TYPE  216  223
   clus
vv  DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE
  0                             9                             216
  1                             1                             223
[1] 2 2
[1] FALSE
D80V6, binary
                                 cls
clus                                0   1
  DEL PEAK 22(10Q23.31) MUTATED     3   0
  DEL PEAK 22(10Q23.31) WILD-TYPE 275   9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(10Q23.31) MUTATED      3    0
  DEL PEAK 22(10Q23.31) WILD-TYPE  275    9
   clus
vv  DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE
  0                             3                             275
  1                             0                               9
[1] 2 2
[1] FALSE
D80V7, binary
                                 cls
clus                                0   1
  DEL PEAK 22(10Q23.31) MUTATED     7   5
  DEL PEAK 22(10Q23.31) WILD-TYPE 358 129
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(10Q23.31) MUTATED      7    5
  DEL PEAK 22(10Q23.31) WILD-TYPE  358  129
        clus
vv       DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE
  FEMALE                             7                             358
  MALE                               5                             129
[1] 2 2
[1] FALSE
D80V8, binary
                                 cls
clus                                0   1
  DEL PEAK 22(10Q23.31) MUTATED     3   8
  DEL PEAK 22(10Q23.31) WILD-TYPE 182 282
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(10Q23.31) MUTATED      3    8
  DEL PEAK 22(10Q23.31) WILD-TYPE  182  282
     clus
vv    DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE
  NO                              3                             182
  YES                             8                             282
[1] 2 2
[1] FALSE
                                 vv
clus                              OTHER  SPECIFY
  DEL PEAK 22(10Q23.31) MUTATED                0
  DEL PEAK 22(10Q23.31) WILD-TYPE              8
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 22(10Q23.31) MUTATED                                               7
  DEL PEAK 22(10Q23.31) WILD-TYPE                                           348
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 22(10Q23.31) MUTATED                                                                        5
  DEL PEAK 22(10Q23.31) WILD-TYPE                                                                     95
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 22(10Q23.31) MUTATED                                                                     0
  DEL PEAK 22(10Q23.31) WILD-TYPE                                                                  36
D80V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 22(10Q23.31) MUTATED
  OTHER  SPECIFY                                                                                     0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      7
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             5
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                0
                                                                        clus
vv                                                                       DEL PEAK 22(10Q23.31) WILD-TYPE
  OTHER  SPECIFY                                                                                       8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      348
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                              95
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V10, binary
                                 cls
clus                                0   1
  DEL PEAK 22(10Q23.31) MUTATED    10   0
  DEL PEAK 22(10Q23.31) WILD-TYPE 410  17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(10Q23.31) MUTATED     10    0
  DEL PEAK 22(10Q23.31) WILD-TYPE  410   17
     clus
vv    DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE
  NO                             10                             410
  YES                             0                              17
[1] 2 2
[1] FALSE
                                 vv
clus                              MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 22(10Q23.31) MUTATED              2                       0   10
  DEL PEAK 22(10Q23.31) WILD-TYPE          130                      18  320
                                 vv
clus                              VERY ADVANCED (T4B)
  DEL PEAK 22(10Q23.31) MUTATED                     0
  DEL PEAK 22(10Q23.31) WILD-TYPE                   1
D80V11, multiclass
                         clus
vv                        DEL PEAK 22(10Q23.31) MUTATED
  MINIMAL (T3)                                        2
  MODERATE/ADVANCED (T4A)                             0
  NONE                                               10
  VERY ADVANCED (T4B)                                 0
                         clus
vv                        DEL PEAK 22(10Q23.31) WILD-TYPE
  MINIMAL (T3)                                        130
  MODERATE/ADVANCED (T4A)                              18
  NONE                                                320
  VERY ADVANCED (T4B)                                   1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 22(10Q23.31) MUTATED    12   0   0   0
  DEL PEAK 22(10Q23.31) WILD-TYPE 371  51   4  30
D80V12, multiclass
    clus
vv   DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE
  R0                            12                             371
  R1                             0                              51
  R2                             0                               4
  RX                             0                              30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V13, continuous
D80V14, binary
                                 cls
clus                                0   1
  DEL PEAK 22(10Q23.31) MUTATED     5   6
  DEL PEAK 22(10Q23.31) WILD-TYPE 220 258
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(10Q23.31) MUTATED      5    6
  DEL PEAK 22(10Q23.31) WILD-TYPE  220  258
            clus
vv           DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE
  MULTIFOCAL                             5                             220
  UNIFOCAL                               6                             258
[1] 2 2
[1] FALSE
D80V15, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 22(10Q23.31) MUTATED                                  0     1
  DEL PEAK 22(10Q23.31) WILD-TYPE                                1    51
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(10Q23.31) MUTATED                           0     7
  DEL PEAK 22(10Q23.31) WILD-TYPE                        27   321
D80V16, multiclass
                                  clus
vv                                 DEL PEAK 22(10Q23.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                    0
  WHITE                                                        7
                                  clus
vv                                 DEL PEAK 22(10Q23.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         51
  BLACK OR AFRICAN AMERICAN                                     27
  WHITE                                                        321
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V17, binary
                                 cls
clus                                0   1
  DEL PEAK 22(10Q23.31) MUTATED     0   9
  DEL PEAK 22(10Q23.31) WILD-TYPE  38 350
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(10Q23.31) MUTATED      0    9
  DEL PEAK 22(10Q23.31) WILD-TYPE   38  350
                        clus
vv                       DEL PEAK 22(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                             9
                        clus
vv                       DEL PEAK 22(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                  38
  NOT HISPANIC OR LATINO                             350
[1] 2 2
[1] FALSE

Clustering(81) Variable = DEL PEAK 23(11P15.1) MUTATION ANALYSIS
D81V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(11P15.1) MUTATED     6   1
  DEL PEAK 23(11P15.1) WILD-TYPE 475  15
  DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE 
                             7                            490 
  DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE 
                             1                             15 
$`DEL PEAK 23(11P15.1) MUTATED`
TCGA-BJ-A190 TCGA-EL-A3GP TCGA-EL-A4K6 TCGA-EL-A4KI TCGA-EM-A22N TCGA-FE-A239 
       20.58        49.51        44.15        23.90        10.65        33.63 
TCGA-FY-A3I5 
        7.82 

$`DEL PEAK 23(11P15.1) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        42.08        51.39        41.52         4.83        44.35 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
       42.15        21.04        35.54        32.45        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.08        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        30.61         0.16         0.23        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        33.50         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        69.57        57.11       108.36        64.87 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K7 TCGA-EL-A4K9 
       31.04        34.39        30.51        53.36        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       43.59        24.30        27.06        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
       48.49        18.05        19.79        19.46        78.61        57.01 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       54.08        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       44.19        41.29        14.24        47.57        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         6.05         2.99        12.30        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        40.34        19.73        32.32        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.46        17.29        14.60        22.52        30.94        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR 
       14.14        33.07        13.38         8.35        29.72        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        47.38        21.01        12.07        17.49 
TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 
       17.39        16.18        15.02        14.50        15.06         7.33 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
        0.49         9.24        13.91        38.66        38.86        29.95 
TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       29.85        13.51        12.79        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        5.33        26.37        26.37        22.45        21.53        60.49 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       24.46        13.68        81.93        81.70        77.56        70.42 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       56.58        60.20        63.39        65.29        18.38        63.45 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       88.41        58.75        37.25        52.60        54.35        83.34 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       84.89       123.32       100.57        95.34        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       98.20        28.24        50.40        79.10        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       87.62        77.82        75.42        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       94.59        84.85        80.58        66.84        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      166.62        24.72        43.99        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       39.95        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       71.08         4.11         1.05        13.28         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON 
      116.09         1.25        20.42        17.82         0.99        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
       13.91        16.27        15.68        16.57        18.08         0.30 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
        0.76        17.06        17.36        15.16         6.58        22.49 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04         1.35        21.60         1.68        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46         2.99        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        18.51        16.90        21.83        31.10         8.22 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
       25.64        17.23        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW 
       27.85        24.69        22.29         5.75         2.47         2.60 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       43.69        18.64        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       33.24        33.40        40.37        21.83         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45        30.21        23.93        12.89 

  DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE 
                          7.82                           0.16 
  DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE 
                         49.51                         169.32 
  DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE 
                         23.90                          30.61 
[1] "7.8 - 49.5 (23.9)"  "0.2 - 169.3 (30.6)"
[1] "hr=" "7.9"
D81V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 23(11P15.1) MUTATED         1        1         4        1         0
  DEL PEAK 23(11P15.1) WILD-TYPE     281       49       107        1        46
                                vv
clus                             STAGE IVC
  DEL PEAK 23(11P15.1) MUTATED           0
  DEL PEAK 23(11P15.1) WILD-TYPE         6
D81V3, multiclass
           clus
vv          DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE
  STAGE I                              1                            281
  STAGE II                             1                             49
  STAGE III                            4                            107
  STAGE IV                             1                              1
  STAGE IVA                            0                             46
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 23(11P15.1) MUTATED     1   1   4   1
  DEL PEAK 23(11P15.1) WILD-TYPE 141 164 163  22
D81V4, multiclass
    clus
vv   DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE
  T1                            1                            141
  T2                            1                            164
  T3                            4                            163
  T4                            1                             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"
D81V5, binary
                                cls
clus                               0   1
  DEL PEAK 23(11P15.1) MUTATED     5   2
  DEL PEAK 23(11P15.1) WILD-TYPE 220 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11P15.1) MUTATED      5    2
  DEL PEAK 23(11P15.1) WILD-TYPE  220  222
   clus
vv  DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE
  0                            5                            220
  1                            2                            222
[1] 2 2
[1] FALSE
D81V6, binary
                                cls
clus                               0   1
  DEL PEAK 23(11P15.1) MUTATED     1   0
  DEL PEAK 23(11P15.1) WILD-TYPE 277   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11P15.1) MUTATED      1    0
  DEL PEAK 23(11P15.1) WILD-TYPE  277    9
   clus
vv  DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE
  0                            1                            277
  1                            0                              9
[1] 2 2
[1] FALSE
D81V7, binary
                                cls
clus                               0   1
  DEL PEAK 23(11P15.1) MUTATED     2   5
  DEL PEAK 23(11P15.1) WILD-TYPE 363 129
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11P15.1) MUTATED      2    5
  DEL PEAK 23(11P15.1) WILD-TYPE  363  129
        clus
vv       DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE
  FEMALE                            2                            363
  MALE                              5                            129
[1] 2 2
[1] FALSE
D81V8, binary
                                cls
clus                               0   1
  DEL PEAK 23(11P15.1) MUTATED     1   5
  DEL PEAK 23(11P15.1) WILD-TYPE 184 285
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11P15.1) MUTATED      1    5
  DEL PEAK 23(11P15.1) WILD-TYPE  184  285
     clus
vv    DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE
  NO                             1                            184
  YES                            5                            285
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 23(11P15.1) MUTATED                0
  DEL PEAK 23(11P15.1) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 23(11P15.1) MUTATED                                               5
  DEL PEAK 23(11P15.1) WILD-TYPE                                           350
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 23(11P15.1) MUTATED                                                                        2
  DEL PEAK 23(11P15.1) WILD-TYPE                                                                     98
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 23(11P15.1) MUTATED                                                                     0
  DEL PEAK 23(11P15.1) WILD-TYPE                                                                  36
D81V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 23(11P15.1) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     5
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       DEL PEAK 23(11P15.1) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V10, binary
                                cls
clus                               0   1
  DEL PEAK 23(11P15.1) MUTATED     6   0
  DEL PEAK 23(11P15.1) WILD-TYPE 414  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11P15.1) MUTATED      6    0
  DEL PEAK 23(11P15.1) WILD-TYPE  414   17
     clus
vv    DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE
  NO                             6                            414
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 23(11P15.1) MUTATED              3                       0    4
  DEL PEAK 23(11P15.1) WILD-TYPE          129                      18  326
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 23(11P15.1) MUTATED                     0
  DEL PEAK 23(11P15.1) WILD-TYPE                   1
D81V11, multiclass
                         clus
vv                        DEL PEAK 23(11P15.1) MUTATED
  MINIMAL (T3)                                       3
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               4
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK 23(11P15.1) WILD-TYPE
  MINIMAL (T3)                                       129
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               326
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 23(11P15.1) MUTATED     6   0   0   1
  DEL PEAK 23(11P15.1) WILD-TYPE 377  51   4  29
D81V12, multiclass
    clus
vv   DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE
  R0                            6                            377
  R1                            0                             51
  R2                            0                              4
  RX                            1                             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"
D81V13, continuous
D81V14, binary
                                cls
clus                               0   1
  DEL PEAK 23(11P15.1) MUTATED     4   3
  DEL PEAK 23(11P15.1) WILD-TYPE 221 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11P15.1) MUTATED      4    3
  DEL PEAK 23(11P15.1) WILD-TYPE  221  261
            clus
vv           DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE
  MULTIFOCAL                            4                            221
  UNIFOCAL                              3                            261
[1] 2 2
[1] FALSE
D81V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 23(11P15.1) MUTATED                                  0     0
  DEL PEAK 23(11P15.1) WILD-TYPE                                1    52
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(11P15.1) MUTATED                           1     5
  DEL PEAK 23(11P15.1) WILD-TYPE                        26   323
D81V16, multiclass
                                  clus
vv                                 DEL PEAK 23(11P15.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                       5
                                  clus
vv                                 DEL PEAK 23(11P15.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        52
  BLACK OR AFRICAN AMERICAN                                    26
  WHITE                                                       323
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V17, binary
                                cls
clus                               0   1
  DEL PEAK 23(11P15.1) MUTATED     0   6
  DEL PEAK 23(11P15.1) WILD-TYPE  38 353
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11P15.1) MUTATED      0    6
  DEL PEAK 23(11P15.1) WILD-TYPE   38  353
                        clus
vv                       DEL PEAK 23(11P15.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            6
                        clus
vv                       DEL PEAK 23(11P15.1) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            353
[1] 2 2
[1] FALSE

Clustering(82) Variable = DEL PEAK 24(13Q12.13) MUTATION ANALYSIS
D82V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 24(13Q12.13) MUTATED    15   2
  DEL PEAK 24(13Q12.13) WILD-TYPE 466  14
  DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE 
                             17                             480 
  DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE 
                              2                              14 
$`DEL PEAK 24(13Q12.13) MUTATED`
TCGA-BJ-A3F0 TCGA-BJ-A45C TCGA-DJ-A13P TCGA-DJ-A2Q2 TCGA-DJ-A3UY TCGA-EL-A3T0 
       13.94         7.99       169.32         6.77        35.87       142.52 
TCGA-EM-A1YB TCGA-EM-A22M TCGA-EM-A22Q TCGA-EM-A2OX TCGA-EM-A3O3 TCGA-EM-A3SU 
       19.46        14.53        14.24        19.73        14.50        29.95 
TCGA-ET-A39N TCGA-ET-A40S TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3W9 
      123.32        40.21        33.63         7.82         0.76 

$`DEL PEAK 24(13Q12.13) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3PR TCGA-BJ-A3PT 
       20.48        18.97         7.04        16.01        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
       18.64        10.88        21.01         3.45        23.84        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
       15.45        21.63        23.18        19.43        23.47        12.66 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
       12.43        12.66        35.84        21.63        50.17        37.64 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M 
       25.12        14.70        14.27         2.76         9.96        48.79 
TCGA-DJ-A13O TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
       38.17        18.58         8.71        56.19        23.38        43.17 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       52.37         8.32        11.01       135.91        30.61        44.98 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
       42.51        14.96        17.59         6.02        42.58        47.41 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
       17.56        10.09         7.82        30.58        35.41        27.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
       26.20        38.83        33.96        31.99        34.85        28.96 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.78         8.42        34.36        37.74        40.24        33.93 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
       37.48        36.46        35.11        39.09        35.90        33.53 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       35.18        15.88        36.92        31.04        32.42        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU 
       16.41        19.56        36.33        32.81        36.33        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       59.57        11.34        40.96        36.99        20.22        30.61 
TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       42.54        19.20        23.21        21.27        20.48        24.82 
TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI 
       22.92        21.01        18.97         7.76        35.67         3.12 
TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       36.43        24.76        17.23        27.62        30.87        21.34 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       33.04        34.78        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       47.21        66.38        80.52        63.19        52.44        39.95 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
       31.23        35.67        31.27        29.98        31.50        31.04 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 
        0.72         0.26         3.02        25.45        30.61         0.16 
TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M 
        0.23        14.96         7.69        33.50         0.39         0.39 
TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR 
       31.66        26.73       155.54        97.74       158.83         7.66 
TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX 
       45.53        60.95       157.15        37.94        57.01       106.62 
TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 
        4.18        79.50       139.86        98.53        69.57        57.11 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS 
      108.36        64.87        49.51        50.24       115.10        65.39 
TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
      136.01        50.37        50.20       147.75       101.13       139.99 
TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
       49.32        33.50        43.36        49.71        83.57       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 
      150.48       108.66        57.63        17.52        52.50        29.65 
TCGA-EL-A3N3 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      147.42       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
      107.47         5.72        66.90        82.82        89.56        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       51.78        62.30        36.03        53.06        47.38        65.49 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       61.22        60.16         7.07        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        37.94        31.04        34.39        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       44.15        41.13        47.84        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J 
       19.79        78.61        57.01        54.08        14.73        14.50 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A2CJ 
       15.75        10.45        10.65        44.19        41.29        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
       17.88        13.18        23.51         6.05         2.99        12.30 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OY TCGA-EM-A2OZ 
       48.46        13.15        22.16        40.34        32.32        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ 
       17.59        17.46        17.29        14.60        22.52        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        33.07        13.38         8.35        29.72 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        47.38        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O7 
       17.49        17.39        16.18        15.02        15.06         7.33 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SX 
        0.49         9.24        13.91        38.66        38.86        29.85 
TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       13.51        12.79        84.59        29.33        21.34         5.33 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
       26.37        26.37        22.45        21.53        60.49        24.46 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
       13.68        81.93        81.70        77.56        70.42        56.58 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       60.20        63.39        65.29        18.38        63.45        88.41 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       58.75        37.25        52.60        54.35        83.34         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       80.88        33.24       106.09       107.41       108.46        84.89 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
      100.57        95.34        94.13        55.10        98.20        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
       50.40        79.10        76.64         5.79        87.62        77.82 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       75.42        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
       43.99        46.26        44.38        37.48        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA 
      117.40        66.77       112.80        39.95        81.83       106.36 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD 
       85.15        85.68        78.77        71.08         4.11         1.05 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       13.28         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       17.82         0.99        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       16.57        18.08         0.30        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58        22.49        19.04         1.35        21.60         1.68 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46         2.99        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        18.51        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
       31.10         8.22        25.64        17.23        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
      113.85        26.70        43.69        18.64        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET 
       84.72        35.28        33.24        33.40        40.37        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        9.50        36.10        32.45        30.21        23.93        12.89 

  DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE 
                           0.76                            0.16 
  DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE 
                         169.32                          166.62 
  DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE 
                         19.460                          30.905 
[1] "0.8 - 169.3 (19.5)" "0.2 - 166.6 (30.9)"
[1] "hr=" "4.5"
D82V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 24(13Q12.13) MUTATED         7        4         6        0         1
  DEL PEAK 24(13Q12.13) WILD-TYPE     275       46       105        2        45
                                 vv
clus                              STAGE IVC
  DEL PEAK 24(13Q12.13) MUTATED           0
  DEL PEAK 24(13Q12.13) WILD-TYPE         6
D82V3, multiclass
           clus
vv          DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE
  STAGE I                               7                             275
  STAGE II                              4                              46
  STAGE III                             6                             105
  STAGE IV                              0                               2
  STAGE IVA                             1                              45
  STAGE IVC                             0                               6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 24(13Q12.13) MUTATED     5   6   7   0
  DEL PEAK 24(13Q12.13) WILD-TYPE 137 159 160  23
D82V4, multiclass
    clus
vv   DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE
  T1                             5                             137
  T2                             6                             159
  T3                             7                             160
  T4                             0                              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"
D82V5, binary
                                 cls
clus                                0   1
  DEL PEAK 24(13Q12.13) MUTATED    11   4
  DEL PEAK 24(13Q12.13) WILD-TYPE 214 220
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(13Q12.13) MUTATED     11    4
  DEL PEAK 24(13Q12.13) WILD-TYPE  214  220
   clus
vv  DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE
  0                            11                             214
  1                             4                             220
[1] 2 2
[1] FALSE
D82V6, binary
                                 cls
clus                                0   1
  DEL PEAK 24(13Q12.13) MUTATED     6   0
  DEL PEAK 24(13Q12.13) WILD-TYPE 272   9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(13Q12.13) MUTATED      6    0
  DEL PEAK 24(13Q12.13) WILD-TYPE  272    9
   clus
vv  DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE
  0                             6                             272
  1                             0                               9
[1] 2 2
[1] FALSE
D82V7, binary
                                 cls
clus                                0   1
  DEL PEAK 24(13Q12.13) MUTATED    11   7
  DEL PEAK 24(13Q12.13) WILD-TYPE 354 127
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(13Q12.13) MUTATED     11    7
  DEL PEAK 24(13Q12.13) WILD-TYPE  354  127
        clus
vv       DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE
  FEMALE                            11                             354
  MALE                               7                             127
[1] 2 2
[1] FALSE
D82V8, binary
                                 cls
clus                                0   1
  DEL PEAK 24(13Q12.13) MUTATED     4  11
  DEL PEAK 24(13Q12.13) WILD-TYPE 181 279
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(13Q12.13) MUTATED      4   11
  DEL PEAK 24(13Q12.13) WILD-TYPE  181  279
     clus
vv    DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE
  NO                              4                             181
  YES                            11                             279
[1] 2 2
[1] FALSE
                                 vv
clus                              OTHER  SPECIFY
  DEL PEAK 24(13Q12.13) MUTATED                0
  DEL PEAK 24(13Q12.13) WILD-TYPE              8
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 24(13Q12.13) MUTATED                                              13
  DEL PEAK 24(13Q12.13) WILD-TYPE                                           342
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 24(13Q12.13) MUTATED                                                                        5
  DEL PEAK 24(13Q12.13) WILD-TYPE                                                                     95
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 24(13Q12.13) MUTATED                                                                     0
  DEL PEAK 24(13Q12.13) WILD-TYPE                                                                  36
D82V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 24(13Q12.13) MUTATED
  OTHER  SPECIFY                                                                                     0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     13
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             5
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                0
                                                                        clus
vv                                                                       DEL PEAK 24(13Q12.13) WILD-TYPE
  OTHER  SPECIFY                                                                                       8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      342
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                              95
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V10, binary
                                 cls
clus                                0   1
  DEL PEAK 24(13Q12.13) MUTATED    13   4
  DEL PEAK 24(13Q12.13) WILD-TYPE 407  13
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(13Q12.13) MUTATED     13    4
  DEL PEAK 24(13Q12.13) WILD-TYPE  407   13
     clus
vv    DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE
  NO                             13                             407
  YES                             4                              13
[1] 2 2
[1] FALSE
                                 vv
clus                              MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 24(13Q12.13) MUTATED              3                       0   15
  DEL PEAK 24(13Q12.13) WILD-TYPE          129                      18  315
                                 vv
clus                              VERY ADVANCED (T4B)
  DEL PEAK 24(13Q12.13) MUTATED                     0
  DEL PEAK 24(13Q12.13) WILD-TYPE                   1
D82V11, multiclass
                         clus
vv                        DEL PEAK 24(13Q12.13) MUTATED
  MINIMAL (T3)                                        3
  MODERATE/ADVANCED (T4A)                             0
  NONE                                               15
  VERY ADVANCED (T4B)                                 0
                         clus
vv                        DEL PEAK 24(13Q12.13) WILD-TYPE
  MINIMAL (T3)                                        129
  MODERATE/ADVANCED (T4A)                              18
  NONE                                                315
  VERY ADVANCED (T4B)                                   1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 24(13Q12.13) MUTATED    14   2   0   1
  DEL PEAK 24(13Q12.13) WILD-TYPE 369  49   4  29
D82V12, multiclass
    clus
vv   DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE
  R0                            14                             369
  R1                             2                              49
  R2                             0                               4
  RX                             1                              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"
D82V13, continuous
D82V14, binary
                                 cls
clus                                0   1
  DEL PEAK 24(13Q12.13) MUTATED     9   9
  DEL PEAK 24(13Q12.13) WILD-TYPE 216 255
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(13Q12.13) MUTATED      9    9
  DEL PEAK 24(13Q12.13) WILD-TYPE  216  255
            clus
vv           DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE
  MULTIFOCAL                             9                             216
  UNIFOCAL                               9                             255
[1] 2 2
[1] FALSE
D82V15, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 24(13Q12.13) MUTATED                                  0     1
  DEL PEAK 24(13Q12.13) WILD-TYPE                                1    51
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(13Q12.13) MUTATED                           1    11
  DEL PEAK 24(13Q12.13) WILD-TYPE                        26   317
D82V16, multiclass
                                  clus
vv                                 DEL PEAK 24(13Q12.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                    1
  WHITE                                                       11
                                  clus
vv                                 DEL PEAK 24(13Q12.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         51
  BLACK OR AFRICAN AMERICAN                                     26
  WHITE                                                        317
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V17, binary
                                 cls
clus                                0   1
  DEL PEAK 24(13Q12.13) MUTATED     0  13
  DEL PEAK 24(13Q12.13) WILD-TYPE  38 346
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(13Q12.13) MUTATED      0   13
  DEL PEAK 24(13Q12.13) WILD-TYPE   38  346
                        clus
vv                       DEL PEAK 24(13Q12.13) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            13
                        clus
vv                       DEL PEAK 24(13Q12.13) WILD-TYPE
  HISPANIC OR LATINO                                  38
  NOT HISPANIC OR LATINO                             346
[1] 2 2
[1] FALSE

Clustering(83) Variable = DEL PEAK 25(13Q22.1) MUTATION ANALYSIS
D83V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(13Q22.1) MUTATED    16   2
  DEL PEAK 25(13Q22.1) WILD-TYPE 465  14
  DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE 
                            18                            479 
  DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE 
                             2                             14 
$`DEL PEAK 25(13Q22.1) MUTATED`
TCGA-BJ-A2N9 TCGA-BJ-A3F0 TCGA-BJ-A45C TCGA-CE-A13K TCGA-DJ-A13P TCGA-DJ-A1QN 
       20.48        13.94         7.99        12.66       169.32        42.58 
TCGA-DJ-A2Q2 TCGA-EM-A1YB TCGA-EM-A22M TCGA-EM-A22Q TCGA-EM-A2OX TCGA-ET-A39N 
        6.77        19.46        14.53        14.24        19.73       123.32 
TCGA-ET-A40S TCGA-FE-A235 TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3W9 TCGA-L6-A4EP 
       40.21       117.40        33.63         7.82         0.76        33.40 

$`DEL PEAK 25(13Q22.1) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
       18.97         7.04        16.01        36.39        23.31        18.64 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
       10.88        21.01         3.45        23.84        28.44        15.45 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD 
       21.63        23.18        19.43        23.47        12.30        12.79 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 
       12.46        11.38        10.68        15.02        12.43        12.66 
TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       35.84        21.63        50.17        37.64        15.85        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J 
       18.84        30.12        11.57        30.02        25.12        14.70 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13R 
       14.27         2.76         9.96        48.79        38.17        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        23.38        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       11.01       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
       17.59         6.02        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
       30.58        35.41        27.45        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
       37.74        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        30.61         0.16         0.23        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        33.50         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        69.57        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       49.51        50.24       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       150.48       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        89.56        78.97        51.78 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        47.38        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       60.16         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        47.84        43.59        24.30        27.06        23.90 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       78.61        57.01        54.08        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.45        10.65        44.19        41.29        47.57        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       13.18        23.51         6.05         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       13.15        22.16        40.34        32.32        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.46        17.29        14.60        22.52        30.94        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR 
       14.14        33.07        13.38         8.35        29.72        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        47.38        21.01        12.07        17.49 
TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 
       17.39        16.18        15.02        14.50        15.06         7.33 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
        0.49         9.24        13.91        38.66        38.86        29.95 
TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       29.85        13.51        12.79        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        5.33        26.37        26.37        22.45        21.53        60.49 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       24.46        13.68        81.93        81.70        77.56        70.42 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       56.58        60.20        63.39        65.29        18.38        63.45 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       88.41        58.75        37.25        52.60        54.35        83.34 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89       100.57        95.34        94.13        55.10        98.20 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24        50.40        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       77.82        75.42        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40T TCGA-ET-A4KN 
       24.72        43.99        46.26        44.38        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA 
       68.22        66.77       112.80        39.95        81.83       106.36 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD 
       85.15        85.68        78.77        71.08         4.11         1.05 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       13.28         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       17.82         0.99        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K 
       16.57        18.08         0.30        17.06        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58        22.49        19.04         1.35        21.60         1.68 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46         2.99        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y 
       18.61        48.92        47.41        18.51        16.90        21.83 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
       31.10         8.22        25.64        17.23        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J 
        2.47         2.60         0.20       143.57        15.98        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 
      113.85        26.70        43.69        18.64        32.45        87.39 
TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       84.72        35.28        33.24        40.37        21.83         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       36.10        32.45        30.21        23.93        12.89 

  DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE 
                          0.76                           0.16 
  DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE 
                        169.32                         166.62 
  DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE 
                        19.595                         30.870 
[1] "0.8 - 169.3 (19.6)" "0.2 - 166.6 (30.9)"
[1] "hr=" "4.3"
D83V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 25(13Q22.1) MUTATED        10        4         4        0         1
  DEL PEAK 25(13Q22.1) WILD-TYPE     272       46       107        2        45
                                vv
clus                             STAGE IVC
  DEL PEAK 25(13Q22.1) MUTATED           0
  DEL PEAK 25(13Q22.1) WILD-TYPE         6
D83V3, multiclass
           clus
vv          DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE
  STAGE I                             10                            272
  STAGE II                             4                             46
  STAGE III                            4                            107
  STAGE IV                             0                              2
  STAGE IVA                            1                             45
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 25(13Q22.1) MUTATED     5   7   7   0
  DEL PEAK 25(13Q22.1) WILD-TYPE 137 158 160  23
D83V4, multiclass
    clus
vv   DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE
  T1                            5                            137
  T2                            7                            158
  T3                            7                            160
  T4                            0                             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"
D83V5, binary
                                cls
clus                               0   1
  DEL PEAK 25(13Q22.1) MUTATED    13   3
  DEL PEAK 25(13Q22.1) WILD-TYPE 212 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(13Q22.1) MUTATED     13    3
  DEL PEAK 25(13Q22.1) WILD-TYPE  212  221
   clus
vv  DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE
  0                           13                            212
  1                            3                            221
[1] 2 2
[1] FALSE
D83V6, binary
                                cls
clus                               0   1
  DEL PEAK 25(13Q22.1) MUTATED     8   0
  DEL PEAK 25(13Q22.1) WILD-TYPE 270   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(13Q22.1) MUTATED      8    0
  DEL PEAK 25(13Q22.1) WILD-TYPE  270    9
   clus
vv  DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE
  0                            8                            270
  1                            0                              9
[1] 2 2
[1] FALSE
D83V7, binary
                                cls
clus                               0   1
  DEL PEAK 25(13Q22.1) MUTATED    12   7
  DEL PEAK 25(13Q22.1) WILD-TYPE 353 127
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(13Q22.1) MUTATED     12    7
  DEL PEAK 25(13Q22.1) WILD-TYPE  353  127
        clus
vv       DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE
  FEMALE                           12                            353
  MALE                              7                            127
[1] 2 2
[1] FALSE
D83V8, binary
                                cls
clus                               0   1
  DEL PEAK 25(13Q22.1) MUTATED     6  10
  DEL PEAK 25(13Q22.1) WILD-TYPE 179 280
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(13Q22.1) MUTATED      6   10
  DEL PEAK 25(13Q22.1) WILD-TYPE  179  280
     clus
vv    DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE
  NO                             6                            179
  YES                           10                            280
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 25(13Q22.1) MUTATED                0
  DEL PEAK 25(13Q22.1) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 25(13Q22.1) MUTATED                                              14
  DEL PEAK 25(13Q22.1) WILD-TYPE                                           341
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 25(13Q22.1) MUTATED                                                                        5
  DEL PEAK 25(13Q22.1) WILD-TYPE                                                                     95
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 25(13Q22.1) MUTATED                                                                     0
  DEL PEAK 25(13Q22.1) WILD-TYPE                                                                  36
D83V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 25(13Q22.1) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    14
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            5
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       DEL PEAK 25(13Q22.1) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     341
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             95
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V10, binary
                                cls
clus                               0   1
  DEL PEAK 25(13Q22.1) MUTATED    13   4
  DEL PEAK 25(13Q22.1) WILD-TYPE 407  13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(13Q22.1) MUTATED     13    4
  DEL PEAK 25(13Q22.1) WILD-TYPE  407   13
     clus
vv    DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE
  NO                            13                            407
  YES                            4                             13
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 25(13Q22.1) MUTATED              3                       0   16
  DEL PEAK 25(13Q22.1) WILD-TYPE          129                      18  314
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 25(13Q22.1) MUTATED                     0
  DEL PEAK 25(13Q22.1) WILD-TYPE                   1
D83V11, multiclass
                         clus
vv                        DEL PEAK 25(13Q22.1) MUTATED
  MINIMAL (T3)                                       3
  MODERATE/ADVANCED (T4A)                            0
  NONE                                              16
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK 25(13Q22.1) WILD-TYPE
  MINIMAL (T3)                                       129
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               314
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 25(13Q22.1) MUTATED    14   3   0   1
  DEL PEAK 25(13Q22.1) WILD-TYPE 369  48   4  29
D83V12, multiclass
    clus
vv   DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE
  R0                           14                            369
  R1                            3                             48
  R2                            0                              4
  RX                            1                             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"
D83V13, continuous
D83V14, binary
                                cls
clus                               0   1
  DEL PEAK 25(13Q22.1) MUTATED    10   9
  DEL PEAK 25(13Q22.1) WILD-TYPE 215 255
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(13Q22.1) MUTATED     10    9
  DEL PEAK 25(13Q22.1) WILD-TYPE  215  255
            clus
vv           DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE
  MULTIFOCAL                           10                            215
  UNIFOCAL                              9                            255
[1] 2 2
[1] FALSE
D83V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 25(13Q22.1) MUTATED                                  0     3
  DEL PEAK 25(13Q22.1) WILD-TYPE                                1    49
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(13Q22.1) MUTATED                           1    11
  DEL PEAK 25(13Q22.1) WILD-TYPE                        26   317
D83V16, multiclass
                                  clus
vv                                 DEL PEAK 25(13Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                      11
                                  clus
vv                                 DEL PEAK 25(13Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        49
  BLACK OR AFRICAN AMERICAN                                    26
  WHITE                                                       317
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V17, binary
                                cls
clus                               0   1
  DEL PEAK 25(13Q22.1) MUTATED     0  16
  DEL PEAK 25(13Q22.1) WILD-TYPE  38 343
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(13Q22.1) MUTATED      0   16
  DEL PEAK 25(13Q22.1) WILD-TYPE   38  343
                        clus
vv                       DEL PEAK 25(13Q22.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           16
                        clus
vv                       DEL PEAK 25(13Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            343
[1] 2 2
[1] FALSE

Clustering(84) Variable = DEL PEAK 27(15Q25.3) MUTATION ANALYSIS
D84V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(15Q25.3) MUTATED     9   0
  DEL PEAK 27(15Q25.3) WILD-TYPE 472  16
  DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE 
                             9                            488 
  DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE 
                             0                             16 
$`DEL PEAK 27(15Q25.3) MUTATED`
TCGA-BJ-A3F0 TCGA-DJ-A4UR TCGA-EL-A3GO TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A2OY 
       13.94        34.78        64.87        54.08        14.73        32.32 
TCGA-EM-A3O9 TCGA-ET-A39N TCGA-FY-A3I5 
        9.24       123.32         7.82 

$`DEL PEAK 27(15Q25.3) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3PR TCGA-BJ-A3PT 
       20.48        18.97         7.04        16.01        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP 
       42.58        47.41        17.56        10.09         7.82        30.58 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UT 
       17.23        27.62        30.87        21.34        33.04        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        52.44        39.95        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GP TCGA-EL-A3GQ 
       98.53        69.57        57.11       108.36        49.51        50.24 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
      115.10        65.39       136.01        50.37        50.20       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       83.57       139.00       150.48       108.66        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       52.50        29.65       147.42       142.52       129.57        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      132.07        98.24        41.29       107.47         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM 
       82.82        89.56        78.97        51.78        62.30        36.03 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        65.49        61.22        60.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       34.39        30.51        53.36        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       43.59        24.30        27.06        23.90        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        48.49        18.05        19.79        19.46        78.61 
TCGA-EM-A1YD TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N 
       57.01        14.50        15.75        10.45        14.53        10.65 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       44.19        41.29        14.24        47.57        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         6.05         2.99        12.30        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        40.34        19.73        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       33.07        13.38         8.35        29.72        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        47.38        21.01        12.07        17.49        17.39 
TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 
       16.18        15.02        14.50        15.06         7.33         0.49 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       13.91        38.66        38.86        29.95        29.85        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        84.59        29.33        21.34         5.33        26.37 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
       26.37        22.45        21.53        60.49        24.46        13.68 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       81.93        81.70        77.56        70.42        56.58        60.20 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       63.39        65.29        18.38        63.45        88.41        58.75 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       37.25        52.60        54.35        83.34         2.66        80.88 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O 
       33.24       106.09       107.41       108.46        84.89       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       95.34        94.13        55.10        98.20        28.24        50.40 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
       79.10        76.64         5.79        87.62        77.82        75.42 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
       46.65        52.47       116.78        94.59        84.85        80.58 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
       66.84        43.73        62.83       166.62        24.72        43.99 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
       46.26        44.38        40.21        37.48        33.17        31.40 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      117.40        66.77       112.80        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        1.05        13.28         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       20.42        17.82         0.99        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08         0.30         0.76        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.36        15.16         6.58        22.49        19.04         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       21.60         1.68        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
        2.99        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90        21.83        31.10         8.22        25.64        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF 
       43.17        27.19        11.24        31.82        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F 
       22.29         5.75         2.47         2.60         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       23.93        12.89 

  DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE 
                          7.82                           0.16 
  DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE 
                        123.32                         169.32 
  DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE 
                         32.32                          30.61 
[1] "7.8 - 123.3 (32.3)" "0.2 - 169.3 (30.6)"
[1] "hr="     "9200000"
D84V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 27(15Q25.3) MUTATED         4        3         2        0         0
  DEL PEAK 27(15Q25.3) WILD-TYPE     278       47       109        2        46
                                vv
clus                             STAGE IVC
  DEL PEAK 27(15Q25.3) MUTATED           0
  DEL PEAK 27(15Q25.3) WILD-TYPE         6
D84V3, multiclass
           clus
vv          DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE
  STAGE I                              4                            278
  STAGE II                             3                             47
  STAGE III                            2                            109
  STAGE IV                             0                              2
  STAGE IVA                            0                             46
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 27(15Q25.3) MUTATED     1   3   5   0
  DEL PEAK 27(15Q25.3) WILD-TYPE 141 162 162  23
D84V4, multiclass
    clus
vv   DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE
  T1                            1                            141
  T2                            3                            162
  T3                            5                            162
  T4                            0                             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"
D84V5, binary
                                cls
clus                               0   1
  DEL PEAK 27(15Q25.3) MUTATED     7   1
  DEL PEAK 27(15Q25.3) WILD-TYPE 218 223
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q25.3) MUTATED      7    1
  DEL PEAK 27(15Q25.3) WILD-TYPE  218  223
   clus
vv  DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE
  0                            7                            218
  1                            1                            223
[1] 2 2
[1] FALSE
D84V6, binary
                                cls
clus                               0   1
  DEL PEAK 27(15Q25.3) MUTATED     2   1
  DEL PEAK 27(15Q25.3) WILD-TYPE 276   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q25.3) MUTATED      2    1
  DEL PEAK 27(15Q25.3) WILD-TYPE  276    8
   clus
vv  DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE
  0                            2                            276
  1                            1                              8
[1] 2 2
[1] FALSE
D84V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(15Q25.3) MUTATED     8   1
  DEL PEAK 27(15Q25.3) WILD-TYPE 357 133
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q25.3) MUTATED      8    1
  DEL PEAK 27(15Q25.3) WILD-TYPE  357  133
        clus
vv       DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE
  FEMALE                            8                            357
  MALE                              1                            133
[1] 2 2
[1] FALSE
D84V8, binary
                                cls
clus                               0   1
  DEL PEAK 27(15Q25.3) MUTATED     2   6
  DEL PEAK 27(15Q25.3) WILD-TYPE 183 284
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q25.3) MUTATED      2    6
  DEL PEAK 27(15Q25.3) WILD-TYPE  183  284
     clus
vv    DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE
  NO                             2                            183
  YES                            6                            284
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 27(15Q25.3) MUTATED                0
  DEL PEAK 27(15Q25.3) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 27(15Q25.3) MUTATED                                               4
  DEL PEAK 27(15Q25.3) WILD-TYPE                                           351
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 27(15Q25.3) MUTATED                                                                        5
  DEL PEAK 27(15Q25.3) WILD-TYPE                                                                     95
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 27(15Q25.3) MUTATED                                                                     0
  DEL PEAK 27(15Q25.3) WILD-TYPE                                                                  36
D84V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 27(15Q25.3) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            5
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       DEL PEAK 27(15Q25.3) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             95
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V10, binary
                                cls
clus                               0   1
  DEL PEAK 27(15Q25.3) MUTATED     8   0
  DEL PEAK 27(15Q25.3) WILD-TYPE 412  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q25.3) MUTATED      8    0
  DEL PEAK 27(15Q25.3) WILD-TYPE  412   17
     clus
vv    DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE
  NO                             8                            412
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 27(15Q25.3) MUTATED              2                       0    7
  DEL PEAK 27(15Q25.3) WILD-TYPE          130                      18  323
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 27(15Q25.3) MUTATED                     0
  DEL PEAK 27(15Q25.3) WILD-TYPE                   1
D84V11, multiclass
                         clus
vv                        DEL PEAK 27(15Q25.3) MUTATED
  MINIMAL (T3)                                       2
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               7
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK 27(15Q25.3) WILD-TYPE
  MINIMAL (T3)                                       130
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               323
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 27(15Q25.3) MUTATED     8   1   0   0
  DEL PEAK 27(15Q25.3) WILD-TYPE 375  50   4  30
D84V12, multiclass
    clus
vv   DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE
  R0                            8                            375
  R1                            1                             50
  R2                            0                              4
  RX                            0                             30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V13, continuous
D84V14, binary
                                cls
clus                               0   1
  DEL PEAK 27(15Q25.3) MUTATED     4   5
  DEL PEAK 27(15Q25.3) WILD-TYPE 221 259
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q25.3) MUTATED      4    5
  DEL PEAK 27(15Q25.3) WILD-TYPE  221  259
            clus
vv           DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE
  MULTIFOCAL                            4                            221
  UNIFOCAL                              5                            259
[1] 2 2
[1] FALSE
D84V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 27(15Q25.3) MUTATED                                  0     1
  DEL PEAK 27(15Q25.3) WILD-TYPE                                1    51
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(15Q25.3) MUTATED                           0     4
  DEL PEAK 27(15Q25.3) WILD-TYPE                        27   324
D84V16, multiclass
                                  clus
vv                                 DEL PEAK 27(15Q25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       4
                                  clus
vv                                 DEL PEAK 27(15Q25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        51
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V17, binary
                                cls
clus                               0   1
  DEL PEAK 27(15Q25.3) MUTATED     1   4
  DEL PEAK 27(15Q25.3) WILD-TYPE  37 355
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q25.3) MUTATED      1    4
  DEL PEAK 27(15Q25.3) WILD-TYPE   37  355
                        clus
vv                       DEL PEAK 27(15Q25.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                            4
                        clus
vv                       DEL PEAK 27(15Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                 37
  NOT HISPANIC OR LATINO                            355
[1] 2 2
[1] FALSE

Clustering(85) Variable = DEL PEAK 29(16Q23.3) MUTATION ANALYSIS
D85V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(16Q23.3) MUTATED     5   1
  DEL PEAK 29(16Q23.3) WILD-TYPE 476  15
  DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE 
                             6                            491 
  DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE 
                             1                             15 
$`DEL PEAK 29(16Q23.3) MUTATED`
TCGA-DJ-A3V7 TCGA-EL-A3GP TCGA-EL-A3H5 TCGA-EL-A3MX TCGA-ET-A2N4 TCGA-ET-A3BT 
       23.21        49.51        83.57        57.63         2.66        87.62 

$`DEL PEAK 29(16Q23.3) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
       30.58        35.41        27.45        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74         6.77        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        36.33        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       35.87        40.96        36.99        20.22        30.61        42.54 
TCGA-DJ-A3V5 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       19.20        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        30.61         0.16         0.23        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        33.50         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        69.57        57.11       108.36        64.87 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MY TCGA-EL-A3MZ 
       49.71       139.00       150.48       108.66        17.52        52.50 
TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       29.65       147.42       142.52       129.57        32.48       132.07 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
       98.24        41.29       107.47         5.72        66.90        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN 
       89.56        78.97        51.78        62.30        36.03        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        65.49        61.22        60.16         7.07        59.44 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       57.47        34.72        45.96        37.94        31.04        34.39 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        53.36        44.15        41.13        47.84        43.59 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       24.30        27.06        23.90        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
       48.49        18.05        19.79        19.46        78.61        57.01 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       54.08        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.65        44.19        41.29        14.24        47.57        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       13.18        23.51         6.05         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        40.34        19.73        32.32        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ 
       17.59        17.46        17.29        14.60        22.52        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        33.07        13.38         8.35        29.72 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        47.38        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 
       17.49        17.39        16.18        15.02        14.50        15.06 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33         0.49         9.24        13.91        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       29.95        29.85        13.51        12.79        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
       21.34         5.33        26.37        26.37        22.45        21.53 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       60.49        24.46        13.68        81.93        81.70        77.56 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       70.42        56.58        60.20        63.39        65.29        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       63.45        88.41        58.75        37.25        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
       83.34        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       84.89       123.32       100.57        95.34        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       98.20        28.24        50.40        79.10        76.64         5.79 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       77.82        75.42        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       117.40        66.77       112.80        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       33.63        81.83       106.36        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       71.08         4.11         1.05        13.28         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
      116.09         1.25        20.42        17.82         7.82         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
        0.30         0.76        17.06        17.36        15.16         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
       22.49        19.04         1.35        21.60         1.68        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46         2.99        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        8.22        25.64        17.23        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
       26.70        43.69        18.64        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       36.10        32.45        30.21        23.93        12.89 

  DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE 
                          2.66                           0.16 
  DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE 
                         87.62                         169.32 
  DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE 
                         53.57                          30.61 
[1] "2.7 - 87.6 (53.6)"  "0.2 - 169.3 (30.6)"
[1] "hr=" "3.5"
D85V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 29(16Q23.3) MUTATED         0        0         3        0         2
  DEL PEAK 29(16Q23.3) WILD-TYPE     282       50       108        2        44
                                vv
clus                             STAGE IVC
  DEL PEAK 29(16Q23.3) MUTATED           1
  DEL PEAK 29(16Q23.3) WILD-TYPE         5
D85V3, multiclass
           clus
vv          DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE
  STAGE I                              0                            282
  STAGE II                             0                             50
  STAGE III                            3                            108
  STAGE IV                             0                              2
  STAGE IVA                            2                             44
  STAGE IVC                            1                              5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 29(16Q23.3) MUTATED     0   1   3   2
  DEL PEAK 29(16Q23.3) WILD-TYPE 142 164 164  21
D85V4, multiclass
    clus
vv   DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE
  T1                            0                            142
  T2                            1                            164
  T3                            3                            164
  T4                            2                             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"
D85V5, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q23.3) MUTATED     2   4
  DEL PEAK 29(16Q23.3) WILD-TYPE 223 220
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q23.3) MUTATED      2    4
  DEL PEAK 29(16Q23.3) WILD-TYPE  223  220
   clus
vv  DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE
  0                            2                            223
  1                            4                            220
[1] 2 2
[1] FALSE
D85V6, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q23.3) MUTATED     3   1
  DEL PEAK 29(16Q23.3) WILD-TYPE 275   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q23.3) MUTATED      3    1
  DEL PEAK 29(16Q23.3) WILD-TYPE  275    8
   clus
vv  DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE
  0                            3                            275
  1                            1                              8
[1] 2 2
[1] FALSE
D85V7, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q23.3) MUTATED     5   1
  DEL PEAK 29(16Q23.3) WILD-TYPE 360 133
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q23.3) MUTATED      5    1
  DEL PEAK 29(16Q23.3) WILD-TYPE  360  133
        clus
vv       DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE
  FEMALE                            5                            360
  MALE                              1                            133
[1] 2 2
[1] FALSE
D85V8, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q23.3) MUTATED     1   5
  DEL PEAK 29(16Q23.3) WILD-TYPE 184 285
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q23.3) MUTATED      1    5
  DEL PEAK 29(16Q23.3) WILD-TYPE  184  285
     clus
vv    DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE
  NO                             1                            184
  YES                            5                            285
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 29(16Q23.3) MUTATED                0
  DEL PEAK 29(16Q23.3) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 29(16Q23.3) MUTATED                                               3
  DEL PEAK 29(16Q23.3) WILD-TYPE                                           352
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 29(16Q23.3) MUTATED                                                                        1
  DEL PEAK 29(16Q23.3) WILD-TYPE                                                                     99
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 29(16Q23.3) MUTATED                                                                     2
  DEL PEAK 29(16Q23.3) WILD-TYPE                                                                  34
D85V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 29(16Q23.3) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               2
                                                                        clus
vv                                                                       DEL PEAK 29(16Q23.3) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             99
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                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"
D85V10, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q23.3) MUTATED     5   1
  DEL PEAK 29(16Q23.3) WILD-TYPE 415  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q23.3) MUTATED      5    1
  DEL PEAK 29(16Q23.3) WILD-TYPE  415   16
     clus
vv    DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE
  NO                             5                            415
  YES                            1                             16
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 29(16Q23.3) MUTATED              3                       1    2
  DEL PEAK 29(16Q23.3) WILD-TYPE          129                      17  328
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 29(16Q23.3) MUTATED                     0
  DEL PEAK 29(16Q23.3) WILD-TYPE                   1
D85V11, multiclass
                         clus
vv                        DEL PEAK 29(16Q23.3) MUTATED
  MINIMAL (T3)                                       3
  MODERATE/ADVANCED (T4A)                            1
  NONE                                               2
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK 29(16Q23.3) WILD-TYPE
  MINIMAL (T3)                                       129
  MODERATE/ADVANCED (T4A)                             17
  NONE                                               328
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 29(16Q23.3) MUTATED     3   1   0   2
  DEL PEAK 29(16Q23.3) WILD-TYPE 380  50   4  28
D85V12, multiclass
    clus
vv   DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE
  R0                            3                            380
  R1                            1                             50
  R2                            0                              4
  RX                            2                             28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V13, continuous
D85V14, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q23.3) MUTATED     3   3
  DEL PEAK 29(16Q23.3) WILD-TYPE 222 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q23.3) MUTATED      3    3
  DEL PEAK 29(16Q23.3) WILD-TYPE  222  261
            clus
vv           DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE
  MULTIFOCAL                            3                            222
  UNIFOCAL                              3                            261
[1] 2 2
[1] FALSE
D85V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 29(16Q23.3) MUTATED                                  0     0
  DEL PEAK 29(16Q23.3) WILD-TYPE                                1    52
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(16Q23.3) MUTATED                           1     5
  DEL PEAK 29(16Q23.3) WILD-TYPE                        26   323
D85V16, multiclass
                                  clus
vv                                 DEL PEAK 29(16Q23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                       5
                                  clus
vv                                 DEL PEAK 29(16Q23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        52
  BLACK OR AFRICAN AMERICAN                                    26
  WHITE                                                       323
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V17, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q23.3) MUTATED     0   6
  DEL PEAK 29(16Q23.3) WILD-TYPE  38 353
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q23.3) MUTATED      0    6
  DEL PEAK 29(16Q23.3) WILD-TYPE   38  353
                        clus
vv                       DEL PEAK 29(16Q23.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            6
                        clus
vv                       DEL PEAK 29(16Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            353
[1] 2 2
[1] FALSE

Clustering(86) Variable = DEL PEAK 30(17P13.1) MUTATION ANALYSIS
D86V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(17P13.1) MUTATED     8   0
  DEL PEAK 30(17P13.1) WILD-TYPE 473  16
  DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE 
                             8                            489 
  DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE 
                             0                             16 
$`DEL PEAK 30(17P13.1) MUTATED`
TCGA-E8-A432 TCGA-EL-A3D5 TCGA-EL-A3ZM TCGA-EM-A1YE TCGA-EM-A3O9 TCGA-EM-A3OB 
       30.61        57.11        36.03        54.08         9.24        38.66 
TCGA-FE-A22Z TCGA-FE-A238 
       73.74        39.95 

$`DEL PEAK 30(17P13.1) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
       30.58        35.41        27.45        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74         6.77        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        36.33        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       35.87        40.96        36.99        20.22        30.61        42.54 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20        23.21        21.27        20.48        24.82        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ 
       21.01        18.97         7.76        35.67         3.12        36.43 
TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ 
       24.76        17.23        27.62        30.87        21.34        33.04 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       34.78        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        80.52        63.19        52.44        39.95        31.23 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       35.67        31.27        29.98        31.50        31.04         0.72 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        0.26         3.02        25.45         0.16         0.23        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        33.50         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
      139.86        98.53        69.57       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        65.49        61.22        60.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       34.39        30.51        53.36        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       43.59        24.30        27.06        23.90        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        48.49        18.05        19.79        19.46        78.61 
TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       57.01        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.65        44.19        41.29        14.24        47.57        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       13.18        23.51         6.05         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        40.34        19.73        32.32        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ 
       17.59        17.46        17.29        14.60        22.52        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        33.07        13.38         8.35        29.72 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        47.38        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 
       17.49        17.39        16.18        15.02        14.50        15.06 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
        7.33         0.49        13.91        38.86        29.95        29.85 
TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       13.51        12.79        84.59        29.33        21.34         5.33 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
       26.37        26.37        22.45        21.53        60.49        24.46 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
       13.68        81.93        81.70        77.56        70.42        56.58 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       60.20        63.39        65.29        18.38        63.45        88.41 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       58.75        37.25        52.60        54.35        83.34         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       80.88        33.24       106.09       107.41       108.46        84.89 
TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
      123.32       100.57        95.34        94.13        55.10        98.20 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24        50.40        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       77.82        75.42        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72        43.99        46.26        44.38        40.21        37.48 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       33.17        31.40        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A239 TCGA-FE-A23A 
       68.22       117.40        66.77       112.80        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
      106.36        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        1.05        13.28         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
       20.42        17.82         7.82         0.99        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08         0.30         0.76 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16         6.58        22.49        19.04 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35        21.60         1.68        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46         2.99        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       18.51        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       17.23        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY 
       24.69        22.29         5.75         2.47         2.60         0.20 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
      143.57        15.98        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
       18.64        32.45        87.39        84.72        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       33.40        40.37        21.83         9.50        36.10        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       30.21        23.93        12.89 

  DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE 
                          9.24                           0.16 
  DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE 
                         73.74                         169.32 
  DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE 
                        39.305                         30.510 
[1] "9.2 - 73.7 (39.3)"  "0.2 - 169.3 (30.5)"
[1] "hr="     "9200000"
D86V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 30(17P13.1) MUTATED         4        2         0        0         2
  DEL PEAK 30(17P13.1) WILD-TYPE     278       48       111        2        44
                                vv
clus                             STAGE IVC
  DEL PEAK 30(17P13.1) MUTATED           0
  DEL PEAK 30(17P13.1) WILD-TYPE         6
D86V3, multiclass
           clus
vv          DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE
  STAGE I                              4                            278
  STAGE II                             2                             48
  STAGE III                            0                            111
  STAGE IV                             0                              2
  STAGE IVA                            2                             44
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 30(17P13.1) MUTATED     0   3   3   2
  DEL PEAK 30(17P13.1) WILD-TYPE 142 162 164  21
D86V4, multiclass
    clus
vv   DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE
  T1                            0                            142
  T2                            3                            162
  T3                            3                            164
  T4                            2                             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"
D86V5, binary
                                cls
clus                               0   1
  DEL PEAK 30(17P13.1) MUTATED     5   3
  DEL PEAK 30(17P13.1) WILD-TYPE 220 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(17P13.1) MUTATED      5    3
  DEL PEAK 30(17P13.1) WILD-TYPE  220  221
   clus
vv  DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE
  0                            5                            220
  1                            3                            221
[1] 2 2
[1] FALSE
D86V6, binary
                                cls
clus                               0   1
  DEL PEAK 30(17P13.1) MUTATED     3   0
  DEL PEAK 30(17P13.1) WILD-TYPE 275   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(17P13.1) MUTATED      3    0
  DEL PEAK 30(17P13.1) WILD-TYPE  275    9
   clus
vv  DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE
  0                            3                            275
  1                            0                              9
[1] 2 2
[1] FALSE
D86V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(17P13.1) MUTATED     6   2
  DEL PEAK 30(17P13.1) WILD-TYPE 359 132
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(17P13.1) MUTATED      6    2
  DEL PEAK 30(17P13.1) WILD-TYPE  359  132
        clus
vv       DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE
  FEMALE                            6                            359
  MALE                              2                            132
[1] 2 2
[1] FALSE
D86V8, binary
                                cls
clus                               0   1
  DEL PEAK 30(17P13.1) MUTATED     4   4
  DEL PEAK 30(17P13.1) WILD-TYPE 181 286
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(17P13.1) MUTATED      4    4
  DEL PEAK 30(17P13.1) WILD-TYPE  181  286
     clus
vv    DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE
  NO                             4                            181
  YES                            4                            286
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 30(17P13.1) MUTATED                0
  DEL PEAK 30(17P13.1) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 30(17P13.1) MUTATED                                               4
  DEL PEAK 30(17P13.1) WILD-TYPE                                           351
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 30(17P13.1) MUTATED                                                                        4
  DEL PEAK 30(17P13.1) WILD-TYPE                                                                     96
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 30(17P13.1) MUTATED                                                                     0
  DEL PEAK 30(17P13.1) WILD-TYPE                                                                  36
D86V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 30(17P13.1) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            4
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       DEL PEAK 30(17P13.1) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             96
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V10, binary
                                cls
clus                               0   1
  DEL PEAK 30(17P13.1) MUTATED     7   1
  DEL PEAK 30(17P13.1) WILD-TYPE 413  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(17P13.1) MUTATED      7    1
  DEL PEAK 30(17P13.1) WILD-TYPE  413   16
     clus
vv    DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE
  NO                             7                            413
  YES                            1                             16
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 30(17P13.1) MUTATED              2                       2    4
  DEL PEAK 30(17P13.1) WILD-TYPE          130                      16  326
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 30(17P13.1) MUTATED                     0
  DEL PEAK 30(17P13.1) WILD-TYPE                   1
D86V11, multiclass
                         clus
vv                        DEL PEAK 30(17P13.1) MUTATED
  MINIMAL (T3)                                       2
  MODERATE/ADVANCED (T4A)                            2
  NONE                                               4
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK 30(17P13.1) WILD-TYPE
  MINIMAL (T3)                                       130
  MODERATE/ADVANCED (T4A)                             16
  NONE                                               326
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 30(17P13.1) MUTATED     6   2   0   0
  DEL PEAK 30(17P13.1) WILD-TYPE 377  49   4  30
D86V12, multiclass
    clus
vv   DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE
  R0                            6                            377
  R1                            2                             49
  R2                            0                              4
  RX                            0                             30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V13, continuous
D86V14, binary
                                cls
clus                               0   1
  DEL PEAK 30(17P13.1) MUTATED     3   5
  DEL PEAK 30(17P13.1) WILD-TYPE 222 259
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(17P13.1) MUTATED      3    5
  DEL PEAK 30(17P13.1) WILD-TYPE  222  259
            clus
vv           DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE
  MULTIFOCAL                            3                            222
  UNIFOCAL                              5                            259
[1] 2 2
[1] FALSE
D86V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 30(17P13.1) MUTATED                                  0     1
  DEL PEAK 30(17P13.1) WILD-TYPE                                1    51
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(17P13.1) MUTATED                           0     3
  DEL PEAK 30(17P13.1) WILD-TYPE                        27   325
D86V16, multiclass
                                  clus
vv                                 DEL PEAK 30(17P13.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       3
                                  clus
vv                                 DEL PEAK 30(17P13.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        51
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V17, binary
                                cls
clus                               0   1
  DEL PEAK 30(17P13.1) MUTATED     0   4
  DEL PEAK 30(17P13.1) WILD-TYPE  38 355
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(17P13.1) MUTATED      0    4
  DEL PEAK 30(17P13.1) WILD-TYPE   38  355
                        clus
vv                       DEL PEAK 30(17P13.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            4
                        clus
vv                       DEL PEAK 30(17P13.1) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            355
[1] 2 2
[1] FALSE

Clustering(87) Variable = DEL PEAK 31(18Q12.3) MUTATION ANALYSIS
D87V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(18Q12.3) MUTATED     4   0
  DEL PEAK 31(18Q12.3) WILD-TYPE 477  16
  DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE 
                             4                            493 
  DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE 
                             0                             16 
$`DEL PEAK 31(18Q12.3) MUTATED`
TCGA-DJ-A2Q0 TCGA-EM-A1YE TCGA-EM-A3SY TCGA-ET-A3BP 
       34.36        54.08        13.51        79.10 

$`DEL PEAK 31(18Q12.3) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 
       15.12        42.08        51.39        41.52        20.58         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       23.31        18.64         7.99        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 
       23.84        28.44        15.45        21.63        23.18        19.43 
TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 
       23.47        12.66        12.30        12.79        12.46        11.38 
TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 
       10.68        15.02        12.43        12.66        35.84        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA 
       50.17        37.64        15.85        18.54        18.84        30.12 
TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 
       11.57        30.02        25.12        14.70        14.27         2.76 
TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        9.96        48.79        38.17       169.32        18.58         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       56.19        23.38        43.17        52.37         8.32        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      135.91        30.61        44.98        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
       30.58        35.41        27.45        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
       31.99        34.85        28.96         8.78         8.42        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        32.42        31.46        16.41        19.56        36.33 
TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       32.81        36.33        17.69        59.57        11.34        35.87 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       40.96        36.99        20.22        30.61        42.54        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
       23.21        21.27        20.48        24.82        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       18.97         7.76        35.67         3.12        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.23        27.62        30.87        21.34        33.04        34.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
        3.02        25.45        30.61         0.16         0.23        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        33.50         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        69.57        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       49.51        50.24       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       150.48       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        89.56        78.97        51.78 
TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       62.30        36.03        53.06        47.38        65.49        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       60.16         7.07        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        34.39        30.51        53.36        44.15 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        47.84        43.59        24.30        27.06        23.90 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.46        78.61        57.01        14.73        14.50        15.75 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       47.57        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       12.30        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       32.32        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       22.52        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33         0.49         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.66        38.86        29.95        29.85        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
      107.41       108.46        84.89       123.32       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BQ 
       94.13        55.10        98.20        28.24        50.40        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.79        87.62        77.82        75.42        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       62.83       166.62        24.72        43.99        46.26        44.38 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       40.21        37.48        33.17        31.40        73.74        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
      112.80        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        13.28 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10       116.09         1.25        20.42        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        7.82         0.99        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08         0.30         0.76        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       15.16         6.58        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83        31.10         8.22        25.64        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        23.93 
TCGA-QD-A8IV 
       12.89 

  DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE 
                         13.51                           0.16 
  DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE 
                         79.10                         169.32 
  DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE 
                         44.22                          30.61 
[1] "13.5 - 79.1 (44.2)" "0.2 - 169.3 (30.6)"
[1] "hr="     "9100000"
D87V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 31(18Q12.3) MUTATED         2        2         0        0         0
  DEL PEAK 31(18Q12.3) WILD-TYPE     280       48       111        2        46
                                vv
clus                             STAGE IVC
  DEL PEAK 31(18Q12.3) MUTATED           0
  DEL PEAK 31(18Q12.3) WILD-TYPE         6
D87V3, multiclass
           clus
vv          DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE
  STAGE I                              2                            280
  STAGE II                             2                             48
  STAGE III                            0                            111
  STAGE IV                             0                              2
  STAGE IVA                            0                             46
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 31(18Q12.3) MUTATED     1   3   0   0
  DEL PEAK 31(18Q12.3) WILD-TYPE 141 162 167  23
D87V4, multiclass
    clus
vv   DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE
  T1                            1                            141
  T2                            3                            162
  T3                            0                            167
  T4                            0                             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"
D87V5, binary
                                cls
clus                               0   1
  DEL PEAK 31(18Q12.3) MUTATED     2   1
  DEL PEAK 31(18Q12.3) WILD-TYPE 223 223
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(18Q12.3) MUTATED      2    1
  DEL PEAK 31(18Q12.3) WILD-TYPE  223  223
   clus
vv  DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE
  0                            2                            223
  1                            1                            223
[1] 2 2
[1] FALSE
D87V6, binary
                                cls
clus                               0   1
  DEL PEAK 31(18Q12.3) MUTATED     1   0
  DEL PEAK 31(18Q12.3) WILD-TYPE 277   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(18Q12.3) MUTATED      1    0
  DEL PEAK 31(18Q12.3) WILD-TYPE  277    9
   clus
vv  DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE
  0                            1                            277
  1                            0                              9
[1] 2 2
[1] FALSE
D87V7, binary
                                cls
clus                               0   1
  DEL PEAK 31(18Q12.3) MUTATED     3   1
  DEL PEAK 31(18Q12.3) WILD-TYPE 362 133
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(18Q12.3) MUTATED      3    1
  DEL PEAK 31(18Q12.3) WILD-TYPE  362  133
        clus
vv       DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE
  FEMALE                            3                            362
  MALE                              1                            133
[1] 2 2
[1] FALSE
D87V8, binary
                                cls
clus                               0   1
  DEL PEAK 31(18Q12.3) MUTATED     2   2
  DEL PEAK 31(18Q12.3) WILD-TYPE 183 288
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(18Q12.3) MUTATED      2    2
  DEL PEAK 31(18Q12.3) WILD-TYPE  183  288
     clus
vv    DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE
  NO                             2                            183
  YES                            2                            288
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 31(18Q12.3) MUTATED                0
  DEL PEAK 31(18Q12.3) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 31(18Q12.3) MUTATED                                               2
  DEL PEAK 31(18Q12.3) WILD-TYPE                                           353
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 31(18Q12.3) MUTATED                                                                        2
  DEL PEAK 31(18Q12.3) WILD-TYPE                                                                     98
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 31(18Q12.3) MUTATED                                                                     0
  DEL PEAK 31(18Q12.3) WILD-TYPE                                                                  36
D87V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 31(18Q12.3) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       DEL PEAK 31(18Q12.3) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     353
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V10, binary
                                cls
clus                               0   1
  DEL PEAK 31(18Q12.3) MUTATED     4   0
  DEL PEAK 31(18Q12.3) WILD-TYPE 416  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(18Q12.3) MUTATED      4    0
  DEL PEAK 31(18Q12.3) WILD-TYPE  416   17
     clus
vv    DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE
  NO                             4                            416
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 31(18Q12.3) MUTATED              0                       0    4
  DEL PEAK 31(18Q12.3) WILD-TYPE          132                      18  326
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 31(18Q12.3) MUTATED                     0
  DEL PEAK 31(18Q12.3) WILD-TYPE                   1
D87V11, multiclass
                         clus
vv                        DEL PEAK 31(18Q12.3) MUTATED
  MINIMAL (T3)                                       0
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               4
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK 31(18Q12.3) WILD-TYPE
  MINIMAL (T3)                                       132
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               326
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 31(18Q12.3) MUTATED     4   0   0   0
  DEL PEAK 31(18Q12.3) WILD-TYPE 379  51   4  30
D87V12, multiclass
    clus
vv   DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE
  R0                            4                            379
  R1                            0                             51
  R2                            0                              4
  RX                            0                             30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V13, continuous
D87V14, binary
                                cls
clus                               0   1
  DEL PEAK 31(18Q12.3) MUTATED     1   3
  DEL PEAK 31(18Q12.3) WILD-TYPE 224 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(18Q12.3) MUTATED      1    3
  DEL PEAK 31(18Q12.3) WILD-TYPE  224  261
            clus
vv           DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE
  MULTIFOCAL                            1                            224
  UNIFOCAL                              3                            261
[1] 2 2
[1] FALSE
D87V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 31(18Q12.3) MUTATED                                  0     0
  DEL PEAK 31(18Q12.3) WILD-TYPE                                1    52
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(18Q12.3) MUTATED                           0     2
  DEL PEAK 31(18Q12.3) WILD-TYPE                        27   326
D87V16, multiclass
[1] "Remove cluster labels:"       "DEL PEAK 31(18Q12.3) MUTATED"
clus
  DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE 
                             2                            406 
                    TCGA-4C-A93U                     TCGA-BJ-A0YZ 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A0Z2                     TCGA-BJ-A0Z3 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A0Z5                     TCGA-BJ-A0Z9 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A0ZA                     TCGA-BJ-A0ZB 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A0ZC                     TCGA-BJ-A0ZE 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A0ZG                     TCGA-BJ-A0ZH 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A0ZJ                     TCGA-BJ-A18Y 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A18Z                     TCGA-BJ-A190 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A191                     TCGA-BJ-A192 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A28R                     TCGA-BJ-A28S 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A28T                     TCGA-BJ-A28V 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A28W                     TCGA-BJ-A28X 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A28Z                     TCGA-BJ-A290 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A291                     TCGA-BJ-A2N7 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A2N8                     TCGA-BJ-A2N9 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A2NA                     TCGA-BJ-A2P4 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A3EZ                     TCGA-BJ-A3F0 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A3PR                     TCGA-BJ-A3PT 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A3PU                     TCGA-BJ-A45C 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A45D                     TCGA-BJ-A45E 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A45F                     TCGA-BJ-A45G 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A45H                     TCGA-BJ-A45I 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A45J                     TCGA-BJ-A45K 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A4O8                     TCGA-BJ-A4O9 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-CE-A13K                     TCGA-CE-A27D 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-CE-A3MD                     TCGA-CE-A3ME 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-CE-A481                     TCGA-CE-A482 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-CE-A483                     TCGA-CE-A484 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-CE-A485                     TCGA-DE-A0XZ 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DE-A0Y2                     TCGA-DE-A0Y3 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DE-A2OL                     TCGA-DE-A3KN 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DE-A4M8                     TCGA-DE-A4M9 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DE-A4MA                     TCGA-DE-A4MB 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DE-A4MC                     TCGA-DE-A4MD 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DE-A69J                     TCGA-DE-A69K 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DE-A7U5                     TCGA-DJ-A13L 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A13M                     TCGA-DJ-A13O 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A13P                     TCGA-DJ-A13R 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A13S                     TCGA-DJ-A13T 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A13U                     TCGA-DJ-A13W 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A1QD                     TCGA-DJ-A1QE 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A1QF                     TCGA-DJ-A1QG 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A1QH                     TCGA-DJ-A1QI 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A1QM                     TCGA-DJ-A1QO 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A1QQ                     TCGA-DJ-A2PN 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A2PO                     TCGA-DJ-A2PQ 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A2PR                     TCGA-DJ-A2PS 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A2PT                     TCGA-DJ-A2PU 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A2PV                     TCGA-DJ-A2PW 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A2PX                     TCGA-DJ-A2PY 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A2PZ                     TCGA-DJ-A2Q1 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A2Q2                     TCGA-DJ-A2Q3 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A2Q4                     TCGA-DJ-A2Q5 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A2Q6                     TCGA-DJ-A2Q7 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A2Q9                     TCGA-DJ-A2QA 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A2QB                     TCGA-DJ-A3UK 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A3UM                     TCGA-DJ-A3UN 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A3UO                     TCGA-DJ-A3UQ 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A3UR                     TCGA-DJ-A3US 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A3UT                     TCGA-DJ-A3UU 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A3UW                     TCGA-DJ-A3UX 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A3UY                     TCGA-DJ-A3UZ 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A3V2                     TCGA-DJ-A3V3 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A3V4                     TCGA-DJ-A3V5 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A3V7                     TCGA-DJ-A3V8 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A3V9                     TCGA-DJ-A3VD 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A3VE                     TCGA-DJ-A3VF 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A3VG                     TCGA-DJ-A3VI 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A3VJ                     TCGA-DJ-A3VK 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A3VL                     TCGA-DJ-A3VM 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A4UL                     TCGA-DJ-A4UP 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A4UQ                     TCGA-DJ-A4UR 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A4UT                     TCGA-DJ-A4UW 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A4V0                     TCGA-DJ-A4V4 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A4V5                     TCGA-DO-A1JZ 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DO-A1K0                     TCGA-DO-A2HM 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-E3-A3DY                     TCGA-E3-A3DZ 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-E3-A3E0                     TCGA-E3-A3E1 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-E3-A3E2                     TCGA-E3-A3E3 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-E3-A3E5                     TCGA-E8-A242 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-E8-A2EA                     TCGA-E8-A3X7 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-E8-A413                     TCGA-E8-A414 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-E8-A415                     TCGA-E8-A416 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-E8-A417                     TCGA-E8-A418 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-E8-A419                     TCGA-E8-A432 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-E8-A433                     TCGA-E8-A434 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-E8-A436                     TCGA-E8-A437 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-E8-A438                     TCGA-E8-A44K 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-E8-A44M                     TCGA-EL-A3CL 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3CM                     TCGA-EL-A3CN 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3CO                     TCGA-EL-A3CP 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3CR                     TCGA-EL-A3CS 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3CT                     TCGA-EL-A3CU 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3CV                     TCGA-EL-A3CW 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3CX                     TCGA-EL-A3CY 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3CZ                     TCGA-EL-A3D0 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3D1                     TCGA-EL-A3D4 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3D5                     TCGA-EL-A3D6 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3GO                     TCGA-EL-A3GP 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3GQ                     TCGA-EL-A3GR 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3GS                     TCGA-EL-A3GU 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3GV                     TCGA-EL-A3GW 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3GX                     TCGA-EL-A3GY 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3GZ                     TCGA-EL-A3H1 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3H2                     TCGA-EL-A3H3 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3H4                     TCGA-EL-A3H5 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3H7                     TCGA-EL-A3H8 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3MW                     TCGA-EL-A3MX 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3MY                     TCGA-EL-A3MZ 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3N2                     TCGA-EL-A3N3 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3T0                     TCGA-EL-A3T1 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3T2                     TCGA-EL-A3T3 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3T6                     TCGA-EL-A3T7 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3T8                     TCGA-EL-A3T9 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3TA                     TCGA-EL-A3TB 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3ZG                     TCGA-EL-A3ZH 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3ZK                     TCGA-EL-A3ZL 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3ZN                     TCGA-EL-A3ZO 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3ZP                     TCGA-EL-A3ZQ 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3ZR                     TCGA-EL-A3ZS 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3ZT                     TCGA-EL-A4JV 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A4JW                     TCGA-EL-A4JX 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A4JZ                     TCGA-EL-A4K0 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A4K1                     TCGA-EL-A4K2 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A4K4                     TCGA-EL-A4K6 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A4K7                     TCGA-EL-A4K9 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A4KD                     TCGA-EL-A4KG 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A4KH                     TCGA-EL-A4KI 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EM-A22M                     TCGA-EM-A22O 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EM-A2OV                     TCGA-EM-A3AI 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A25G                     TCGA-ET-A25I 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A25J                     TCGA-ET-A25K 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A25L                     TCGA-ET-A25M 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A25N                     TCGA-ET-A25O 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A25P                     TCGA-ET-A25R 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A2MX                     TCGA-ET-A2MY 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A2MZ                     TCGA-ET-A2N0 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A2N1                     TCGA-ET-A2N3 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A2N4                     TCGA-ET-A2N5 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A39I                     TCGA-ET-A39J 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A39K                     TCGA-ET-A39M 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A39N                     TCGA-ET-A39O 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A39P                     TCGA-ET-A39R 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A39S                     TCGA-ET-A39T 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A3BN                     TCGA-ET-A3BO 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A3BQ                     TCGA-ET-A3BS 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A3BT                     TCGA-ET-A3BU 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A3BV                     TCGA-ET-A3BW 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A3BX                     TCGA-ET-A3DO 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A3DP                     TCGA-ET-A3DQ 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A3DR                     TCGA-ET-A3DS 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A3DT                     TCGA-ET-A3DU 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A3DV                     TCGA-ET-A3DW 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A40P                     TCGA-ET-A40Q 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A40R                     TCGA-ET-A40S 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A40T                     TCGA-ET-A4KN 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A4KQ                     TCGA-FE-A22Z 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-FE-A230                     TCGA-FE-A231 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-FE-A232                     TCGA-FE-A233 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-FE-A234                     TCGA-FE-A235 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-FE-A236                     TCGA-FE-A237 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-FE-A238                     TCGA-FE-A239 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-FE-A23A                     TCGA-FE-A3PA 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-FE-A3PB                     TCGA-FE-A3PC 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-FE-A3PD                     TCGA-FK-A3S3 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-FK-A3SB                     TCGA-FK-A3SD 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-FK-A3SE                     TCGA-FK-A3SG 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-FK-A3SH                     TCGA-FK-A4UB 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-FY-A2QD                     TCGA-FY-A3BL 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-FY-A3I4                     TCGA-FY-A3I5 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-FY-A3NM                     TCGA-FY-A3ON 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-FY-A3R6                     TCGA-FY-A3R7 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-FY-A3R8                     TCGA-FY-A3R9 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-FY-A3RA                     TCGA-FY-A3W9 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-FY-A3WA                     TCGA-FY-A3YR 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-FY-A40K                     TCGA-FY-A40L 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-FY-A40M                     TCGA-FY-A40N 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-FY-A4B0                     TCGA-FY-A4B3 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-FY-A4B4                     TCGA-FY-A76V 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-GE-A2C6                     TCGA-H2-A26U 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-H2-A2K9                     TCGA-H2-A3RH 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-H2-A3RI                     TCGA-H2-A421 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-H2-A422                     TCGA-IM-A3EB 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-IM-A3ED                     TCGA-IM-A3U2 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-IM-A3U3                     TCGA-IM-A41Y 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-IM-A41Z                     TCGA-IM-A420 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-IM-A4EB                     TCGA-J8-A3NZ 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-J8-A3O0                     TCGA-J8-A3O1 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-J8-A3O2                     TCGA-J8-A3YD 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-J8-A3YE                     TCGA-J8-A3YF 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-J8-A3YG                     TCGA-J8-A3YH 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-J8-A42S                     TCGA-J8-A4HW 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-J8-A4HY                     TCGA-KS-A41F 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-KS-A41I                     TCGA-KS-A41J 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-KS-A41L                     TCGA-KS-A4I1 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-KS-A4I3                     TCGA-KS-A4I5 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-KS-A4I7                     TCGA-KS-A4I9 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-KS-A4IB                     TCGA-KS-A4IC 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-KS-A4ID                     TCGA-L6-A4EP 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-L6-A4EQ                     TCGA-L6-A4ET 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-L6-A4EU                     TCGA-MK-A4N6 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-MK-A4N7                     TCGA-MK-A4N9 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-MK-A84Z                     TCGA-QD-A8IV 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
D87V17, binary
                                cls
clus                               0   1
  DEL PEAK 31(18Q12.3) MUTATED     1   1
  DEL PEAK 31(18Q12.3) WILD-TYPE  37 358
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(18Q12.3) MUTATED      1    1
  DEL PEAK 31(18Q12.3) WILD-TYPE   37  358
                        clus
vv                       DEL PEAK 31(18Q12.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                            1
                        clus
vv                       DEL PEAK 31(18Q12.3) WILD-TYPE
  HISPANIC OR LATINO                                 37
  NOT HISPANIC OR LATINO                            358
[1] 2 2
[1] FALSE

Clustering(88) Variable = DEL PEAK 32(19P13.2) MUTATION ANALYSIS
D88V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 32(19P13.2) MUTATED     5   1
  DEL PEAK 32(19P13.2) WILD-TYPE 476  15
  DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE 
                             6                            491 
  DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE 
                             1                             15 
$`DEL PEAK 32(19P13.2) MUTATED`
TCGA-BJ-A0YZ TCGA-BJ-A192 TCGA-EL-A3D5 TCGA-EL-A3H2 TCGA-ET-A39N TCGA-FY-A3WA 
       24.79        44.35        57.11        33.50       123.32        17.06 

$`DEL PEAK 32(19P13.2) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
        4.24        13.78        49.78        16.34        14.73        41.33 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73        25.48        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A28R 
       42.08        51.39        41.52        20.58         4.83        42.15 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04        35.54        32.45        11.31        30.97        11.08 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       30.21        22.88        18.38        16.57        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        7.99        10.88        21.01         3.45        23.84        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
       15.45        21.63        23.18        19.43        23.47        12.66 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
       12.43        12.66        35.84        21.63        50.17        37.64 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M 
       25.12        14.70        14.27         2.76         9.96        48.79 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       38.17       169.32        18.58         8.71        56.19        23.38 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       43.17        52.37         8.32        11.01       135.91        30.61 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       44.98        42.51        14.96        17.59         6.02        42.58 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
       47.41        17.56        10.09         7.82        30.58        35.41 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       27.45        26.20        38.83        33.96        31.99        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       28.96         8.78         8.42        34.36        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24        33.93        37.48        36.46        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        33.53        35.18        15.88        36.92        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       32.42        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        17.69        59.57        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        42.54        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL 
        7.76        35.67         3.12        36.43        24.76        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        21.34        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        52.44        39.95        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       98.53        69.57       108.36        64.87        49.51        50.24 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
      115.10        65.39       136.01        50.37        50.20       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 
      101.13       139.99        49.32        43.36        49.71        83.57 
TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ 
      139.00       150.48       108.66        57.63        17.52        52.50 
TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       29.65       147.42       142.52       129.57        32.48       132.07 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
       98.24        41.29       107.47         5.72        66.90        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN 
       89.56        78.97        51.78        62.30        36.03        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        65.49        61.22        60.16         7.07        59.44 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       57.47        34.72        45.96        37.94        31.04        34.39 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        53.36        44.15        41.13        47.84        43.59 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       24.30        27.06        23.90        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
       48.49        18.05        19.79        19.46        78.61        57.01 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       54.08        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.65        44.19        41.29        14.24        47.57        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       13.18        23.51         6.05         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        40.34        19.73        32.32        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ 
       17.59        17.46        17.29        14.60        22.52        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        33.07        13.38         8.35        29.72 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        47.38        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 
       17.49        17.39        16.18        15.02        14.50        15.06 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33         0.49         9.24        13.91        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       29.95        29.85        13.51        12.79        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
       21.34         5.33        26.37        26.37        22.45        21.53 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       60.49        24.46        13.68        81.93        81.70        77.56 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       70.42        56.58        60.20        63.39        65.29        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       63.45        88.41        58.75        37.25        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       83.34         2.66        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
      108.46        84.89       100.57        95.34        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       98.20        28.24        50.40        79.10        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       87.62        77.82        75.42        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       94.59        84.85        80.58        66.84        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      166.62        24.72        43.99        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        13.28         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 
       48.10       116.09         1.25        20.42        17.82         7.82 
TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
        0.99        19.56        13.91        16.27        15.68        16.57 
TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
       18.08         0.30         0.76        17.36        15.16         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
       22.49        19.04         1.35        21.60         1.68        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
       17.00        21.67        12.46         2.99        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       48.92        47.41        18.51        16.90        21.83        31.10 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        8.22        25.64        17.23        43.17        27.19        11.24 
TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S 
       31.82        27.85        24.69        22.29         5.75         2.47 
TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.60         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
       26.70        43.69        18.64        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU 
       35.28        33.24        33.40        40.37        21.83         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       36.10        32.45        30.21        23.93        12.89 

  DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE 
                         17.06                           0.16 
  DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE 
                        123.32                         169.32 
  DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE 
                        38.925                         30.610 
[1] "17.1 - 123.3 (38.9)" "0.2 - 169.3 (30.6)" 
[1] "hr=" "4.2"
D88V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 32(19P13.2) MUTATED         4        2         1        0         0
  DEL PEAK 32(19P13.2) WILD-TYPE     278       48       110        2        46
                                vv
clus                             STAGE IVC
  DEL PEAK 32(19P13.2) MUTATED           0
  DEL PEAK 32(19P13.2) WILD-TYPE         6
D88V3, multiclass
           clus
vv          DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE
  STAGE I                              4                            278
  STAGE II                             2                             48
  STAGE III                            1                            110
  STAGE IV                             0                              2
  STAGE IVA                            0                             46
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 32(19P13.2) MUTATED     2   2   3   0
  DEL PEAK 32(19P13.2) WILD-TYPE 140 163 164  23
D88V4, multiclass
    clus
vv   DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE
  T1                            2                            140
  T2                            2                            163
  T3                            3                            164
  T4                            0                             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"
D88V5, binary
                                cls
clus                               0   1
  DEL PEAK 32(19P13.2) MUTATED     2   1
  DEL PEAK 32(19P13.2) WILD-TYPE 223 223
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(19P13.2) MUTATED      2    1
  DEL PEAK 32(19P13.2) WILD-TYPE  223  223
   clus
vv  DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE
  0                            2                            223
  1                            1                            223
[1] 2 2
[1] FALSE
D88V6, binary
                                cls
clus                               0   1
  DEL PEAK 32(19P13.2) MUTATED     3   0
  DEL PEAK 32(19P13.2) WILD-TYPE 275   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(19P13.2) MUTATED      3    0
  DEL PEAK 32(19P13.2) WILD-TYPE  275    9
   clus
vv  DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE
  0                            3                            275
  1                            0                              9
[1] 2 2
[1] FALSE
D88V7, binary
                                cls
clus                               0   1
  DEL PEAK 32(19P13.2) MUTATED     4   3
  DEL PEAK 32(19P13.2) WILD-TYPE 361 131
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(19P13.2) MUTATED      4    3
  DEL PEAK 32(19P13.2) WILD-TYPE  361  131
        clus
vv       DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE
  FEMALE                            4                            361
  MALE                              3                            131
[1] 2 2
[1] FALSE
D88V8, binary
                                cls
clus                               0   1
  DEL PEAK 32(19P13.2) MUTATED     3   3
  DEL PEAK 32(19P13.2) WILD-TYPE 182 287
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(19P13.2) MUTATED      3    3
  DEL PEAK 32(19P13.2) WILD-TYPE  182  287
     clus
vv    DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE
  NO                             3                            182
  YES                            3                            287
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 32(19P13.2) MUTATED                0
  DEL PEAK 32(19P13.2) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 32(19P13.2) MUTATED                                               6
  DEL PEAK 32(19P13.2) WILD-TYPE                                           349
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 32(19P13.2) MUTATED                                                                        1
  DEL PEAK 32(19P13.2) WILD-TYPE                                                                     99
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 32(19P13.2) MUTATED                                                                     0
  DEL PEAK 32(19P13.2) WILD-TYPE                                                                  36
D88V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 32(19P13.2) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     6
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       DEL PEAK 32(19P13.2) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     349
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             99
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V10, binary
                                cls
clus                               0   1
  DEL PEAK 32(19P13.2) MUTATED     5   2
  DEL PEAK 32(19P13.2) WILD-TYPE 415  15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(19P13.2) MUTATED      5    2
  DEL PEAK 32(19P13.2) WILD-TYPE  415   15
     clus
vv    DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE
  NO                             5                            415
  YES                            2                             15
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 32(19P13.2) MUTATED              2                       0    5
  DEL PEAK 32(19P13.2) WILD-TYPE          130                      18  325
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 32(19P13.2) MUTATED                     0
  DEL PEAK 32(19P13.2) WILD-TYPE                   1
D88V11, multiclass
                         clus
vv                        DEL PEAK 32(19P13.2) MUTATED
  MINIMAL (T3)                                       2
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               5
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK 32(19P13.2) WILD-TYPE
  MINIMAL (T3)                                       130
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               325
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 32(19P13.2) MUTATED     4   2   0   1
  DEL PEAK 32(19P13.2) WILD-TYPE 379  49   4  29
D88V12, multiclass
    clus
vv   DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE
  R0                            4                            379
  R1                            2                             49
  R2                            0                              4
  RX                            1                             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"
D88V13, continuous
[1] "Remove cluster labels:"       "DEL PEAK 32(19P13.2) MUTATED"
clus
  DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE 
                             1                            384 
                    TCGA-4C-A93U                     TCGA-BJ-A0Z0 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A0Z3                     TCGA-BJ-A0Z9 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A0ZA                     TCGA-BJ-A0ZB 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A0ZH                     TCGA-BJ-A0ZJ 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A18Y                     TCGA-BJ-A18Z 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A190                     TCGA-BJ-A191 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A28R                     TCGA-BJ-A28T 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A28W                     TCGA-BJ-A28X 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A28Z                     TCGA-BJ-A290 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A291                     TCGA-BJ-A2N8 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A2N9                     TCGA-BJ-A2NA 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A3EZ                     TCGA-BJ-A3PR 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A3PU                     TCGA-BJ-A45C 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A45D                     TCGA-BJ-A45E 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A45G                     TCGA-BJ-A45I 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A45J                     TCGA-BJ-A45K 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A4O8                     TCGA-BJ-A4O9 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-CE-A13K                     TCGA-CE-A3MD 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-CE-A483                     TCGA-CE-A484 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-CE-A485                     TCGA-DE-A0XZ 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DE-A0Y2                     TCGA-DE-A0Y3 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DE-A3KN                     TCGA-DE-A4M8 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DE-A4MA                     TCGA-DE-A4MB 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DE-A4MC                     TCGA-DE-A4MD 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DE-A69K                     TCGA-DE-A7U5 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A13M                     TCGA-DJ-A13O 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A13R                     TCGA-DJ-A13T 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A13V                     TCGA-DJ-A13W 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A13X                     TCGA-DJ-A1QG 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A1QH                     TCGA-DJ-A1QM 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A2PO                     TCGA-DJ-A2PP 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A2PQ                     TCGA-DJ-A2PR 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A2PS                     TCGA-DJ-A2PT 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A2PU                     TCGA-DJ-A2PV 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A2PW                     TCGA-DJ-A2PX 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A2PY                     TCGA-DJ-A2PZ 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A2Q0                     TCGA-DJ-A2Q1 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A2Q2                     TCGA-DJ-A2Q3 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A2Q4                     TCGA-DJ-A2Q5 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A2Q6                     TCGA-DJ-A2Q7 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A2Q8                     TCGA-DJ-A2Q9 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A2QA                     TCGA-DJ-A2QB 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A3UK                     TCGA-DJ-A3UM 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A3UN                     TCGA-DJ-A3UO 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A3UP                     TCGA-DJ-A3UQ 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A3UR                     TCGA-DJ-A3UU 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A3UW                     TCGA-DJ-A3UX 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A3UZ                     TCGA-DJ-A3V0 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A3V2                     TCGA-DJ-A3V3 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A3V4                     TCGA-DJ-A3V5 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A3V7                     TCGA-DJ-A3V8 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A3V9                     TCGA-DJ-A3VA 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A3VB                     TCGA-DJ-A3VD 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A3VF                     TCGA-DJ-A3VG 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A3VI                     TCGA-DJ-A3VJ 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A3VK                     TCGA-DJ-A3VL 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A4UL                     TCGA-DJ-A4UP 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A4UQ                     TCGA-DJ-A4UR 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A4UW                     TCGA-DJ-A4V2 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A4V5                     TCGA-DO-A1K0 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DO-A2HM                     TCGA-E3-A3DY 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-E3-A3DZ                     TCGA-E3-A3E0 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-E3-A3E1                     TCGA-E3-A3E2 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-E3-A3E3                     TCGA-E3-A3E5 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-E8-A242                     TCGA-E8-A2EA 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-E8-A414                     TCGA-E8-A415 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-E8-A417                     TCGA-E8-A419 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-E8-A433                     TCGA-E8-A436 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-E8-A438                     TCGA-E8-A44K 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3CM                     TCGA-EL-A3CN 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3CO                     TCGA-EL-A3CR 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3CS                     TCGA-EL-A3CT 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3CU                     TCGA-EL-A3CV 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3CW                     TCGA-EL-A3CX 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3CY                     TCGA-EL-A3CZ 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3D0                     TCGA-EL-A3D1 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3D4                     TCGA-EL-A3D6 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3GO                     TCGA-EL-A3GP 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3GQ                     TCGA-EL-A3GS 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3GU                     TCGA-EL-A3GV 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3GX                     TCGA-EL-A3H3 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3H4                     TCGA-EL-A3H5 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3H7                     TCGA-EL-A3H8 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3MW                     TCGA-EL-A3MX 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3MZ                     TCGA-EL-A3N2 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3T0                     TCGA-EL-A3T1 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3T2                     TCGA-EL-A3TB 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3ZH                     TCGA-EL-A3ZK 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3ZL                     TCGA-EL-A3ZM 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3ZN                     TCGA-EL-A3ZO 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3ZP                     TCGA-EL-A3ZS 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A4JV                     TCGA-EL-A4JW 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A4JX                     TCGA-EL-A4JZ 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A4K0                     TCGA-EL-A4K1 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A4K2                     TCGA-EL-A4K4 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A4K6                     TCGA-EL-A4K7 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A4KD                     TCGA-EL-A4KG 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A4KI                     TCGA-EM-A1CS 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A1CT                     TCGA-EM-A1CU 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A1CV                     TCGA-EM-A1CW 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A1YC                     TCGA-EM-A1YD 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A1YE                     TCGA-EM-A22I 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A22J                     TCGA-EM-A22K 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A22L                     TCGA-EM-A22M 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A22N                     TCGA-EM-A22O 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A22P                     TCGA-EM-A22Q 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A2CK                     TCGA-EM-A2CN 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A2CP                     TCGA-EM-A2CQ 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A2CT                     TCGA-EM-A2CU 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A2OV                     TCGA-EM-A2OX 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A2OY                     TCGA-EM-A2OZ 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A2P0                     TCGA-EM-A2P1 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A2P2                     TCGA-EM-A3AJ 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A3AK                     TCGA-EM-A3AL 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A3AN                     TCGA-EM-A3AO 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A3AQ                     TCGA-EM-A3AR 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A3FJ                     TCGA-EM-A3FK 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A3FM                     TCGA-EM-A3FN 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A3FO                     TCGA-EM-A3FP 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A3FQ                     TCGA-EM-A3FR 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A3O3                     TCGA-EM-A3O8 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A3O9                     TCGA-EM-A3OA 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A3OB                     TCGA-EM-A3ST 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A3SU                     TCGA-EM-A3SX 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A3SZ                     TCGA-EM-A4FF 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A4FM                     TCGA-EM-A4FN 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A4FO                     TCGA-EM-A4FQ 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A4FR                     TCGA-EM-A4FV 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A4G1                     TCGA-ET-A25G 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-ET-A25I                     TCGA-ET-A25J 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-ET-A25K                     TCGA-ET-A25L 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-ET-A25M                     TCGA-ET-A25N 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-ET-A25O                     TCGA-ET-A25P 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-ET-A2MX                     TCGA-ET-A2MZ 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-ET-A2N0                     TCGA-ET-A2N1 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-ET-A2N4                     TCGA-ET-A39K 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-ET-A39L                     TCGA-ET-A39O 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-ET-A39P                     TCGA-ET-A39R 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-ET-A39S                     TCGA-ET-A39T 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-ET-A3BO                     TCGA-ET-A3BP 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-ET-A3BQ                     TCGA-ET-A3BS 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-ET-A3BT                     TCGA-ET-A3BU 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-ET-A3BV                     TCGA-ET-A3BX 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-ET-A3DQ                     TCGA-ET-A3DR 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-ET-A3DS                     TCGA-ET-A3DT 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-ET-A3DU                     TCGA-ET-A3DV 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-ET-A3DW                     TCGA-ET-A40P 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-ET-A40Q                     TCGA-ET-A40R 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-ET-A40S                     TCGA-ET-A40T 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-ET-A4KN                     TCGA-FE-A22Z 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-FE-A230                     TCGA-FE-A231 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-FE-A232                     TCGA-FE-A233 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-FE-A234                     TCGA-FE-A235 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-FE-A236                     TCGA-FE-A237 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-FE-A238                     TCGA-FE-A239 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-FE-A23A                     TCGA-FE-A3PB 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-FE-A3PC                     TCGA-FE-A3PD 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-FK-A3S3                     TCGA-FK-A3SB 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-FK-A3SE                     TCGA-FK-A3SG 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-FK-A3SH                     TCGA-FK-A4UB 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-FY-A2QD                     TCGA-FY-A3I4 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-FY-A3I5                     TCGA-FY-A3NM 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-FY-A3NN                     TCGA-FY-A3ON 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-FY-A3R6                     TCGA-FY-A3R7 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-FY-A3R9                     TCGA-FY-A3TY 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-FY-A3W9                     TCGA-FY-A3YR 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-FY-A40K                     TCGA-FY-A40L 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-FY-A40M                     TCGA-FY-A40N 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-FY-A4B3                     TCGA-FY-A4B4 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-GE-A2C6                     TCGA-H2-A26U 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-H2-A2K9                     TCGA-H2-A3RH 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-H2-A3RI                     TCGA-H2-A421 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-H2-A422                     TCGA-IM-A3EB 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-IM-A3ED                     TCGA-IM-A3U2 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-IM-A3U3                     TCGA-IM-A41Y 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-IM-A41Z                     TCGA-IM-A420 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-IM-A4EB                     TCGA-J8-A3NZ 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-J8-A3O0                     TCGA-J8-A3O1 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-J8-A3O2                     TCGA-J8-A3YD 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-J8-A3YE                     TCGA-J8-A3YF 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-J8-A3YG                     TCGA-J8-A3YH 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-J8-A42S                     TCGA-J8-A4HW 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-J8-A4HY                     TCGA-KS-A41F 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-KS-A41I                     TCGA-KS-A41J 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-KS-A41L                     TCGA-KS-A4I1 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-KS-A4I3                     TCGA-KS-A4I5 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-KS-A4I7                     TCGA-KS-A4I9 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-KS-A4IB                     TCGA-KS-A4IC 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-KS-A4ID                     TCGA-L6-A4EP 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-L6-A4EQ                     TCGA-L6-A4EU 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-MK-A4N6                     TCGA-MK-A4N7 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-MK-A4N9                     TCGA-QD-A8IV 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
D88V14, binary
                                cls
clus                               0   1
  DEL PEAK 32(19P13.2) MUTATED     2   5
  DEL PEAK 32(19P13.2) WILD-TYPE 223 259
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(19P13.2) MUTATED      2    5
  DEL PEAK 32(19P13.2) WILD-TYPE  223  259
            clus
vv           DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE
  MULTIFOCAL                            2                            223
  UNIFOCAL                              5                            259
[1] 2 2
[1] FALSE
D88V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 32(19P13.2) MUTATED                                  0     0
  DEL PEAK 32(19P13.2) WILD-TYPE                                1    52
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(19P13.2) MUTATED                           0     7
  DEL PEAK 32(19P13.2) WILD-TYPE                        27   321
D88V16, multiclass
                                  clus
vv                                 DEL PEAK 32(19P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       7
                                  clus
vv                                 DEL PEAK 32(19P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        52
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       321
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V17, binary
                                cls
clus                               0   1
  DEL PEAK 32(19P13.2) MUTATED     0   6
  DEL PEAK 32(19P13.2) WILD-TYPE  38 353
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(19P13.2) MUTATED      0    6
  DEL PEAK 32(19P13.2) WILD-TYPE   38  353
                        clus
vv                       DEL PEAK 32(19P13.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            6
                        clus
vv                       DEL PEAK 32(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            353
[1] 2 2
[1] FALSE

Clustering(89) Variable = DEL PEAK 33(19P13.12) MUTATION ANALYSIS
D89V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 33(19P13.12) MUTATED     6   1
  DEL PEAK 33(19P13.12) WILD-TYPE 475  15
  DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE 
                              7                             490 
  DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE 
                              1                              15 
$`DEL PEAK 33(19P13.12) MUTATED`
TCGA-BJ-A0YZ TCGA-DE-A69J TCGA-EL-A3D5 TCGA-EL-A3H2 TCGA-ET-A39N TCGA-FY-A2QD 
       24.79        14.70        57.11        33.50       123.32         1.25 
TCGA-FY-A3WA 
       17.06 

$`DEL PEAK 33(19P13.12) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
        4.24        13.78        49.78        16.34        14.73        41.33 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73        25.48        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       42.08        51.39        41.52        20.58         4.83        44.35 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
       42.15        21.04        35.54        32.45        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.08        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       15.02        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       37.64        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M 
       30.02        25.12        14.27         2.76         9.96        48.79 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       38.17       169.32        18.58         8.71        56.19        23.38 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       43.17        52.37         8.32        11.01       135.91        30.61 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       44.98        42.51        14.96        17.59         6.02        42.58 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
       47.41        17.56        10.09         7.82        30.58        35.41 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       27.45        26.20        38.83        33.96        31.99        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       28.96         8.78         8.42        34.36        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24        33.93        37.48        36.46        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        33.53        35.18        15.88        36.92        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       32.42        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        17.69        59.57        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        42.54        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL 
        7.76        35.67         3.12        36.43        24.76        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        21.34        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        52.44        39.95        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       98.53        69.57       108.36        64.87        49.51        50.24 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
      115.10        65.39       136.01        50.37        50.20       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 
      101.13       139.99        49.32        43.36        49.71        83.57 
TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ 
      139.00       150.48       108.66        57.63        17.52        52.50 
TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       29.65       147.42       142.52       129.57        32.48       132.07 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
       98.24        41.29       107.47         5.72        66.90        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN 
       89.56        78.97        51.78        62.30        36.03        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        65.49        61.22        60.16         7.07        59.44 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       57.47        34.72        45.96        37.94        31.04        34.39 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        53.36        44.15        41.13        47.84        43.59 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       24.30        27.06        23.90        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
       48.49        18.05        19.79        19.46        78.61        57.01 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       54.08        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.65        44.19        41.29        14.24        47.57        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT 
       13.18        23.51         6.05         2.99        12.30        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        40.34        19.73        32.32        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ 
       17.59        17.46        17.29        14.60        22.52        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        33.07        13.38         8.35        29.72 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        47.38        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 
       17.49        17.39        16.18        15.02        14.50        15.06 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33         0.49         9.24        13.91        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       29.95        29.85        13.51        12.79        84.59        29.33 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
       21.34         5.33        26.37        26.37        22.45        21.53 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       60.49        24.46        13.68        81.93        81.70        77.56 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       70.42        56.58        60.20        63.39        65.29        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       63.45        88.41        58.75        37.25        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       83.34         2.66        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
      108.46        84.89       100.57        95.34        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       98.20        28.24        50.40        79.10        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       87.62        77.82        75.42        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       94.59        84.85        80.58        66.84        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      166.62        24.72        43.99        46.26        44.38        40.21 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       37.48        33.17        31.40        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       39.95        33.63        81.83       106.36        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        13.28         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
       48.10       116.09        20.42        17.82         7.82         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M 
        0.30         0.76        17.36        15.16         6.58        22.49 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
       19.04         1.35        21.60         1.68        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46         2.99        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 
       47.41        18.51        16.90        21.83        31.10         8.22 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
       25.64        17.23        43.17        27.19        11.24        31.82 
TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW 
       27.85        24.69        22.29         5.75         2.47         2.60 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        0.20       143.57        15.98        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       43.69        18.64        32.45        87.39        84.72        35.28 
TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       33.24        33.40        40.37        21.83         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45        30.21        23.93        12.89 

  DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE 
                           1.25                            0.16 
  DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE 
                         123.32                          169.32 
  DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE 
                          24.79                           30.61 
[1] "1.2 - 123.3 (24.8)" "0.2 - 169.3 (30.6)"
[1] "hr=" "4.7"
D89V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 33(19P13.12) MUTATED         5        2         0        0         0
  DEL PEAK 33(19P13.12) WILD-TYPE     277       48       111        2        46
                                 vv
clus                              STAGE IVC
  DEL PEAK 33(19P13.12) MUTATED           0
  DEL PEAK 33(19P13.12) WILD-TYPE         6
D89V3, multiclass
           clus
vv          DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE
  STAGE I                               5                             277
  STAGE II                              2                              48
  STAGE III                             0                             111
  STAGE IV                              0                               2
  STAGE IVA                             0                              46
  STAGE IVC                             0                               6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 33(19P13.12) MUTATED     3   3   2   0
  DEL PEAK 33(19P13.12) WILD-TYPE 139 162 165  23
D89V4, multiclass
    clus
vv   DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE
  T1                             3                             139
  T2                             3                             162
  T3                             2                             165
  T4                             0                              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"
D89V5, binary
                                 cls
clus                                0   1
  DEL PEAK 33(19P13.12) MUTATED     3   1
  DEL PEAK 33(19P13.12) WILD-TYPE 222 223
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(19P13.12) MUTATED      3    1
  DEL PEAK 33(19P13.12) WILD-TYPE  222  223
   clus
vv  DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE
  0                             3                             222
  1                             1                             223
[1] 2 2
[1] FALSE
D89V6, binary
                                 cls
clus                                0   1
  DEL PEAK 33(19P13.12) MUTATED     3   0
  DEL PEAK 33(19P13.12) WILD-TYPE 275   9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(19P13.12) MUTATED      3    0
  DEL PEAK 33(19P13.12) WILD-TYPE  275    9
   clus
vv  DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE
  0                             3                             275
  1                             0                               9
[1] 2 2
[1] FALSE
D89V7, binary
                                 cls
clus                                0   1
  DEL PEAK 33(19P13.12) MUTATED     5   3
  DEL PEAK 33(19P13.12) WILD-TYPE 360 131
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(19P13.12) MUTATED      5    3
  DEL PEAK 33(19P13.12) WILD-TYPE  360  131
        clus
vv       DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE
  FEMALE                             5                             360
  MALE                               3                             131
[1] 2 2
[1] FALSE
D89V8, binary
                                 cls
clus                                0   1
  DEL PEAK 33(19P13.12) MUTATED     2   4
  DEL PEAK 33(19P13.12) WILD-TYPE 183 286
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(19P13.12) MUTATED      2    4
  DEL PEAK 33(19P13.12) WILD-TYPE  183  286
     clus
vv    DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE
  NO                              2                             183
  YES                             4                             286
[1] 2 2
[1] FALSE
                                 vv
clus                              OTHER  SPECIFY
  DEL PEAK 33(19P13.12) MUTATED                0
  DEL PEAK 33(19P13.12) WILD-TYPE              8
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 33(19P13.12) MUTATED                                               7
  DEL PEAK 33(19P13.12) WILD-TYPE                                           348
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 33(19P13.12) MUTATED                                                                        1
  DEL PEAK 33(19P13.12) WILD-TYPE                                                                     99
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 33(19P13.12) MUTATED                                                                     0
  DEL PEAK 33(19P13.12) WILD-TYPE                                                                  36
D89V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 33(19P13.12) MUTATED
  OTHER  SPECIFY                                                                                     0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      7
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                0
                                                                        clus
vv                                                                       DEL PEAK 33(19P13.12) WILD-TYPE
  OTHER  SPECIFY                                                                                       8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      348
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                              99
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V10, binary
                                 cls
clus                                0   1
  DEL PEAK 33(19P13.12) MUTATED     5   2
  DEL PEAK 33(19P13.12) WILD-TYPE 415  15
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(19P13.12) MUTATED      5    2
  DEL PEAK 33(19P13.12) WILD-TYPE  415   15
     clus
vv    DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE
  NO                              5                             415
  YES                             2                              15
[1] 2 2
[1] FALSE
                                 vv
clus                              MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 33(19P13.12) MUTATED              1                       0    7
  DEL PEAK 33(19P13.12) WILD-TYPE          131                      18  323
                                 vv
clus                              VERY ADVANCED (T4B)
  DEL PEAK 33(19P13.12) MUTATED                     0
  DEL PEAK 33(19P13.12) WILD-TYPE                   1
D89V11, multiclass
                         clus
vv                        DEL PEAK 33(19P13.12) MUTATED
  MINIMAL (T3)                                        1
  MODERATE/ADVANCED (T4A)                             0
  NONE                                                7
  VERY ADVANCED (T4B)                                 0
                         clus
vv                        DEL PEAK 33(19P13.12) WILD-TYPE
  MINIMAL (T3)                                        131
  MODERATE/ADVANCED (T4A)                              18
  NONE                                                323
  VERY ADVANCED (T4B)                                   1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 33(19P13.12) MUTATED     5   2   0   0
  DEL PEAK 33(19P13.12) WILD-TYPE 378  49   4  30
D89V12, multiclass
    clus
vv   DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE
  R0                             5                             378
  R1                             2                              49
  R2                             0                               4
  RX                             0                              30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V13, continuous
[1] "Remove cluster labels:"        "DEL PEAK 33(19P13.12) MUTATED"
clus
  DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE 
                              2                             383 
                     TCGA-4C-A93U                      TCGA-BJ-A0Z0 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A0Z3                      TCGA-BJ-A0Z9 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A0ZA                      TCGA-BJ-A0ZB 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A0ZH                      TCGA-BJ-A0ZJ 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A18Y                      TCGA-BJ-A18Z 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A190                      TCGA-BJ-A191 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A28R                      TCGA-BJ-A28T 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A28W                      TCGA-BJ-A28X 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A28Z                      TCGA-BJ-A290 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A291                      TCGA-BJ-A2N8 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A2N9                      TCGA-BJ-A2NA 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A3EZ                      TCGA-BJ-A3PR 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A3PU                      TCGA-BJ-A45C 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A45D                      TCGA-BJ-A45E 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A45G                      TCGA-BJ-A45I 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A45J                      TCGA-BJ-A45K 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A4O8                      TCGA-BJ-A4O9 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-CE-A13K                      TCGA-CE-A3MD 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-CE-A483                      TCGA-CE-A484 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-CE-A485                      TCGA-DE-A0XZ 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DE-A0Y2                      TCGA-DE-A0Y3 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DE-A3KN                      TCGA-DE-A4M8 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DE-A4MA                      TCGA-DE-A4MB 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DE-A4MC                      TCGA-DE-A4MD 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DE-A69K                      TCGA-DE-A7U5 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A13M                      TCGA-DJ-A13O 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A13R                      TCGA-DJ-A13T 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A13V                      TCGA-DJ-A13W 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A13X                      TCGA-DJ-A1QG 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A1QH                      TCGA-DJ-A1QM 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A2PO                      TCGA-DJ-A2PP 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A2PQ                      TCGA-DJ-A2PR 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A2PS                      TCGA-DJ-A2PT 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A2PU                      TCGA-DJ-A2PV 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A2PW                      TCGA-DJ-A2PX 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A2PY                      TCGA-DJ-A2PZ 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A2Q0                      TCGA-DJ-A2Q1 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A2Q2                      TCGA-DJ-A2Q3 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A2Q4                      TCGA-DJ-A2Q5 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A2Q6                      TCGA-DJ-A2Q7 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A2Q8                      TCGA-DJ-A2Q9 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A2QA                      TCGA-DJ-A2QB 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A3UK                      TCGA-DJ-A3UM 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A3UN                      TCGA-DJ-A3UO 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A3UP                      TCGA-DJ-A3UQ 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A3UR                      TCGA-DJ-A3UU 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A3UW                      TCGA-DJ-A3UX 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A3UZ                      TCGA-DJ-A3V0 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A3V2                      TCGA-DJ-A3V3 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A3V4                      TCGA-DJ-A3V5 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A3V7                      TCGA-DJ-A3V8 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A3V9                      TCGA-DJ-A3VA 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A3VB                      TCGA-DJ-A3VD 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A3VF                      TCGA-DJ-A3VG 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A3VI                      TCGA-DJ-A3VJ 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A3VK                      TCGA-DJ-A3VL 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A4UL                      TCGA-DJ-A4UP 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A4UQ                      TCGA-DJ-A4UR 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A4UW                      TCGA-DJ-A4V2 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A4V5                      TCGA-DO-A1K0 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DO-A2HM                      TCGA-E3-A3DY 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-E3-A3DZ                      TCGA-E3-A3E0 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-E3-A3E1                      TCGA-E3-A3E2 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-E3-A3E3                      TCGA-E3-A3E5 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-E8-A242                      TCGA-E8-A2EA 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-E8-A414                      TCGA-E8-A415 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-E8-A417                      TCGA-E8-A419 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-E8-A433                      TCGA-E8-A436 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-E8-A438                      TCGA-E8-A44K 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3CM                      TCGA-EL-A3CN 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3CO                      TCGA-EL-A3CR 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3CS                      TCGA-EL-A3CT 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3CU                      TCGA-EL-A3CV 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3CW                      TCGA-EL-A3CX 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3CY                      TCGA-EL-A3CZ 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3D0                      TCGA-EL-A3D1 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3D4                      TCGA-EL-A3D6 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3GO                      TCGA-EL-A3GP 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3GQ                      TCGA-EL-A3GS 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3GU                      TCGA-EL-A3GV 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3GX                      TCGA-EL-A3H3 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3H4                      TCGA-EL-A3H5 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3H7                      TCGA-EL-A3H8 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3MW                      TCGA-EL-A3MX 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3MZ                      TCGA-EL-A3N2 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3T0                      TCGA-EL-A3T1 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3T2                      TCGA-EL-A3TB 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3ZH                      TCGA-EL-A3ZK 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3ZL                      TCGA-EL-A3ZM 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3ZN                      TCGA-EL-A3ZO 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3ZP                      TCGA-EL-A3ZS 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A4JV                      TCGA-EL-A4JW 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A4JX                      TCGA-EL-A4JZ 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A4K0                      TCGA-EL-A4K1 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A4K2                      TCGA-EL-A4K4 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A4K6                      TCGA-EL-A4K7 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A4KD                      TCGA-EL-A4KG 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A4KI                      TCGA-EM-A1CS 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A1CT                      TCGA-EM-A1CU 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A1CV                      TCGA-EM-A1CW 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A1YC                      TCGA-EM-A1YD 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A1YE                      TCGA-EM-A22I 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A22J                      TCGA-EM-A22K 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A22L                      TCGA-EM-A22M 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A22N                      TCGA-EM-A22O 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A22P                      TCGA-EM-A22Q 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A2CK                      TCGA-EM-A2CN 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A2CP                      TCGA-EM-A2CQ 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A2CT                      TCGA-EM-A2CU 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A2OV                      TCGA-EM-A2OX 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A2OY                      TCGA-EM-A2OZ 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A2P0                      TCGA-EM-A2P1 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A2P2                      TCGA-EM-A3AJ 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A3AK                      TCGA-EM-A3AL 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A3AN                      TCGA-EM-A3AO 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A3AQ                      TCGA-EM-A3AR 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A3FJ                      TCGA-EM-A3FK 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A3FM                      TCGA-EM-A3FN 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A3FO                      TCGA-EM-A3FP 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A3FQ                      TCGA-EM-A3FR 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A3O3                      TCGA-EM-A3O8 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A3O9                      TCGA-EM-A3OA 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A3OB                      TCGA-EM-A3ST 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A3SU                      TCGA-EM-A3SX 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A3SZ                      TCGA-EM-A4FF 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A4FM                      TCGA-EM-A4FN 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A4FO                      TCGA-EM-A4FQ 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A4FR                      TCGA-EM-A4FV 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A4G1                      TCGA-ET-A25G 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-ET-A25I                      TCGA-ET-A25J 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-ET-A25K                      TCGA-ET-A25L 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-ET-A25M                      TCGA-ET-A25N 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-ET-A25O                      TCGA-ET-A25P 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-ET-A2MX                      TCGA-ET-A2MZ 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-ET-A2N0                      TCGA-ET-A2N1 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-ET-A2N4                      TCGA-ET-A39K 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-ET-A39L                      TCGA-ET-A39O 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-ET-A39P                      TCGA-ET-A39R 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-ET-A39S                      TCGA-ET-A39T 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-ET-A3BO                      TCGA-ET-A3BP 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-ET-A3BQ                      TCGA-ET-A3BS 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-ET-A3BT                      TCGA-ET-A3BU 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-ET-A3BV                      TCGA-ET-A3BX 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-ET-A3DQ                      TCGA-ET-A3DR 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-ET-A3DS                      TCGA-ET-A3DT 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-ET-A3DU                      TCGA-ET-A3DV 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-ET-A3DW                      TCGA-ET-A40P 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-ET-A40Q                      TCGA-ET-A40R 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-ET-A40S                      TCGA-ET-A40T 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-ET-A4KN                      TCGA-FE-A22Z 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-FE-A230                      TCGA-FE-A231 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-FE-A232                      TCGA-FE-A233 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-FE-A234                      TCGA-FE-A235 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-FE-A236                      TCGA-FE-A237 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-FE-A238                      TCGA-FE-A239 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-FE-A23A                      TCGA-FE-A3PB 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-FE-A3PC                      TCGA-FE-A3PD 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-FK-A3S3                      TCGA-FK-A3SB 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-FK-A3SE                      TCGA-FK-A3SG 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-FK-A3SH                      TCGA-FK-A4UB 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-FY-A3I4                      TCGA-FY-A3I5 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-FY-A3NM                      TCGA-FY-A3NN 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-FY-A3ON                      TCGA-FY-A3R6 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-FY-A3R7                      TCGA-FY-A3R9 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-FY-A3TY                      TCGA-FY-A3W9 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-FY-A3YR                      TCGA-FY-A40K 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-FY-A40L                      TCGA-FY-A40M 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-FY-A40N                      TCGA-FY-A4B3 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-FY-A4B4                      TCGA-GE-A2C6 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-H2-A26U                      TCGA-H2-A2K9 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-H2-A3RH                      TCGA-H2-A3RI 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-H2-A421                      TCGA-H2-A422 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-IM-A3EB                      TCGA-IM-A3ED 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-IM-A3U2                      TCGA-IM-A3U3 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-IM-A41Y                      TCGA-IM-A41Z 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-IM-A420                      TCGA-IM-A4EB 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-J8-A3NZ                      TCGA-J8-A3O0 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-J8-A3O1                      TCGA-J8-A3O2 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-J8-A3YD                      TCGA-J8-A3YE 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-J8-A3YF                      TCGA-J8-A3YG 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-J8-A3YH                      TCGA-J8-A42S 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-J8-A4HW                      TCGA-J8-A4HY 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-KS-A41F                      TCGA-KS-A41I 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-KS-A41J                      TCGA-KS-A41L 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-KS-A4I1                      TCGA-KS-A4I3 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-KS-A4I5                      TCGA-KS-A4I7 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-KS-A4I9                      TCGA-KS-A4IB 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-KS-A4IC                      TCGA-KS-A4ID 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-L6-A4EP                      TCGA-L6-A4EQ 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-L6-A4EU                      TCGA-MK-A4N6 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-MK-A4N7                      TCGA-MK-A4N9 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-QD-A8IV 
"DEL PEAK 33(19P13.12) WILD-TYPE" 
D89V14, binary
                                 cls
clus                                0   1
  DEL PEAK 33(19P13.12) MUTATED     4   4
  DEL PEAK 33(19P13.12) WILD-TYPE 221 260
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(19P13.12) MUTATED      4    4
  DEL PEAK 33(19P13.12) WILD-TYPE  221  260
            clus
vv           DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE
  MULTIFOCAL                             4                             221
  UNIFOCAL                               4                             260
[1] 2 2
[1] FALSE
D89V15, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 33(19P13.12) MUTATED                                  0     0
  DEL PEAK 33(19P13.12) WILD-TYPE                                1    52
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(19P13.12) MUTATED                           2     6
  DEL PEAK 33(19P13.12) WILD-TYPE                        25   322
D89V16, multiclass
                                  clus
vv                                 DEL PEAK 33(19P13.12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                    2
  WHITE                                                        6
                                  clus
vv                                 DEL PEAK 33(19P13.12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         52
  BLACK OR AFRICAN AMERICAN                                     25
  WHITE                                                        322
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V17, binary
                                 cls
clus                                0   1
  DEL PEAK 33(19P13.12) MUTATED     0   8
  DEL PEAK 33(19P13.12) WILD-TYPE  38 351
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(19P13.12) MUTATED      0    8
  DEL PEAK 33(19P13.12) WILD-TYPE   38  351
                        clus
vv                       DEL PEAK 33(19P13.12) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                             8
                        clus
vv                       DEL PEAK 33(19P13.12) WILD-TYPE
  HISPANIC OR LATINO                                  38
  NOT HISPANIC OR LATINO                             351
[1] 2 2
[1] FALSE

Clustering(90) Variable = DEL PEAK 36(21Q21.1) MUTATION ANALYSIS
D90V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 36(21Q21.1) MUTATED     9   0
  DEL PEAK 36(21Q21.1) WILD-TYPE 472  16
  DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE 
                             9                            488 
  DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE 
                             0                             16 
$`DEL PEAK 36(21Q21.1) MUTATED`
TCGA-BJ-A190 TCGA-CE-A485 TCGA-DJ-A2Q0 TCGA-E8-A432 TCGA-EM-A22P TCGA-EM-A2OY 
       20.58        12.66        34.36        30.61        41.29        32.32 
TCGA-ET-A25L TCGA-FY-A3I5 TCGA-J8-A4HW 
       56.58         7.82         2.60 

$`DEL PEAK 36(21Q21.1) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 
        4.24        24.79        13.78        49.78        16.34        14.73 
TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG 
       41.33        18.87         4.01        11.57        16.73        25.48 
TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 
       15.12        42.08        51.39        41.52         4.83        44.35 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
       42.15        21.04        35.54        32.45        11.31        30.97 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       11.08        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
       18.97         7.04        16.01        13.94        36.39        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         7.99        10.88        21.01         3.45        23.84 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       28.44        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
       12.66        12.30        12.79        12.46        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
       15.02        12.43        35.84        21.63        50.17        37.64 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M 
       25.12        14.70        14.27         2.76         9.96        48.79 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       38.17       169.32        18.58         8.71        56.19        23.38 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       43.17        52.37         8.32        11.01       135.91        30.61 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       44.98        42.51        14.96        17.59         6.02        42.58 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
       47.41        17.56        10.09         7.82        30.58        35.41 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       27.45        26.20        38.83        33.96        31.99        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
       28.96         8.78         8.42        37.74         6.77        40.24 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
       33.93        37.48        36.46        35.11        39.09        35.90 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       33.53        35.18        15.88        36.92        31.04        32.42 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       31.46        16.41        19.56        36.33        32.81        36.33 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        59.57        11.34        35.87        40.96        36.99 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        42.54        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM 
       35.67         3.12        36.43        24.76        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       30.87        21.34        33.04        34.78        27.06        26.93 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       35.54         3.12        15.81        35.38        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        92.55        47.21        66.38        80.52        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 
       52.44        39.95        31.23        35.67        31.27        29.98 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 
       31.50        31.04         0.72         0.26         3.02        25.45 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
        0.16         0.23        14.96         7.69        33.50         0.39 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
        0.39        31.66        26.73       155.54        97.74       158.83 
TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
        7.66        45.53        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 
      106.62         4.18        79.50       139.86        98.53        69.57 
TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR 
       57.11       108.36        64.87        49.51        50.24       115.10 
TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY 
       65.39       136.01        50.37        50.20       147.75       101.13 
TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 
      139.99        49.32        33.50        43.36        49.71        83.57 
TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ 
      139.00       150.48       108.66        57.63        17.52        52.50 
TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       29.65       147.42       142.52       129.57        32.48       132.07 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
       98.24        41.29       107.47         5.72        66.90        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZM TCGA-EL-A3ZN 
       89.56        78.97        51.78        62.30        36.03        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        65.49        61.22        60.16         7.07        59.44 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       57.47        34.72        45.96        37.94        31.04        34.39 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        53.36        44.15        41.13        47.84        43.59 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       24.30        27.06        23.90        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
       48.49        18.05        19.79        19.46        78.61        57.01 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       54.08        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       10.65        44.19        14.24        47.57        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         6.05         2.99        12.30        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        40.34        19.73        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       33.07        13.38         8.35        29.72        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        47.38        21.01        12.07        17.49        17.39 
TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 
       16.18        15.02        14.50        15.06         7.33         0.49 
TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
        9.24        13.91        38.66        38.86        29.95        29.85 
TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       13.51        12.79        84.59        29.33        21.34         5.33 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
       26.37        26.37        22.45        21.53        60.49        24.46 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25M 
       13.68        81.93        81.70        77.56        70.42        60.20 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       63.39        65.29        18.38        63.45        88.41        58.75 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       37.25        52.60        54.35        83.34         2.66        80.88 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
       33.24       106.09       107.41       108.46        84.89       123.32 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
      100.57        95.34        94.13        55.10        98.20        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
       50.40        79.10        76.64         5.79        87.62        77.82 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       75.42        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       117.40        66.77       112.80        39.95        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       81.83       106.36        85.15        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.11         1.05        13.28         0.92        48.10       116.09 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25        20.42        17.82         0.99        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
       16.27        15.68        16.57        18.08         0.30         0.76 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
       17.06        17.36        15.16         6.58        22.49        19.04 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35        21.60         1.68        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46         2.99        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
       18.51        16.90        21.83        31.10         8.22        25.64 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
       17.23        43.17        27.19        11.24        31.82        27.85 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F 
       24.69        22.29         5.75         2.47         0.20       143.57 
TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 
       15.98        15.68       113.85        26.70        43.69        18.64 
TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       32.45        87.39        84.72        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 
TCGA-MK-A84Z TCGA-QD-A8IV 
       23.93        12.89 

  DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE 
                          2.60                           0.16 
  DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE 
                         56.58                         169.32 
  DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE 
                         30.61                          30.61 
[1] "2.6 - 56.6 (30.6)"  "0.2 - 169.3 (30.6)"
[1] "hr="     "9100000"
D90V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 36(21Q21.1) MUTATED         1        4         2        0         2
  DEL PEAK 36(21Q21.1) WILD-TYPE     281       46       109        2        44
                                vv
clus                             STAGE IVC
  DEL PEAK 36(21Q21.1) MUTATED           0
  DEL PEAK 36(21Q21.1) WILD-TYPE         6
D90V3, multiclass
           clus
vv          DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE
  STAGE I                              1                            281
  STAGE II                             4                             46
  STAGE III                            2                            109
  STAGE IV                             0                              2
  STAGE IVA                            2                             44
  STAGE IVC                            0                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 36(21Q21.1) MUTATED     1   6   2   0
  DEL PEAK 36(21Q21.1) WILD-TYPE 141 159 165  23
D90V4, multiclass
    clus
vv   DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE
  T1                            1                            141
  T2                            6                            159
  T3                            2                            165
  T4                            0                             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"
D90V5, binary
                                cls
clus                               0   1
  DEL PEAK 36(21Q21.1) MUTATED     5   4
  DEL PEAK 36(21Q21.1) WILD-TYPE 220 220
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(21Q21.1) MUTATED      5    4
  DEL PEAK 36(21Q21.1) WILD-TYPE  220  220
   clus
vv  DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE
  0                            5                            220
  1                            4                            220
[1] 2 2
[1] FALSE
D90V6, binary
                                cls
clus                               0   1
  DEL PEAK 36(21Q21.1) MUTATED     4   0
  DEL PEAK 36(21Q21.1) WILD-TYPE 274   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(21Q21.1) MUTATED      4    0
  DEL PEAK 36(21Q21.1) WILD-TYPE  274    9
   clus
vv  DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE
  0                            4                            274
  1                            0                              9
[1] 2 2
[1] FALSE
D90V7, binary
                                cls
clus                               0   1
  DEL PEAK 36(21Q21.1) MUTATED     6   3
  DEL PEAK 36(21Q21.1) WILD-TYPE 359 131
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(21Q21.1) MUTATED      6    3
  DEL PEAK 36(21Q21.1) WILD-TYPE  359  131
        clus
vv       DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE
  FEMALE                            6                            359
  MALE                              3                            131
[1] 2 2
[1] FALSE
D90V8, binary
                                cls
clus                               0   1
  DEL PEAK 36(21Q21.1) MUTATED     3   5
  DEL PEAK 36(21Q21.1) WILD-TYPE 182 285
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(21Q21.1) MUTATED      3    5
  DEL PEAK 36(21Q21.1) WILD-TYPE  182  285
     clus
vv    DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE
  NO                             3                            182
  YES                            5                            285
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 36(21Q21.1) MUTATED                0
  DEL PEAK 36(21Q21.1) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 36(21Q21.1) MUTATED                                               6
  DEL PEAK 36(21Q21.1) WILD-TYPE                                           349
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 36(21Q21.1) MUTATED                                                                        2
  DEL PEAK 36(21Q21.1) WILD-TYPE                                                                     98
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 36(21Q21.1) MUTATED                                                                     1
  DEL PEAK 36(21Q21.1) WILD-TYPE                                                                  35
D90V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 36(21Q21.1) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     6
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               1
                                                                        clus
vv                                                                       DEL PEAK 36(21Q21.1) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     349
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V10, binary
                                cls
clus                               0   1
  DEL PEAK 36(21Q21.1) MUTATED     8   0
  DEL PEAK 36(21Q21.1) WILD-TYPE 412  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(21Q21.1) MUTATED      8    0
  DEL PEAK 36(21Q21.1) WILD-TYPE  412   17
     clus
vv    DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE
  NO                             8                            412
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 36(21Q21.1) MUTATED              1                       0    8
  DEL PEAK 36(21Q21.1) WILD-TYPE          131                      18  322
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 36(21Q21.1) MUTATED                     0
  DEL PEAK 36(21Q21.1) WILD-TYPE                   1
D90V11, multiclass
                         clus
vv                        DEL PEAK 36(21Q21.1) MUTATED
  MINIMAL (T3)                                       1
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               8
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK 36(21Q21.1) WILD-TYPE
  MINIMAL (T3)                                       131
  MODERATE/ADVANCED (T4A)                             18
  NONE                                               322
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 36(21Q21.1) MUTATED     7   2   0   0
  DEL PEAK 36(21Q21.1) WILD-TYPE 376  49   4  30
D90V12, multiclass
    clus
vv   DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE
  R0                            7                            376
  R1                            2                             49
  R2                            0                              4
  RX                            0                             30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V13, continuous
D90V14, binary
                                cls
clus                               0   1
  DEL PEAK 36(21Q21.1) MUTATED     6   3
  DEL PEAK 36(21Q21.1) WILD-TYPE 219 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(21Q21.1) MUTATED      6    3
  DEL PEAK 36(21Q21.1) WILD-TYPE  219  261
            clus
vv           DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE
  MULTIFOCAL                            6                            219
  UNIFOCAL                              3                            261
[1] 2 2
[1] FALSE
D90V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 36(21Q21.1) MUTATED                                  0     2
  DEL PEAK 36(21Q21.1) WILD-TYPE                                1    50
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(21Q21.1) MUTATED                           0     5
  DEL PEAK 36(21Q21.1) WILD-TYPE                        27   323
D90V16, multiclass
                                  clus
vv                                 DEL PEAK 36(21Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       5
                                  clus
vv                                 DEL PEAK 36(21Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        50
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       323
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V17, binary
                                cls
clus                               0   1
  DEL PEAK 36(21Q21.1) MUTATED     0   6
  DEL PEAK 36(21Q21.1) WILD-TYPE  38 353
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(21Q21.1) MUTATED      0    6
  DEL PEAK 36(21Q21.1) WILD-TYPE   38  353
                        clus
vv                       DEL PEAK 36(21Q21.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            6
                        clus
vv                       DEL PEAK 36(21Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            353
[1] 2 2
[1] FALSE

Clustering(91) Variable = DEL PEAK 37(22Q12.3) MUTATION ANALYSIS
D91V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 37(22Q12.3) MUTATED    89   1
  DEL PEAK 37(22Q12.3) WILD-TYPE 392  15
  DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE 
                            90                            407 
  DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE 
                             1                             15 
$`DEL PEAK 37(22Q12.3) MUTATED`
TCGA-4C-A93U TCGA-BJ-A0Z2 TCGA-BJ-A0Z5 TCGA-BJ-A0ZH TCGA-BJ-A18Y TCGA-BJ-A190 
        4.24        49.78        14.73        15.12        51.39        20.58 
TCGA-BJ-A2P4 TCGA-BJ-A3PT TCGA-BJ-A45D TCGA-BJ-A45F TCGA-CE-A484 TCGA-DE-A0XZ 
        7.04        23.31        10.88         3.45        12.43        35.84 
TCGA-DE-A4M8 TCGA-DJ-A13M TCGA-DJ-A13T TCGA-DJ-A1QG TCGA-DJ-A1QN TCGA-DJ-A2PS 
       18.54        48.79        56.19        44.98        42.58        26.20 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q7 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A3UK TCGA-DJ-A3UN 
       34.36        35.11        33.53        35.18        36.92        32.42 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3VK TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-E3-A3DZ 
       31.46        16.41        24.76        27.62        34.78        47.21 
TCGA-E3-A3E5 TCGA-E8-A432 TCGA-E8-A434 TCGA-EL-A3CL TCGA-EL-A3D0 TCGA-EL-A3D1 
       39.95        30.61         0.23        31.66       139.86        98.53 
TCGA-EL-A3D4 TCGA-EL-A3GP TCGA-EL-A3GW TCGA-EL-A3T2 TCGA-EL-A3ZL TCGA-EL-A3ZR 
       69.57        49.51        50.20        32.48        62.30        60.16 
TCGA-EL-A4JV TCGA-EL-A4JZ TCGA-EL-A4K6 TCGA-EL-A4K9 TCGA-EL-A4KI TCGA-EM-A1CS 
       57.47        37.94        44.15        47.84        23.90        26.86 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22P TCGA-EM-A2CJ TCGA-EM-A2OX 
       15.75        10.45        14.53        41.29        47.57        19.73 
TCGA-EM-A2OY TCGA-EM-A3AP TCGA-EM-A3FO TCGA-EM-A3O9 TCGA-EM-A3SX TCGA-EM-A3SZ 
       32.32         8.35        17.49         9.24        29.85        12.79 
TCGA-EM-A4FO TCGA-EM-A4FR TCGA-EM-A4FU TCGA-ET-A25L TCGA-ET-A25O TCGA-ET-A2N4 
       26.37        21.53        60.49        56.58        65.29         2.66 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A3BP TCGA-ET-A3DS TCGA-ET-A40P 
      108.46        84.89       123.32        79.10        66.84        43.99 
TCGA-ET-A40T TCGA-FE-A237 TCGA-FE-A3PB TCGA-FY-A3R7 TCGA-FY-A3W9 TCGA-FY-A3WA 
       37.48       112.80        85.15        16.27         0.76        17.06 
TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-IM-A3U3 TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3YD 
       21.60        12.53        16.90        31.10        43.17        31.82 
TCGA-J8-A3YH TCGA-KS-A41I TCGA-KS-A4I7 TCGA-KS-A4IB TCGA-MK-A84Z TCGA-QD-A8IV 
        5.75        15.98        32.45        84.72        23.93        12.89 

$`DEL PEAK 37(22Q12.3) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB 
       24.79        13.78        16.34        41.33        18.87         4.01 
TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZJ TCGA-BJ-A18Z TCGA-BJ-A191 
       11.57        16.73        25.48        42.08        41.52         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PU 
       20.48        18.97        16.01        13.94        36.39        18.64 
TCGA-BJ-A45C TCGA-BJ-A45E TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J 
        7.99        21.01        23.84        28.44        15.45        21.63 
TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD 
       23.18        19.43        23.47        12.66        12.30        12.79 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A485 TCGA-DE-A0Y2 
       12.46        11.38        10.68        15.02        12.66        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       50.17        37.64        15.85        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13U TCGA-DJ-A13V 
       38.17       169.32        18.58         8.71        23.38        43.17 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QH 
       52.37         8.32        11.01       135.91        30.61        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       14.96        17.59         6.02        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.82        30.58        35.41        27.45        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
       31.99        34.85        28.96         8.78         8.42        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 
        6.77        40.24        33.93        37.48        36.46        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QC TCGA-DJ-A3UM TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       35.90        15.88        31.04        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        17.69        59.57        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        42.54        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A4UL 
        7.76        35.67         3.12        36.43        17.23        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       21.34        33.04        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA 
       66.38        80.52        63.19        52.44        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
        3.02        25.45         0.16        14.96         7.69        33.50 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
        0.39         0.39        26.73       155.54        97.74       158.83 
TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
        7.66        45.53        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62         4.18        79.50        57.11       108.36        64.87 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GX 
       50.24       115.10        65.39       136.01        50.37       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       83.57       139.00       150.48       108.66        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T3 
       52.50        29.65       147.42       142.52       129.57       132.07 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
       98.24        41.29       107.47         5.72        66.90        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO 
       89.56        78.97        51.78        36.03        53.06        47.38 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JW TCGA-EL-A4JX 
       65.49        61.22         7.07        59.44        34.72        45.96 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K7 TCGA-EL-A4KD 
       31.04        34.39        30.51        53.36        41.13        43.59 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       24.30        27.06        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I 
       19.79        19.46        78.61        57.01        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22Q TCGA-EM-A2CK TCGA-EM-A2CL 
       14.50        10.65        44.19        14.24        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         6.05         2.99        12.30        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       22.16        40.34        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
       13.38        29.72        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       21.01        12.07        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
       15.06         7.33         0.49        13.91        38.66        38.86 
TCGA-EM-A3SU TCGA-EM-A3SY TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       29.95        13.51        84.59        29.33        21.34         5.33 
TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       26.37        22.45        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25P TCGA-ET-A25R 
       77.56        70.42        60.20        63.39        18.38        63.45 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       88.41        58.75        37.25        52.60        54.35        83.34 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39O TCGA-ET-A39P 
       80.88        33.24       106.09       107.41       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BQ 
       94.13        55.10        98.20        28.24        50.40        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.79        87.62        77.82        75.42        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU 
      116.78        94.59        84.85        80.58        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A4KN 
      166.62        24.72        46.26        44.38        40.21        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
       68.22       117.40        66.77        39.95        33.63        81.83 
TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD 
      106.36        85.68        78.77        71.08         4.11         1.05 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       13.28         0.92        48.10       116.09         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R8 
       17.82         7.82         0.99        19.56        13.91        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L 
       16.57        18.08         0.30        17.36        15.16         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A76V TCGA-H2-A26U TCGA-H2-A2K9 
       22.49        19.04         1.35         1.68        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       12.46         2.99        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A41Y TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O1 
       18.51        21.83         8.22        25.64        17.23        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A42S TCGA-J8-A4HW 
       11.24        27.85        24.69        22.29         2.47         2.60 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
        0.20       143.57        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       18.64        87.39        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       21.83         9.50        36.10        32.45        30.21 

  DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE 
                          0.23                           0.16 
  DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE 
                        139.86                         169.32 
  DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE 
                         32.37                          30.12 
[1] "0.2 - 139.9 (32.4)" "0.2 - 169.3 (30.1)"
[1] "hr=" "3.2"
D91V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 37(22Q12.3) MUTATED        49       10        18        1        11
  DEL PEAK 37(22Q12.3) WILD-TYPE     233       40        93        1        35
                                vv
clus                             STAGE IVC
  DEL PEAK 37(22Q12.3) MUTATED           1
  DEL PEAK 37(22Q12.3) WILD-TYPE         5
D91V3, multiclass
           clus
vv          DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE
  STAGE I                             49                            233
  STAGE II                            10                             40
  STAGE III                           18                             93
  STAGE IV                             1                              1
  STAGE IVA                           11                             35
  STAGE IVC                            1                              5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 37(22Q12.3) MUTATED    25  33  28   4
  DEL PEAK 37(22Q12.3) WILD-TYPE 117 132 139  19
D91V4, multiclass
    clus
vv   DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE
  T1                           25                            117
  T2                           33                            132
  T3                           28                            139
  T4                            4                             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"
D91V5, binary
                                cls
clus                               0   1
  DEL PEAK 37(22Q12.3) MUTATED    45  37
  DEL PEAK 37(22Q12.3) WILD-TYPE 180 187
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(22Q12.3) MUTATED     45   37
  DEL PEAK 37(22Q12.3) WILD-TYPE  180  187
   clus
vv  DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE
  0                           45                            180
  1                           37                            187
[1] 2 2
[1] FALSE
D91V6, binary
                                cls
clus                               0   1
  DEL PEAK 37(22Q12.3) MUTATED    45   2
  DEL PEAK 37(22Q12.3) WILD-TYPE 233   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(22Q12.3) MUTATED     45    2
  DEL PEAK 37(22Q12.3) WILD-TYPE  233    7
   clus
vv  DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE
  0                           45                            233
  1                            2                              7
[1] 2 2
[1] FALSE
D91V7, binary
                                cls
clus                               0   1
  DEL PEAK 37(22Q12.3) MUTATED    62  28
  DEL PEAK 37(22Q12.3) WILD-TYPE 303 106
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(22Q12.3) MUTATED     62   28
  DEL PEAK 37(22Q12.3) WILD-TYPE  303  106
        clus
vv       DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE
  FEMALE                           62                            303
  MALE                             28                            106
[1] 2 2
[1] FALSE
D91V8, binary
                                cls
clus                               0   1
  DEL PEAK 37(22Q12.3) MUTATED    26  60
  DEL PEAK 37(22Q12.3) WILD-TYPE 159 230
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(22Q12.3) MUTATED     26   60
  DEL PEAK 37(22Q12.3) WILD-TYPE  159  230
     clus
vv    DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE
  NO                            26                            159
  YES                           60                            230
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 37(22Q12.3) MUTATED                1
  DEL PEAK 37(22Q12.3) WILD-TYPE              7
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 37(22Q12.3) MUTATED                                              62
  DEL PEAK 37(22Q12.3) WILD-TYPE                                           293
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 37(22Q12.3) MUTATED                                                                       24
  DEL PEAK 37(22Q12.3) WILD-TYPE                                                                     76
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 37(22Q12.3) MUTATED                                                                     3
  DEL PEAK 37(22Q12.3) WILD-TYPE                                                                  33
D91V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 37(22Q12.3) MUTATED
  OTHER  SPECIFY                                                                                    1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    62
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           24
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               3
                                                                        clus
vv                                                                       DEL PEAK 37(22Q12.3) WILD-TYPE
  OTHER  SPECIFY                                                                                      7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     293
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             76
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                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"
D91V10, binary
                                cls
clus                               0   1
  DEL PEAK 37(22Q12.3) MUTATED    80   1
  DEL PEAK 37(22Q12.3) WILD-TYPE 340  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(22Q12.3) MUTATED     80    1
  DEL PEAK 37(22Q12.3) WILD-TYPE  340   16
     clus
vv    DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE
  NO                            80                            340
  YES                            1                             16
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 37(22Q12.3) MUTATED             19                       2   64
  DEL PEAK 37(22Q12.3) WILD-TYPE          113                      16  266
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 37(22Q12.3) MUTATED                     0
  DEL PEAK 37(22Q12.3) WILD-TYPE                   1
D91V11, multiclass
                         clus
vv                        DEL PEAK 37(22Q12.3) MUTATED
  MINIMAL (T3)                                      19
  MODERATE/ADVANCED (T4A)                            2
  NONE                                              64
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK 37(22Q12.3) WILD-TYPE
  MINIMAL (T3)                                       113
  MODERATE/ADVANCED (T4A)                             16
  NONE                                               266
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 37(22Q12.3) MUTATED    69   6   1   8
  DEL PEAK 37(22Q12.3) WILD-TYPE 314  45   3  22
D91V12, multiclass
    clus
vv   DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE
  R0                           69                            314
  R1                            6                             45
  R2                            1                              3
  RX                            8                             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V13, continuous
D91V14, binary
                                cls
clus                               0   1
  DEL PEAK 37(22Q12.3) MUTATED    46  42
  DEL PEAK 37(22Q12.3) WILD-TYPE 179 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(22Q12.3) MUTATED     46   42
  DEL PEAK 37(22Q12.3) WILD-TYPE  179  222
            clus
vv           DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE
  MULTIFOCAL                           46                            179
  UNIFOCAL                             42                            222
[1] 2 2
[1] FALSE
D91V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 37(22Q12.3) MUTATED                                  0    11
  DEL PEAK 37(22Q12.3) WILD-TYPE                                1    41
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 37(22Q12.3) MUTATED                           7    54
  DEL PEAK 37(22Q12.3) WILD-TYPE                        20   274
D91V16, multiclass
                                  clus
vv                                 DEL PEAK 37(22Q12.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      11
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      54
                                  clus
vv                                 DEL PEAK 37(22Q12.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        41
  BLACK OR AFRICAN AMERICAN                                    20
  WHITE                                                       274
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V17, binary
                                cls
clus                               0   1
  DEL PEAK 37(22Q12.3) MUTATED     6  63
  DEL PEAK 37(22Q12.3) WILD-TYPE  32 296
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(22Q12.3) MUTATED      6   63
  DEL PEAK 37(22Q12.3) WILD-TYPE   32  296
                        clus
vv                       DEL PEAK 37(22Q12.3) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           63
                        clus
vv                       DEL PEAK 37(22Q12.3) WILD-TYPE
  HISPANIC OR LATINO                                 32
  NOT HISPANIC OR LATINO                            296
[1] 2 2
[1] FALSE

Clustering(92) Variable = DEL PEAK 38(22Q13.1) MUTATION ANALYSIS
D92V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 38(22Q13.1) MUTATED    88   1
  DEL PEAK 38(22Q13.1) WILD-TYPE 393  15
  DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE 
                            89                            408 
  DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE 
                             1                             15 
$`DEL PEAK 38(22Q13.1) MUTATED`
TCGA-4C-A93U TCGA-BJ-A0Z2 TCGA-BJ-A0Z5 TCGA-BJ-A0ZH TCGA-BJ-A18Y TCGA-BJ-A190 
        4.24        49.78        14.73        15.12        51.39        20.58 
TCGA-BJ-A2P4 TCGA-BJ-A3PT TCGA-BJ-A45D TCGA-BJ-A45F TCGA-CE-A484 TCGA-DE-A0XZ 
        7.04        23.31        10.88         3.45        12.43        35.84 
TCGA-DE-A4M8 TCGA-DJ-A13M TCGA-DJ-A13T TCGA-DJ-A1QG TCGA-DJ-A1QN TCGA-DJ-A2PS 
       18.54        48.79        56.19        44.98        42.58        26.20 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q7 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A3UK TCGA-DJ-A3UN 
       34.36        35.11        33.53        35.18        36.92        32.42 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3VK TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-E3-A3DZ 
       31.46        16.41        24.76        27.62        34.78        47.21 
TCGA-E3-A3E5 TCGA-E8-A432 TCGA-E8-A434 TCGA-EL-A3CL TCGA-EL-A3D0 TCGA-EL-A3D1 
       39.95        30.61         0.23        31.66       139.86        98.53 
TCGA-EL-A3D4 TCGA-EL-A3GP TCGA-EL-A3GW TCGA-EL-A3T2 TCGA-EL-A3ZL TCGA-EL-A3ZR 
       69.57        49.51        50.20        32.48        62.30        60.16 
TCGA-EL-A4JV TCGA-EL-A4JZ TCGA-EL-A4K6 TCGA-EL-A4K9 TCGA-EL-A4KI TCGA-EM-A1CS 
       57.47        37.94        44.15        47.84        23.90        26.86 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22P TCGA-EM-A2CJ TCGA-EM-A2OY 
       15.75        10.45        14.53        41.29        47.57        32.32 
TCGA-EM-A3AP TCGA-EM-A3FO TCGA-EM-A3O9 TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FO 
        8.35        17.49         9.24        29.85        12.79        26.37 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-ET-A25L TCGA-ET-A25O TCGA-ET-A2N4 TCGA-ET-A39L 
       21.53        60.49        56.58        65.29         2.66       108.46 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A3BP TCGA-ET-A3DS TCGA-ET-A40P TCGA-ET-A40T 
       84.89       123.32        79.10        66.84        43.99        37.48 
TCGA-FE-A237 TCGA-FE-A3PB TCGA-FY-A3R7 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A4B4 
      112.80        85.15        16.27         0.76        17.06        21.60 
TCGA-GE-A2C6 TCGA-IM-A3U3 TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3YD TCGA-J8-A3YH 
       12.53        16.90        31.10        43.17        31.82         5.75 
TCGA-KS-A41I TCGA-KS-A4I7 TCGA-KS-A4IB TCGA-MK-A84Z TCGA-QD-A8IV 
       15.98        32.45        84.72        23.93        12.89 

$`DEL PEAK 38(22Q13.1) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB 
       24.79        13.78        16.34        41.33        18.87         4.01 
TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZJ TCGA-BJ-A18Z TCGA-BJ-A191 
       11.57        16.73        25.48        42.08        41.52         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PU 
       20.48        18.97        16.01        13.94        36.39        18.64 
TCGA-BJ-A45C TCGA-BJ-A45E TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J 
        7.99        21.01        23.84        28.44        15.45        21.63 
TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD 
       23.18        19.43        23.47        12.66        12.30        12.79 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A485 TCGA-DE-A0Y2 
       12.46        11.38        10.68        15.02        12.66        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       50.17        37.64        15.85        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13U TCGA-DJ-A13V 
       38.17       169.32        18.58         8.71        23.38        43.17 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QH 
       52.37         8.32        11.01       135.91        30.61        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       14.96        17.59         6.02        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.82        30.58        35.41        27.45        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
       31.99        34.85        28.96         8.78         8.42        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 
        6.77        40.24        33.93        37.48        36.46        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QC TCGA-DJ-A3UM TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       35.90        15.88        31.04        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        17.69        59.57        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        42.54        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A4UL 
        7.76        35.67         3.12        36.43        17.23        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       21.34        33.04        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA 
       66.38        80.52        63.19        52.44        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
        3.02        25.45         0.16        14.96         7.69        33.50 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
        0.39         0.39        26.73       155.54        97.74       158.83 
TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
        7.66        45.53        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62         4.18        79.50        57.11       108.36        64.87 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GX 
       50.24       115.10        65.39       136.01        50.37       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       83.57       139.00       150.48       108.66        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T3 
       52.50        29.65       147.42       142.52       129.57       132.07 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
       98.24        41.29       107.47         5.72        66.90        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO 
       89.56        78.97        51.78        36.03        53.06        47.38 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JW TCGA-EL-A4JX 
       65.49        61.22         7.07        59.44        34.72        45.96 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K7 TCGA-EL-A4KD 
       31.04        34.39        30.51        53.36        41.13        43.59 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       24.30        27.06        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I 
       19.79        19.46        78.61        57.01        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22Q TCGA-EM-A2CK TCGA-EM-A2CL 
       14.50        10.65        44.19        14.24        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         6.05         2.99        12.30        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        40.34        19.73        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       33.07        13.38        29.72        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       47.38        21.01        12.07        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB 
       14.50        15.06         7.33         0.49        13.91        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SY TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       38.86        29.95        13.51        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        5.33        26.37        22.45        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25P 
       81.70        77.56        70.42        60.20        63.39        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       63.45        88.41        58.75        37.25        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39O 
       83.34        80.88        33.24       106.09       107.41       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       95.34        94.13        55.10        98.20        28.24        50.40 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
       76.64         5.79        87.62        77.82        75.42        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT 
       52.47       116.78        94.59        84.85        80.58        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
       62.83       166.62        24.72        46.26        44.38        40.21 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A238 TCGA-FE-A239 
       24.69        68.22       117.40        66.77        39.95        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
       81.83       106.36        85.68        78.77        71.08         4.11 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        1.05        13.28         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
       20.42        17.82         7.82         0.99        19.56        13.91 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3YR TCGA-FY-A40K 
       15.68        16.57        18.08         0.30        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A76V TCGA-H2-A26U 
        6.58        22.49        19.04         1.35         1.68        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46         2.99        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A41Y TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       47.41        18.51        21.83         8.22        25.64        17.23 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A42S 
       27.19        11.24        27.85        24.69        22.29         2.47 
TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        2.60         0.20       143.57        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       43.69        18.64        87.39        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 

  DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE 
                          0.23                           0.16 
  DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE 
                        139.86                         169.32 
  DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE 
                         32.42                          30.07 
[1] "0.2 - 139.9 (32.4)" "0.2 - 169.3 (30.1)"
[1] "hr=" "3.2"
D92V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 38(22Q13.1) MUTATED        49       10        18        1        10
  DEL PEAK 38(22Q13.1) WILD-TYPE     233       40        93        1        36
                                vv
clus                             STAGE IVC
  DEL PEAK 38(22Q13.1) MUTATED           1
  DEL PEAK 38(22Q13.1) WILD-TYPE         5
D92V3, multiclass
           clus
vv          DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE
  STAGE I                             49                            233
  STAGE II                            10                             40
  STAGE III                           18                             93
  STAGE IV                             1                              1
  STAGE IVA                           10                             36
  STAGE IVC                            1                              5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 38(22Q13.1) MUTATED    24  33  28   4
  DEL PEAK 38(22Q13.1) WILD-TYPE 118 132 139  19
D92V4, multiclass
    clus
vv   DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE
  T1                           24                            118
  T2                           33                            132
  T3                           28                            139
  T4                            4                             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"
D92V5, binary
                                cls
clus                               0   1
  DEL PEAK 38(22Q13.1) MUTATED    45  36
  DEL PEAK 38(22Q13.1) WILD-TYPE 180 188
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(22Q13.1) MUTATED     45   36
  DEL PEAK 38(22Q13.1) WILD-TYPE  180  188
   clus
vv  DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE
  0                           45                            180
  1                           36                            188
[1] 2 2
[1] FALSE
D92V6, binary
                                cls
clus                               0   1
  DEL PEAK 38(22Q13.1) MUTATED    45   2
  DEL PEAK 38(22Q13.1) WILD-TYPE 233   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(22Q13.1) MUTATED     45    2
  DEL PEAK 38(22Q13.1) WILD-TYPE  233    7
   clus
vv  DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE
  0                           45                            233
  1                            2                              7
[1] 2 2
[1] FALSE
D92V7, binary
                                cls
clus                               0   1
  DEL PEAK 38(22Q13.1) MUTATED    62  27
  DEL PEAK 38(22Q13.1) WILD-TYPE 303 107
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(22Q13.1) MUTATED     62   27
  DEL PEAK 38(22Q13.1) WILD-TYPE  303  107
        clus
vv       DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE
  FEMALE                           62                            303
  MALE                             27                            107
[1] 2 2
[1] FALSE
D92V8, binary
                                cls
clus                               0   1
  DEL PEAK 38(22Q13.1) MUTATED    26  59
  DEL PEAK 38(22Q13.1) WILD-TYPE 159 231
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(22Q13.1) MUTATED     26   59
  DEL PEAK 38(22Q13.1) WILD-TYPE  159  231
     clus
vv    DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE
  NO                            26                            159
  YES                           59                            231
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 38(22Q13.1) MUTATED                1
  DEL PEAK 38(22Q13.1) WILD-TYPE              7
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 38(22Q13.1) MUTATED                                              61
  DEL PEAK 38(22Q13.1) WILD-TYPE                                           294
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 38(22Q13.1) MUTATED                                                                       24
  DEL PEAK 38(22Q13.1) WILD-TYPE                                                                     76
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 38(22Q13.1) MUTATED                                                                     3
  DEL PEAK 38(22Q13.1) WILD-TYPE                                                                  33
D92V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 38(22Q13.1) MUTATED
  OTHER  SPECIFY                                                                                    1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    61
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           24
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               3
                                                                        clus
vv                                                                       DEL PEAK 38(22Q13.1) WILD-TYPE
  OTHER  SPECIFY                                                                                      7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     294
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             76
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                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"
D92V10, binary
                                cls
clus                               0   1
  DEL PEAK 38(22Q13.1) MUTATED    79   1
  DEL PEAK 38(22Q13.1) WILD-TYPE 341  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(22Q13.1) MUTATED     79    1
  DEL PEAK 38(22Q13.1) WILD-TYPE  341   16
     clus
vv    DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE
  NO                            79                            341
  YES                            1                             16
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 38(22Q13.1) MUTATED             19                       2   63
  DEL PEAK 38(22Q13.1) WILD-TYPE          113                      16  267
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 38(22Q13.1) MUTATED                     0
  DEL PEAK 38(22Q13.1) WILD-TYPE                   1
D92V11, multiclass
                         clus
vv                        DEL PEAK 38(22Q13.1) MUTATED
  MINIMAL (T3)                                      19
  MODERATE/ADVANCED (T4A)                            2
  NONE                                              63
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK 38(22Q13.1) WILD-TYPE
  MINIMAL (T3)                                       113
  MODERATE/ADVANCED (T4A)                             16
  NONE                                               267
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 38(22Q13.1) MUTATED    68   6   1   8
  DEL PEAK 38(22Q13.1) WILD-TYPE 315  45   3  22
D92V12, multiclass
    clus
vv   DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE
  R0                           68                            315
  R1                            6                             45
  R2                            1                              3
  RX                            8                             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V13, continuous
D92V14, binary
                                cls
clus                               0   1
  DEL PEAK 38(22Q13.1) MUTATED    45  42
  DEL PEAK 38(22Q13.1) WILD-TYPE 180 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(22Q13.1) MUTATED     45   42
  DEL PEAK 38(22Q13.1) WILD-TYPE  180  222
            clus
vv           DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE
  MULTIFOCAL                           45                            180
  UNIFOCAL                             42                            222
[1] 2 2
[1] FALSE
D92V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 38(22Q13.1) MUTATED                                  0    11
  DEL PEAK 38(22Q13.1) WILD-TYPE                                1    41
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 38(22Q13.1) MUTATED                           7    54
  DEL PEAK 38(22Q13.1) WILD-TYPE                        20   274
D92V16, multiclass
                                  clus
vv                                 DEL PEAK 38(22Q13.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      11
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      54
                                  clus
vv                                 DEL PEAK 38(22Q13.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        41
  BLACK OR AFRICAN AMERICAN                                    20
  WHITE                                                       274
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V17, binary
                                cls
clus                               0   1
  DEL PEAK 38(22Q13.1) MUTATED     6  63
  DEL PEAK 38(22Q13.1) WILD-TYPE  32 296
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(22Q13.1) MUTATED      6   63
  DEL PEAK 38(22Q13.1) WILD-TYPE   32  296
                        clus
vv                       DEL PEAK 38(22Q13.1) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           63
                        clus
vv                       DEL PEAK 38(22Q13.1) WILD-TYPE
  HISPANIC OR LATINO                                 32
  NOT HISPANIC OR LATINO                            296
[1] 2 2
[1] FALSE

Clustering(93) Variable = DEL PEAK 39(22Q13.2) MUTATION ANALYSIS
D93V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 39(22Q13.2) MUTATED    88   1
  DEL PEAK 39(22Q13.2) WILD-TYPE 393  15
  DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE 
                            89                            408 
  DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE 
                             1                             15 
$`DEL PEAK 39(22Q13.2) MUTATED`
TCGA-4C-A93U TCGA-BJ-A0Z2 TCGA-BJ-A0Z5 TCGA-BJ-A0ZH TCGA-BJ-A18Y TCGA-BJ-A190 
        4.24        49.78        14.73        15.12        51.39        20.58 
TCGA-BJ-A2P4 TCGA-BJ-A3PT TCGA-BJ-A45D TCGA-BJ-A45F TCGA-CE-A484 TCGA-DE-A0XZ 
        7.04        23.31        10.88         3.45        12.43        35.84 
TCGA-DE-A4M8 TCGA-DJ-A13M TCGA-DJ-A13T TCGA-DJ-A1QG TCGA-DJ-A1QN TCGA-DJ-A2PS 
       18.54        48.79        56.19        44.98        42.58        26.20 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q7 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A3UK TCGA-DJ-A3UN 
       34.36        35.11        33.53        35.18        36.92        32.42 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3VK TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-E3-A3DZ 
       31.46        16.41        24.76        27.62        34.78        47.21 
TCGA-E3-A3E5 TCGA-E8-A432 TCGA-E8-A434 TCGA-EL-A3CL TCGA-EL-A3D0 TCGA-EL-A3D1 
       39.95        30.61         0.23        31.66       139.86        98.53 
TCGA-EL-A3D4 TCGA-EL-A3GP TCGA-EL-A3GW TCGA-EL-A3T2 TCGA-EL-A3ZL TCGA-EL-A3ZR 
       69.57        49.51        50.20        32.48        62.30        60.16 
TCGA-EL-A4JV TCGA-EL-A4JZ TCGA-EL-A4K6 TCGA-EL-A4K9 TCGA-EL-A4KI TCGA-EM-A1CS 
       57.47        37.94        44.15        47.84        23.90        26.86 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22P TCGA-EM-A2CJ TCGA-EM-A2OY 
       15.75        10.45        14.53        41.29        47.57        32.32 
TCGA-EM-A3AP TCGA-EM-A3FO TCGA-EM-A3O9 TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FO 
        8.35        17.49         9.24        29.85        12.79        26.37 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-ET-A25L TCGA-ET-A25O TCGA-ET-A2N4 TCGA-ET-A39L 
       21.53        60.49        56.58        65.29         2.66       108.46 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A3BP TCGA-ET-A3DS TCGA-ET-A40P TCGA-ET-A40T 
       84.89       123.32        79.10        66.84        43.99        37.48 
TCGA-FE-A237 TCGA-FE-A3PB TCGA-FY-A3R7 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A4B4 
      112.80        85.15        16.27         0.76        17.06        21.60 
TCGA-GE-A2C6 TCGA-IM-A3U3 TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3YD TCGA-J8-A3YH 
       12.53        16.90        31.10        43.17        31.82         5.75 
TCGA-KS-A41I TCGA-KS-A4I7 TCGA-KS-A4IB TCGA-MK-A84Z TCGA-QD-A8IV 
       15.98        32.45        84.72        23.93        12.89 

$`DEL PEAK 39(22Q13.2) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB 
       24.79        13.78        16.34        41.33        18.87         4.01 
TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZJ TCGA-BJ-A18Z TCGA-BJ-A191 
       11.57        16.73        25.48        42.08        41.52         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PU 
       20.48        18.97        16.01        13.94        36.39        18.64 
TCGA-BJ-A45C TCGA-BJ-A45E TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J 
        7.99        21.01        23.84        28.44        15.45        21.63 
TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD 
       23.18        19.43        23.47        12.66        12.30        12.79 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A485 TCGA-DE-A0Y2 
       12.46        11.38        10.68        15.02        12.66        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       50.17        37.64        15.85        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13U TCGA-DJ-A13V 
       38.17       169.32        18.58         8.71        23.38        43.17 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QH 
       52.37         8.32        11.01       135.91        30.61        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       14.96        17.59         6.02        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.82        30.58        35.41        27.45        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
       31.99        34.85        28.96         8.78         8.42        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 
        6.77        40.24        33.93        37.48        36.46        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QC TCGA-DJ-A3UM TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       35.90        15.88        31.04        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        17.69        59.57        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        42.54        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A4UL 
        7.76        35.67         3.12        36.43        17.23        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       21.34        33.04        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA 
       66.38        80.52        63.19        52.44        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
        3.02        25.45         0.16        14.96         7.69        33.50 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
        0.39         0.39        26.73       155.54        97.74       158.83 
TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
        7.66        45.53        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62         4.18        79.50        57.11       108.36        64.87 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GX 
       50.24       115.10        65.39       136.01        50.37       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       83.57       139.00       150.48       108.66        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T3 
       52.50        29.65       147.42       142.52       129.57       132.07 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
       98.24        41.29       107.47         5.72        66.90        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO 
       89.56        78.97        51.78        36.03        53.06        47.38 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JW TCGA-EL-A4JX 
       65.49        61.22         7.07        59.44        34.72        45.96 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K7 TCGA-EL-A4KD 
       31.04        34.39        30.51        53.36        41.13        43.59 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       24.30        27.06        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I 
       19.79        19.46        78.61        57.01        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22Q TCGA-EM-A2CK TCGA-EM-A2CL 
       14.50        10.65        44.19        14.24        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         6.05         2.99        12.30        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        40.34        19.73        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       33.07        13.38        29.72        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       47.38        21.01        12.07        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB 
       14.50        15.06         7.33         0.49        13.91        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SY TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       38.86        29.95        13.51        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        5.33        26.37        22.45        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25P 
       81.70        77.56        70.42        60.20        63.39        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       63.45        88.41        58.75        37.25        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39O 
       83.34        80.88        33.24       106.09       107.41       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       95.34        94.13        55.10        98.20        28.24        50.40 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
       76.64         5.79        87.62        77.82        75.42        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT 
       52.47       116.78        94.59        84.85        80.58        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
       62.83       166.62        24.72        46.26        44.38        40.21 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A238 TCGA-FE-A239 
       24.69        68.22       117.40        66.77        39.95        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
       81.83       106.36        85.68        78.77        71.08         4.11 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        1.05        13.28         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
       20.42        17.82         7.82         0.99        19.56        13.91 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3YR TCGA-FY-A40K 
       15.68        16.57        18.08         0.30        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A76V TCGA-H2-A26U 
        6.58        22.49        19.04         1.35         1.68        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB 
       21.67        12.46         2.99        20.05        18.61        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A41Y TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       47.41        18.51        21.83         8.22        25.64        17.23 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A42S 
       27.19        11.24        27.85        24.69        22.29         2.47 
TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 
        2.60         0.20       143.57        15.68       113.85        26.70 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP 
       43.69        18.64        87.39        35.28        33.24        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         9.50        36.10        32.45        30.21 

  DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE 
                          0.23                           0.16 
  DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE 
                        139.86                         169.32 
  DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE 
                         32.42                          30.07 
[1] "0.2 - 139.9 (32.4)" "0.2 - 169.3 (30.1)"
[1] "hr=" "3.2"
D93V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 39(22Q13.2) MUTATED        49       10        18        1        10
  DEL PEAK 39(22Q13.2) WILD-TYPE     233       40        93        1        36
                                vv
clus                             STAGE IVC
  DEL PEAK 39(22Q13.2) MUTATED           1
  DEL PEAK 39(22Q13.2) WILD-TYPE         5
D93V3, multiclass
           clus
vv          DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE
  STAGE I                             49                            233
  STAGE II                            10                             40
  STAGE III                           18                             93
  STAGE IV                             1                              1
  STAGE IVA                           10                             36
  STAGE IVC                            1                              5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 39(22Q13.2) MUTATED    24  33  28   4
  DEL PEAK 39(22Q13.2) WILD-TYPE 118 132 139  19
D93V4, multiclass
    clus
vv   DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE
  T1                           24                            118
  T2                           33                            132
  T3                           28                            139
  T4                            4                             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"
D93V5, binary
                                cls
clus                               0   1
  DEL PEAK 39(22Q13.2) MUTATED    45  36
  DEL PEAK 39(22Q13.2) WILD-TYPE 180 188
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(22Q13.2) MUTATED     45   36
  DEL PEAK 39(22Q13.2) WILD-TYPE  180  188
   clus
vv  DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE
  0                           45                            180
  1                           36                            188
[1] 2 2
[1] FALSE
D93V6, binary
                                cls
clus                               0   1
  DEL PEAK 39(22Q13.2) MUTATED    45   2
  DEL PEAK 39(22Q13.2) WILD-TYPE 233   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(22Q13.2) MUTATED     45    2
  DEL PEAK 39(22Q13.2) WILD-TYPE  233    7
   clus
vv  DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE
  0                           45                            233
  1                            2                              7
[1] 2 2
[1] FALSE
D93V7, binary
                                cls
clus                               0   1
  DEL PEAK 39(22Q13.2) MUTATED    62  27
  DEL PEAK 39(22Q13.2) WILD-TYPE 303 107
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(22Q13.2) MUTATED     62   27
  DEL PEAK 39(22Q13.2) WILD-TYPE  303  107
        clus
vv       DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE
  FEMALE                           62                            303
  MALE                             27                            107
[1] 2 2
[1] FALSE
D93V8, binary
                                cls
clus                               0   1
  DEL PEAK 39(22Q13.2) MUTATED    26  59
  DEL PEAK 39(22Q13.2) WILD-TYPE 159 231
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(22Q13.2) MUTATED     26   59
  DEL PEAK 39(22Q13.2) WILD-TYPE  159  231
     clus
vv    DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE
  NO                            26                            159
  YES                           59                            231
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 39(22Q13.2) MUTATED                1
  DEL PEAK 39(22Q13.2) WILD-TYPE              7
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 39(22Q13.2) MUTATED                                              61
  DEL PEAK 39(22Q13.2) WILD-TYPE                                           294
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 39(22Q13.2) MUTATED                                                                       24
  DEL PEAK 39(22Q13.2) WILD-TYPE                                                                     76
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 39(22Q13.2) MUTATED                                                                     3
  DEL PEAK 39(22Q13.2) WILD-TYPE                                                                  33
D93V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 39(22Q13.2) MUTATED
  OTHER  SPECIFY                                                                                    1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    61
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           24
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               3
                                                                        clus
vv                                                                       DEL PEAK 39(22Q13.2) WILD-TYPE
  OTHER  SPECIFY                                                                                      7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     294
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             76
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                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"
D93V10, binary
                                cls
clus                               0   1
  DEL PEAK 39(22Q13.2) MUTATED    79   1
  DEL PEAK 39(22Q13.2) WILD-TYPE 341  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(22Q13.2) MUTATED     79    1
  DEL PEAK 39(22Q13.2) WILD-TYPE  341   16
     clus
vv    DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE
  NO                            79                            341
  YES                            1                             16
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 39(22Q13.2) MUTATED             19                       2   63
  DEL PEAK 39(22Q13.2) WILD-TYPE          113                      16  267
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 39(22Q13.2) MUTATED                     0
  DEL PEAK 39(22Q13.2) WILD-TYPE                   1
D93V11, multiclass
                         clus
vv                        DEL PEAK 39(22Q13.2) MUTATED
  MINIMAL (T3)                                      19
  MODERATE/ADVANCED (T4A)                            2
  NONE                                              63
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK 39(22Q13.2) WILD-TYPE
  MINIMAL (T3)                                       113
  MODERATE/ADVANCED (T4A)                             16
  NONE                                               267
  VERY ADVANCED (T4B)                                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 39(22Q13.2) MUTATED    68   6   1   8
  DEL PEAK 39(22Q13.2) WILD-TYPE 315  45   3  22
D93V12, multiclass
    clus
vv   DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE
  R0                           68                            315
  R1                            6                             45
  R2                            1                              3
  RX                            8                             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V13, continuous
D93V14, binary
                                cls
clus                               0   1
  DEL PEAK 39(22Q13.2) MUTATED    45  42
  DEL PEAK 39(22Q13.2) WILD-TYPE 180 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(22Q13.2) MUTATED     45   42
  DEL PEAK 39(22Q13.2) WILD-TYPE  180  222
            clus
vv           DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE
  MULTIFOCAL                           45                            180
  UNIFOCAL                             42                            222
[1] 2 2
[1] FALSE
D93V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 39(22Q13.2) MUTATED                                  0    11
  DEL PEAK 39(22Q13.2) WILD-TYPE                                1    41
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 39(22Q13.2) MUTATED                           7    54
  DEL PEAK 39(22Q13.2) WILD-TYPE                        20   274
D93V16, multiclass
                                  clus
vv                                 DEL PEAK 39(22Q13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      11
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      54
                                  clus
vv                                 DEL PEAK 39(22Q13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        41
  BLACK OR AFRICAN AMERICAN                                    20
  WHITE                                                       274
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V17, binary
                                cls
clus                               0   1
  DEL PEAK 39(22Q13.2) MUTATED     6  63
  DEL PEAK 39(22Q13.2) WILD-TYPE  32 296
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(22Q13.2) MUTATED      6   63
  DEL PEAK 39(22Q13.2) WILD-TYPE   32  296
                        clus
vv                       DEL PEAK 39(22Q13.2) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           63
                        clus
vv                       DEL PEAK 39(22Q13.2) WILD-TYPE
  HISPANIC OR LATINO                                 32
  NOT HISPANIC OR LATINO                            296
[1] 2 2
[1] FALSE

Clustering(94) Variable = DEL PEAK 40(22Q13.32) MUTATION ANALYSIS
D94V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 40(22Q13.32) MUTATED    89   1
  DEL PEAK 40(22Q13.32) WILD-TYPE 392  15
  DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE 
                             90                             407 
  DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE 
                              1                              15 
$`DEL PEAK 40(22Q13.32) MUTATED`
TCGA-4C-A93U TCGA-BJ-A0Z2 TCGA-BJ-A0Z5 TCGA-BJ-A0ZH TCGA-BJ-A18Y TCGA-BJ-A190 
        4.24        49.78        14.73        15.12        51.39        20.58 
TCGA-BJ-A2P4 TCGA-BJ-A3PT TCGA-BJ-A45D TCGA-BJ-A45F TCGA-CE-A484 TCGA-DE-A0XZ 
        7.04        23.31        10.88         3.45        12.43        35.84 
TCGA-DE-A4M8 TCGA-DJ-A13M TCGA-DJ-A13T TCGA-DJ-A1QG TCGA-DJ-A1QN TCGA-DJ-A2PS 
       18.54        48.79        56.19        44.98        42.58        26.20 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q7 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A3UK TCGA-DJ-A3UN 
       34.36        35.11        33.53        35.18        36.92        32.42 
TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3VK TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-E3-A3DZ 
       31.46        16.41        24.76        27.62        34.78        47.21 
TCGA-E3-A3E5 TCGA-E8-A432 TCGA-E8-A434 TCGA-EL-A3CL TCGA-EL-A3D0 TCGA-EL-A3D1 
       39.95        30.61         0.23        31.66       139.86        98.53 
TCGA-EL-A3D4 TCGA-EL-A3GP TCGA-EL-A3GW TCGA-EL-A3T2 TCGA-EL-A3ZL TCGA-EL-A3ZR 
       69.57        49.51        50.20        32.48        62.30        60.16 
TCGA-EL-A4JV TCGA-EL-A4JZ TCGA-EL-A4K6 TCGA-EL-A4K9 TCGA-EL-A4KI TCGA-EM-A1CS 
       57.47        37.94        44.15        47.84        23.90        26.86 
TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22P TCGA-EM-A2CJ TCGA-EM-A2OY 
       15.75        10.45        14.53        41.29        47.57        32.32 
TCGA-EM-A3AP TCGA-EM-A3FO TCGA-EM-A3O9 TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FO 
        8.35        17.49         9.24        29.85        12.79        26.37 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-ET-A25L TCGA-ET-A25O TCGA-ET-A2N4 TCGA-ET-A39L 
       21.53        60.49        56.58        65.29         2.66       108.46 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A3BP TCGA-ET-A3DS TCGA-ET-A40P TCGA-ET-A40T 
       84.89       123.32        79.10        66.84        43.99        37.48 
TCGA-FE-A237 TCGA-FE-A3PB TCGA-FY-A3R7 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A4B4 
      112.80        85.15        16.27         0.76        17.06        21.60 
TCGA-GE-A2C6 TCGA-H2-A3RH TCGA-IM-A3U3 TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3YD 
       12.53        12.46        16.90        31.10        43.17        31.82 
TCGA-J8-A3YH TCGA-KS-A41I TCGA-KS-A4I7 TCGA-KS-A4IB TCGA-MK-A84Z TCGA-QD-A8IV 
        5.75        15.98        32.45        84.72        23.93        12.89 

$`DEL PEAK 40(22Q13.32) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB 
       24.79        13.78        16.34        41.33        18.87         4.01 
TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZJ TCGA-BJ-A18Z TCGA-BJ-A191 
       11.57        16.73        25.48        42.08        41.52         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
       44.35        42.15        21.04        35.54        32.45        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       30.97        11.08        30.21        22.88        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PU 
       20.48        18.97        16.01        13.94        36.39        18.64 
TCGA-BJ-A45C TCGA-BJ-A45E TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J 
        7.99        21.01        23.84        28.44        15.45        21.63 
TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD 
       23.18        19.43        23.47        12.66        12.30        12.79 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A485 TCGA-DE-A0Y2 
       12.46        11.38        10.68        15.02        12.66        21.63 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       50.17        37.64        15.85        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L 
       30.02        25.12        14.70        14.27         2.76         9.96 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13U TCGA-DJ-A13V 
       38.17       169.32        18.58         8.71        23.38        43.17 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QH 
       52.37         8.32        11.01       135.91        30.61        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       14.96        17.59         6.02        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.82        30.58        35.41        27.45        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
       31.99        34.85        28.96         8.78         8.42        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 
        6.77        40.24        33.93        37.48        36.46        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QC TCGA-DJ-A3UM TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       35.90        15.88        31.04        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        17.69        59.57        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        42.54        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A4UL 
        7.76        35.67         3.12        36.43        17.23        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       21.34        33.04        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA 
       66.38        80.52        63.19        52.44        31.23        35.67 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       31.27        29.98        31.50        31.04         0.72         0.26 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
        3.02        25.45         0.16        14.96         7.69        33.50 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
        0.39         0.39        26.73       155.54        97.74       158.83 
TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
        7.66        45.53        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      106.62         4.18        79.50        57.11       108.36        64.87 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GX 
       50.24       115.10        65.39       136.01        50.37       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       83.57       139.00       150.48       108.66        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T3 
       52.50        29.65       147.42       142.52       129.57       132.07 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
       98.24        41.29       107.47         5.72        66.90        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO 
       89.56        78.97        51.78        36.03        53.06        47.38 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JW TCGA-EL-A4JX 
       65.49        61.22         7.07        59.44        34.72        45.96 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K7 TCGA-EL-A4KD 
       31.04        34.39        30.51        53.36        41.13        43.59 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       24.30        27.06        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I 
       19.79        19.46        78.61        57.01        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22Q TCGA-EM-A2CK TCGA-EM-A2CL 
       14.50        10.65        44.19        14.24        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         6.05         2.99        12.30        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        40.34        19.73        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       33.07        13.38        29.72        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       47.38        21.01        12.07        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB 
       14.50        15.06         7.33         0.49        13.91        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SY TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       38.86        29.95        13.51        84.59        29.33        21.34 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        5.33        26.37        22.45        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25P 
       81.70        77.56        70.42        60.20        63.39        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       63.45        88.41        58.75        37.25        52.60        54.35 
TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39O 
       83.34        80.88        33.24       106.09       107.41       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       95.34        94.13        55.10        98.20        28.24        50.40 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
       76.64         5.79        87.62        77.82        75.42        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT 
       52.47       116.78        94.59        84.85        80.58        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
       62.83       166.62        24.72        46.26        44.38        40.21 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       33.17        31.40        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A238 TCGA-FE-A239 
       24.69        68.22       117.40        66.77        39.95        33.63 
TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
       81.83       106.36        85.68        78.77        71.08         4.11 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        1.05        13.28         0.92        48.10       116.09         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
       20.42        17.82         7.82         0.99        19.56        13.91 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3YR TCGA-FY-A40K 
       15.68        16.57        18.08         0.30        17.36        15.16 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A76V TCGA-H2-A26U 
        6.58        22.49        19.04         1.35         1.68        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
       21.67         2.99        20.05        18.61        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A41Y TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O1 
       18.51        21.83         8.22        25.64        17.23        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A42S TCGA-J8-A4HW 
       11.24        27.85        24.69        22.29         2.47         2.60 
TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
        0.20       143.57        15.68       113.85        26.70        43.69 
TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       18.64        87.39        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       21.83         9.50        36.10        32.45        30.21 

  DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE 
                           0.23                            0.16 
  DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE 
                         139.86                          169.32 
  DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE 
                          32.37                           30.12 
[1] "0.2 - 139.9 (32.4)" "0.2 - 169.3 (30.1)"
[1] "hr=" "3.2"
D94V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 40(22Q13.32) MUTATED        50       10        18        1        10
  DEL PEAK 40(22Q13.32) WILD-TYPE     232       40        93        1        36
                                 vv
clus                              STAGE IVC
  DEL PEAK 40(22Q13.32) MUTATED           1
  DEL PEAK 40(22Q13.32) WILD-TYPE         5
D94V3, multiclass
           clus
vv          DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE
  STAGE I                              50                             232
  STAGE II                             10                              40
  STAGE III                            18                              93
  STAGE IV                              1                               1
  STAGE IVA                            10                              36
  STAGE IVC                             1                               5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 40(22Q13.32) MUTATED    25  33  28   4
  DEL PEAK 40(22Q13.32) WILD-TYPE 117 132 139  19
D94V4, multiclass
    clus
vv   DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE
  T1                            25                             117
  T2                            33                             132
  T3                            28                             139
  T4                             4                              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"
D94V5, binary
                                 cls
clus                                0   1
  DEL PEAK 40(22Q13.32) MUTATED    46  36
  DEL PEAK 40(22Q13.32) WILD-TYPE 179 188
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(22Q13.32) MUTATED     46   36
  DEL PEAK 40(22Q13.32) WILD-TYPE  179  188
   clus
vv  DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE
  0                            46                             179
  1                            36                             188
[1] 2 2
[1] FALSE
D94V6, binary
                                 cls
clus                                0   1
  DEL PEAK 40(22Q13.32) MUTATED    46   2
  DEL PEAK 40(22Q13.32) WILD-TYPE 232   7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(22Q13.32) MUTATED     46    2
  DEL PEAK 40(22Q13.32) WILD-TYPE  232    7
   clus
vv  DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE
  0                            46                             232
  1                             2                               7
[1] 2 2
[1] FALSE
D94V7, binary
                                 cls
clus                                0   1
  DEL PEAK 40(22Q13.32) MUTATED    63  27
  DEL PEAK 40(22Q13.32) WILD-TYPE 302 107
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(22Q13.32) MUTATED     63   27
  DEL PEAK 40(22Q13.32) WILD-TYPE  302  107
        clus
vv       DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE
  FEMALE                            63                             302
  MALE                              27                             107
[1] 2 2
[1] FALSE
D94V8, binary
                                 cls
clus                                0   1
  DEL PEAK 40(22Q13.32) MUTATED    26  60
  DEL PEAK 40(22Q13.32) WILD-TYPE 159 230
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(22Q13.32) MUTATED     26   60
  DEL PEAK 40(22Q13.32) WILD-TYPE  159  230
     clus
vv    DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE
  NO                             26                             159
  YES                            60                             230
[1] 2 2
[1] FALSE
                                 vv
clus                              OTHER  SPECIFY
  DEL PEAK 40(22Q13.32) MUTATED                1
  DEL PEAK 40(22Q13.32) WILD-TYPE              7
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 40(22Q13.32) MUTATED                                              61
  DEL PEAK 40(22Q13.32) WILD-TYPE                                           294
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 40(22Q13.32) MUTATED                                                                       25
  DEL PEAK 40(22Q13.32) WILD-TYPE                                                                     75
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 40(22Q13.32) MUTATED                                                                     3
  DEL PEAK 40(22Q13.32) WILD-TYPE                                                                  33
D94V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 40(22Q13.32) MUTATED
  OTHER  SPECIFY                                                                                     1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     61
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            25
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                3
                                                                        clus
vv                                                                       DEL PEAK 40(22Q13.32) WILD-TYPE
  OTHER  SPECIFY                                                                                       7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      294
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                              75
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                 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"
D94V10, binary
                                 cls
clus                                0   1
  DEL PEAK 40(22Q13.32) MUTATED    80   1
  DEL PEAK 40(22Q13.32) WILD-TYPE 340  16
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(22Q13.32) MUTATED     80    1
  DEL PEAK 40(22Q13.32) WILD-TYPE  340   16
     clus
vv    DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE
  NO                             80                             340
  YES                             1                              16
[1] 2 2
[1] FALSE
                                 vv
clus                              MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 40(22Q13.32) MUTATED             19                       2   64
  DEL PEAK 40(22Q13.32) WILD-TYPE          113                      16  266
                                 vv
clus                              VERY ADVANCED (T4B)
  DEL PEAK 40(22Q13.32) MUTATED                     0
  DEL PEAK 40(22Q13.32) WILD-TYPE                   1
D94V11, multiclass
                         clus
vv                        DEL PEAK 40(22Q13.32) MUTATED
  MINIMAL (T3)                                       19
  MODERATE/ADVANCED (T4A)                             2
  NONE                                               64
  VERY ADVANCED (T4B)                                 0
                         clus
vv                        DEL PEAK 40(22Q13.32) WILD-TYPE
  MINIMAL (T3)                                        113
  MODERATE/ADVANCED (T4A)                              16
  NONE                                                266
  VERY ADVANCED (T4B)                                   1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 40(22Q13.32) MUTATED    68   6   1   8
  DEL PEAK 40(22Q13.32) WILD-TYPE 315  45   3  22
D94V12, multiclass
    clus
vv   DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE
  R0                            68                             315
  R1                             6                              45
  R2                             1                               3
  RX                             8                              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V13, continuous
D94V14, binary
                                 cls
clus                                0   1
  DEL PEAK 40(22Q13.32) MUTATED    46  42
  DEL PEAK 40(22Q13.32) WILD-TYPE 179 222
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(22Q13.32) MUTATED     46   42
  DEL PEAK 40(22Q13.32) WILD-TYPE  179  222
            clus
vv           DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE
  MULTIFOCAL                            46                             179
  UNIFOCAL                              42                             222
[1] 2 2
[1] FALSE
D94V15, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 40(22Q13.32) MUTATED                                  0    11
  DEL PEAK 40(22Q13.32) WILD-TYPE                                1    41
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 40(22Q13.32) MUTATED                           7    55
  DEL PEAK 40(22Q13.32) WILD-TYPE                        20   273
D94V16, multiclass
                                  clus
vv                                 DEL PEAK 40(22Q13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       11
  BLACK OR AFRICAN AMERICAN                                    7
  WHITE                                                       55
                                  clus
vv                                 DEL PEAK 40(22Q13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         41
  BLACK OR AFRICAN AMERICAN                                     20
  WHITE                                                        273
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V17, binary
                                 cls
clus                                0   1
  DEL PEAK 40(22Q13.32) MUTATED     6  64
  DEL PEAK 40(22Q13.32) WILD-TYPE  32 295
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(22Q13.32) MUTATED      6   64
  DEL PEAK 40(22Q13.32) WILD-TYPE   32  295
                        clus
vv                       DEL PEAK 40(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            64
                        clus
vv                       DEL PEAK 40(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                  32
  NOT HISPANIC OR LATINO                             295
[1] 2 2
[1] FALSE

Clustering(95) Variable = DEL PEAK 41(XQ23) MUTATION ANALYSIS
D95V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 41(XQ23) MUTATED     4   0
  DEL PEAK 41(XQ23) WILD-TYPE 477  16
  DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE 
                          4                         493 
  DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE 
                          0                          16 
$`DEL PEAK 41(XQ23) MUTATED`
TCGA-BJ-A0Z0 TCGA-BJ-A190 TCGA-EM-A1YE TCGA-ET-A40S 
       13.78        20.58        54.08        40.21 

$`DEL PEAK 41(XQ23) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
        4.24        24.79        49.78        16.34        14.73        41.33 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73        25.48        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       42.08        51.39        41.52         4.83        44.35        42.15 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04        35.54        32.45        11.31        30.97        11.08 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       30.21        22.88        18.38        16.57        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        7.99        10.88        21.01         3.45        23.84        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
       15.45        21.63        23.18        19.43        23.47        12.66 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
       12.43        12.66        35.84        21.63        50.17        37.64 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M 
       25.12        14.70        14.27         2.76         9.96        48.79 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       38.17       169.32        18.58         8.71        56.19        23.38 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       43.17        52.37         8.32        11.01       135.91        30.61 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       44.98        42.51        14.96        17.59         6.02        42.58 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
       47.41        17.56        10.09         7.82        30.58        35.41 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       27.45        26.20        38.83        33.96        31.99        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       28.96         8.78         8.42        34.36        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24        33.93        37.48        36.46        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        33.53        35.18        15.88        36.92        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       32.42        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        17.69        59.57        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        42.54        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL 
        7.76        35.67         3.12        36.43        24.76        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        21.34        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        52.44        39.95        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       47.84        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       78.61        57.01        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       14.53        10.65        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
       17.88        13.18        23.51         6.05         2.99        12.30 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       48.46        13.15        22.16        40.34        19.73        32.32 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       33.96        17.59        17.46        17.29        14.60        22.52 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.06         7.33         0.49         9.24        13.91        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.86        29.95        29.85        13.51        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
      107.41       108.46        84.89       123.32       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       94.13        55.10        98.20        28.24        50.40        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
       76.64         5.79        87.62        77.82        75.42        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
       52.47       116.78        94.59        84.85        80.58        66.84 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       43.73        62.83       166.62        24.72        43.99        46.26 
TCGA-ET-A40R TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       44.38        37.48        33.17        31.40        73.74        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
      112.80        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        13.28 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10       116.09         1.25        20.42        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        7.82         0.99        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08         0.30         0.76        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       15.16         6.58        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83        31.10         8.22        25.64        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        23.93 
TCGA-QD-A8IV 
       12.89 

  DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE 
                      13.78                        0.16 
  DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE 
                      54.08                      169.32 
  DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE 
                     30.395                      30.610 
[1] "13.8 - 54.1 (30.4)" "0.2 - 169.3 (30.6)"
[1] "hr="     "3300000"
D95V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 41(XQ23) MUTATED         0        4         0        0         0
  DEL PEAK 41(XQ23) WILD-TYPE     282       46       111        2        46
                             vv
clus                          STAGE IVC
  DEL PEAK 41(XQ23) MUTATED           0
  DEL PEAK 41(XQ23) WILD-TYPE         6
D95V3, multiclass
           clus
vv          DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE
  STAGE I                           0                         282
  STAGE II                          4                          46
  STAGE III                         0                         111
  STAGE IV                          0                           2
  STAGE IVA                         0                          46
  STAGE IVC                         0                           6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK 41(XQ23) MUTATED     0   4   0   0
  DEL PEAK 41(XQ23) WILD-TYPE 142 161 167  23
D95V4, multiclass
    clus
vv   DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE
  T1                         0                         142
  T2                         4                         161
  T3                         0                         167
  T4                         0                          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"
D95V5, binary
                             cls
clus                            0   1
  DEL PEAK 41(XQ23) MUTATED     4   0
  DEL PEAK 41(XQ23) WILD-TYPE 221 224
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 41(XQ23) MUTATED      4    0
  DEL PEAK 41(XQ23) WILD-TYPE  221  224
   clus
vv  DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE
  0                         4                         221
  1                         0                         224
[1] 2 2
[1] FALSE
D95V6, binary
                             cls
clus                            0   1
  DEL PEAK 41(XQ23) MUTATED     0   0
  DEL PEAK 41(XQ23) WILD-TYPE 278   9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 41(XQ23) MUTATED      0    0
  DEL PEAK 41(XQ23) WILD-TYPE  278    9
D95V7, binary
                             cls
clus                            0   1
  DEL PEAK 41(XQ23) MUTATED     1   3
  DEL PEAK 41(XQ23) WILD-TYPE 364 131
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 41(XQ23) MUTATED      1    3
  DEL PEAK 41(XQ23) WILD-TYPE  364  131
        clus
vv       DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE
  FEMALE                         1                         364
  MALE                           3                         131
[1] 2 2
[1] FALSE
D95V8, binary
                             cls
clus                            0   1
  DEL PEAK 41(XQ23) MUTATED     0   4
  DEL PEAK 41(XQ23) WILD-TYPE 185 286
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 41(XQ23) MUTATED      0    4
  DEL PEAK 41(XQ23) WILD-TYPE  185  286
     clus
vv    DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE
  NO                          0                         185
  YES                         4                         286
[1] 2 2
[1] FALSE
                             vv
clus                          OTHER  SPECIFY
  DEL PEAK 41(XQ23) MUTATED                0
  DEL PEAK 41(XQ23) WILD-TYPE              8
                             vv
clus                          THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 41(XQ23) MUTATED                                               3
  DEL PEAK 41(XQ23) WILD-TYPE                                           352
                             vv
clus                          THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 41(XQ23) MUTATED                                                                        1
  DEL PEAK 41(XQ23) WILD-TYPE                                                                     99
                             vv
clus                          THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 41(XQ23) MUTATED                                                                     0
  DEL PEAK 41(XQ23) WILD-TYPE                                                                  36
D95V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 41(XQ23) MUTATED
  OTHER  SPECIFY                                                                                 0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                         1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                            0
                                                                        clus
vv                                                                       DEL PEAK 41(XQ23) WILD-TYPE
  OTHER  SPECIFY                                                                                   8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          99
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                             36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V10, binary
                             cls
clus                            0   1
  DEL PEAK 41(XQ23) MUTATED     2   1
  DEL PEAK 41(XQ23) WILD-TYPE 418  16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 41(XQ23) MUTATED      2    1
  DEL PEAK 41(XQ23) WILD-TYPE  418   16
     clus
vv    DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE
  NO                          2                         418
  YES                         1                          16
[1] 2 2
[1] FALSE
                             vv
clus                          MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 41(XQ23) MUTATED              0                       0    4
  DEL PEAK 41(XQ23) WILD-TYPE          132                      18  326
                             vv
clus                          VERY ADVANCED (T4B)
  DEL PEAK 41(XQ23) MUTATED                     0
  DEL PEAK 41(XQ23) WILD-TYPE                   1
D95V11, multiclass
                         clus
vv                        DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE
  MINIMAL (T3)                                    0                         132
  MODERATE/ADVANCED (T4A)                         0                          18
  NONE                                            4                         326
  VERY ADVANCED (T4B)                             0                           1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 41(XQ23) MUTATED     3   0   0   1
  DEL PEAK 41(XQ23) WILD-TYPE 380  51   4  29
D95V12, multiclass
    clus
vv   DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE
  R0                         3                         380
  R1                         0                          51
  R2                         0                           4
  RX                         1                          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"
D95V13, continuous
D95V14, binary
                             cls
clus                            0   1
  DEL PEAK 41(XQ23) MUTATED     2   2
  DEL PEAK 41(XQ23) WILD-TYPE 223 262
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 41(XQ23) MUTATED      2    2
  DEL PEAK 41(XQ23) WILD-TYPE  223  262
            clus
vv           DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE
  MULTIFOCAL                         2                         223
  UNIFOCAL                           2                         262
[1] 2 2
[1] FALSE
D95V15, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 41(XQ23) MUTATED                                  0     0
  DEL PEAK 41(XQ23) WILD-TYPE                                1    52
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 41(XQ23) MUTATED                           0     2
  DEL PEAK 41(XQ23) WILD-TYPE                        27   326
D95V16, multiclass
[1] "Remove cluster labels:"    "DEL PEAK 41(XQ23) MUTATED"
clus
  DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE 
                          2                         406 
                 TCGA-4C-A93U                  TCGA-BJ-A0YZ 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A0Z2                  TCGA-BJ-A0Z3 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A0Z5                  TCGA-BJ-A0Z9 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A0ZA                  TCGA-BJ-A0ZB 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A0ZC                  TCGA-BJ-A0ZE 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A0ZG                  TCGA-BJ-A0ZH 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A0ZJ                  TCGA-BJ-A18Y 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A18Z                  TCGA-BJ-A191 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A192                  TCGA-BJ-A28R 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A28S                  TCGA-BJ-A28T 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A28V                  TCGA-BJ-A28W 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A28X                  TCGA-BJ-A28Z 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A290                  TCGA-BJ-A291 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A2N7                  TCGA-BJ-A2N8 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A2N9                  TCGA-BJ-A2NA 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A2P4                  TCGA-BJ-A3EZ 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A3F0                  TCGA-BJ-A3PR 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A3PT                  TCGA-BJ-A3PU 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A45C                  TCGA-BJ-A45D 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A45E                  TCGA-BJ-A45F 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A45G                  TCGA-BJ-A45H 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A45I                  TCGA-BJ-A45J 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A45K                  TCGA-BJ-A4O8 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A4O9                  TCGA-CE-A13K 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-CE-A27D                  TCGA-CE-A3MD 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-CE-A3ME                  TCGA-CE-A481 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-CE-A482                  TCGA-CE-A483 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-CE-A484                  TCGA-CE-A485 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DE-A0XZ                  TCGA-DE-A0Y2 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DE-A0Y3                  TCGA-DE-A2OL 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DE-A3KN                  TCGA-DE-A4M8 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DE-A4M9                  TCGA-DE-A4MA 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DE-A4MB                  TCGA-DE-A4MC 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DE-A4MD                  TCGA-DE-A69J 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DE-A69K                  TCGA-DE-A7U5 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A13L                  TCGA-DJ-A13M 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A13O                  TCGA-DJ-A13P 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A13R                  TCGA-DJ-A13S 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A13T                  TCGA-DJ-A13U 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A13W                  TCGA-DJ-A1QD 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A1QE                  TCGA-DJ-A1QF 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A1QG                  TCGA-DJ-A1QH 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A1QI                  TCGA-DJ-A1QM 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A1QO                  TCGA-DJ-A1QQ 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A2PN                  TCGA-DJ-A2PO 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A2PQ                  TCGA-DJ-A2PR 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A2PS                  TCGA-DJ-A2PT 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A2PU                  TCGA-DJ-A2PV 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A2PW                  TCGA-DJ-A2PX 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A2PY                  TCGA-DJ-A2PZ 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A2Q0                  TCGA-DJ-A2Q1 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A2Q2                  TCGA-DJ-A2Q3 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A2Q4                  TCGA-DJ-A2Q5 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A2Q6                  TCGA-DJ-A2Q7 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A2Q9                  TCGA-DJ-A2QA 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A2QB                  TCGA-DJ-A3UK 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A3UM                  TCGA-DJ-A3UN 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A3UO                  TCGA-DJ-A3UQ 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A3UR                  TCGA-DJ-A3US 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A3UT                  TCGA-DJ-A3UU 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A3UW                  TCGA-DJ-A3UX 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A3UY                  TCGA-DJ-A3UZ 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A3V2                  TCGA-DJ-A3V3 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A3V4                  TCGA-DJ-A3V5 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A3V7                  TCGA-DJ-A3V8 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A3V9                  TCGA-DJ-A3VD 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A3VE                  TCGA-DJ-A3VF 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A3VG                  TCGA-DJ-A3VI 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A3VJ                  TCGA-DJ-A3VK 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A3VL                  TCGA-DJ-A3VM 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A4UL                  TCGA-DJ-A4UP 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A4UQ                  TCGA-DJ-A4UR 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A4UT                  TCGA-DJ-A4UW 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A4V0                  TCGA-DJ-A4V4 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A4V5                  TCGA-DO-A1JZ 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DO-A1K0                  TCGA-DO-A2HM 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-E3-A3DY                  TCGA-E3-A3DZ 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-E3-A3E0                  TCGA-E3-A3E1 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-E3-A3E2                  TCGA-E3-A3E3 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-E3-A3E5                  TCGA-E8-A242 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-E8-A2EA                  TCGA-E8-A3X7 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-E8-A413                  TCGA-E8-A414 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-E8-A415                  TCGA-E8-A416 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-E8-A417                  TCGA-E8-A418 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-E8-A419                  TCGA-E8-A432 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-E8-A433                  TCGA-E8-A434 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-E8-A436                  TCGA-E8-A437 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-E8-A438                  TCGA-E8-A44K 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-E8-A44M                  TCGA-EL-A3CL 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3CM                  TCGA-EL-A3CN 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3CO                  TCGA-EL-A3CP 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3CR                  TCGA-EL-A3CS 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3CT                  TCGA-EL-A3CU 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3CV                  TCGA-EL-A3CW 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3CX                  TCGA-EL-A3CY 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3CZ                  TCGA-EL-A3D0 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3D1                  TCGA-EL-A3D4 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3D5                  TCGA-EL-A3D6 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3GO                  TCGA-EL-A3GP 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3GQ                  TCGA-EL-A3GR 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3GS                  TCGA-EL-A3GU 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3GV                  TCGA-EL-A3GW 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3GX                  TCGA-EL-A3GY 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3GZ                  TCGA-EL-A3H1 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3H2                  TCGA-EL-A3H3 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3H4                  TCGA-EL-A3H5 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3H7                  TCGA-EL-A3H8 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3MW                  TCGA-EL-A3MX 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3MY                  TCGA-EL-A3MZ 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3N2                  TCGA-EL-A3N3 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3T0                  TCGA-EL-A3T1 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3T2                  TCGA-EL-A3T3 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3T6                  TCGA-EL-A3T7 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3T8                  TCGA-EL-A3T9 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3TA                  TCGA-EL-A3TB 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3ZG                  TCGA-EL-A3ZH 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3ZK                  TCGA-EL-A3ZL 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3ZN                  TCGA-EL-A3ZO 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3ZP                  TCGA-EL-A3ZQ 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3ZR                  TCGA-EL-A3ZS 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3ZT                  TCGA-EL-A4JV 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A4JW                  TCGA-EL-A4JX 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A4JZ                  TCGA-EL-A4K0 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A4K1                  TCGA-EL-A4K2 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A4K4                  TCGA-EL-A4K6 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A4K7                  TCGA-EL-A4K9 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A4KD                  TCGA-EL-A4KG 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A4KH                  TCGA-EL-A4KI 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EM-A22M                  TCGA-EM-A22O 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EM-A2OV                  TCGA-EM-A3AI 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A25G                  TCGA-ET-A25I 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A25J                  TCGA-ET-A25K 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A25L                  TCGA-ET-A25M 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A25N                  TCGA-ET-A25O 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A25P                  TCGA-ET-A25R 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A2MX                  TCGA-ET-A2MY 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A2MZ                  TCGA-ET-A2N0 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A2N1                  TCGA-ET-A2N3 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A2N4                  TCGA-ET-A2N5 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A39I                  TCGA-ET-A39J 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A39K                  TCGA-ET-A39M 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A39N                  TCGA-ET-A39O 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A39P                  TCGA-ET-A39R 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A39S                  TCGA-ET-A39T 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A3BN                  TCGA-ET-A3BO 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A3BP                  TCGA-ET-A3BQ 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A3BS                  TCGA-ET-A3BT 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A3BU                  TCGA-ET-A3BV 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A3BW                  TCGA-ET-A3BX 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A3DO                  TCGA-ET-A3DP 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A3DQ                  TCGA-ET-A3DR 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A3DS                  TCGA-ET-A3DT 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A3DU                  TCGA-ET-A3DV 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A3DW                  TCGA-ET-A40P 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A40Q                  TCGA-ET-A40R 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A40T                  TCGA-ET-A4KN 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A4KQ                  TCGA-FE-A22Z 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FE-A230                  TCGA-FE-A231 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FE-A232                  TCGA-FE-A233 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FE-A234                  TCGA-FE-A235 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FE-A236                  TCGA-FE-A237 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FE-A238                  TCGA-FE-A239 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FE-A23A                  TCGA-FE-A3PA 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FE-A3PB                  TCGA-FE-A3PC 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FE-A3PD                  TCGA-FK-A3S3 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FK-A3SB                  TCGA-FK-A3SD 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FK-A3SE                  TCGA-FK-A3SG 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FK-A3SH                  TCGA-FK-A4UB 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FY-A2QD                  TCGA-FY-A3BL 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FY-A3I4                  TCGA-FY-A3I5 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FY-A3NM                  TCGA-FY-A3ON 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FY-A3R6                  TCGA-FY-A3R7 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FY-A3R8                  TCGA-FY-A3R9 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FY-A3RA                  TCGA-FY-A3W9 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FY-A3WA                  TCGA-FY-A3YR 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FY-A40K                  TCGA-FY-A40L 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FY-A40M                  TCGA-FY-A40N 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FY-A4B0                  TCGA-FY-A4B3 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FY-A4B4                  TCGA-FY-A76V 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-GE-A2C6                  TCGA-H2-A26U 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-H2-A2K9                  TCGA-H2-A3RH 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-H2-A3RI                  TCGA-H2-A421 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-H2-A422                  TCGA-IM-A3EB 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-IM-A3ED                  TCGA-IM-A3U2 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-IM-A3U3                  TCGA-IM-A41Y 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-IM-A41Z                  TCGA-IM-A420 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-IM-A4EB                  TCGA-J8-A3NZ 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-J8-A3O0                  TCGA-J8-A3O1 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-J8-A3O2                  TCGA-J8-A3YD 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-J8-A3YE                  TCGA-J8-A3YF 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-J8-A3YG                  TCGA-J8-A3YH 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-J8-A42S                  TCGA-J8-A4HW 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-J8-A4HY                  TCGA-KS-A41F 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-KS-A41I                  TCGA-KS-A41J 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-KS-A41L                  TCGA-KS-A4I1 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-KS-A4I3                  TCGA-KS-A4I5 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-KS-A4I7                  TCGA-KS-A4I9 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-KS-A4IB                  TCGA-KS-A4IC 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-KS-A4ID                  TCGA-L6-A4EP 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-L6-A4EQ                  TCGA-L6-A4ET 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-L6-A4EU                  TCGA-MK-A4N6 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-MK-A4N7                  TCGA-MK-A4N9 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-MK-A84Z                  TCGA-QD-A8IV 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
D95V17, binary
                             cls
clus                            0   1
  DEL PEAK 41(XQ23) MUTATED     0   3
  DEL PEAK 41(XQ23) WILD-TYPE  38 356
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 41(XQ23) MUTATED      0    3
  DEL PEAK 41(XQ23) WILD-TYPE   38  356
                        clus
vv                       DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE
  HISPANIC OR LATINO                             0                          38
  NOT HISPANIC OR LATINO                         3                         356
[1] 2 2
[1] FALSE

Clustering(96) Variable = DEL PEAK 42(XQ22.3) MUTATION ANALYSIS
D96V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 42(XQ22.3) MUTATED     4   0
  DEL PEAK 42(XQ22.3) WILD-TYPE 477  16
  DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE 
                            4                           493 
  DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE 
                            0                            16 
$`DEL PEAK 42(XQ22.3) MUTATED`
TCGA-BJ-A0Z0 TCGA-BJ-A190 TCGA-EM-A1YE TCGA-ET-A40S 
       13.78        20.58        54.08        40.21 

$`DEL PEAK 42(XQ22.3) WILD-TYPE`
TCGA-4C-A93U TCGA-BJ-A0YZ TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
        4.24        24.79        49.78        16.34        14.73        41.33 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
       18.87         4.01        11.57        16.73        25.48        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       42.08        51.39        41.52         4.83        44.35        42.15 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04        35.54        32.45        11.31        30.97        11.08 
TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       30.21        22.88        18.38        16.57        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
        7.04        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        7.99        10.88        21.01         3.45        23.84        28.44 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
       15.45        21.63        23.18        19.43        23.47        12.66 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
       12.43        12.66        35.84        21.63        50.17        37.64 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC 
       15.85        18.54        18.84        30.12        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13L TCGA-DJ-A13M 
       25.12        14.70        14.27         2.76         9.96        48.79 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       38.17       169.32        18.58         8.71        56.19        23.38 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       43.17        52.37         8.32        11.01       135.91        30.61 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       44.98        42.51        14.96        17.59         6.02        42.58 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
       47.41        17.56        10.09         7.82        30.58        35.41 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       27.45        26.20        38.83        33.96        31.99        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       28.96         8.78         8.42        34.36        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24        33.93        37.48        36.46        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        33.53        35.18        15.88        36.92        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       32.42        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        17.69        59.57        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       36.99        20.22        30.61        42.54        19.20        23.21 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        24.82        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VI TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL 
        7.76        35.67         3.12        36.43        24.76        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       27.62        30.87        21.34        33.04        34.78        27.06 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       26.93        35.54         3.12        15.81        35.38        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        52.44        39.95        31.23        35.67        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       29.98        31.50        31.04         0.72         0.26         3.02 
TCGA-E8-A419 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       25.45        30.61         0.16         0.23        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       33.50         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        78.97        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       36.03        53.06        47.38        65.49        61.22        60.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        34.39        30.51        53.36        44.15        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       47.84        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       78.61        57.01        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       14.53        10.65        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
       17.88        13.18        23.51         6.05         2.99        12.30 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       48.46        13.15        22.16        40.34        19.73        32.32 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       33.96        17.59        17.46        17.29        14.60        22.52 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        47.38        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.06         7.33         0.49         9.24        13.91        38.66 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       38.86        29.95        29.85        13.51        12.79        84.59 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       29.33        21.34         5.33        26.37        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       21.53        60.49        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       77.56        70.42        56.58        60.20        63.39        65.29 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        63.45        88.41        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       54.35        83.34         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
      107.41       108.46        84.89       123.32       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       94.13        55.10        98.20        28.24        50.40        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
       76.64         5.79        87.62        77.82        75.42        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
       52.47       116.78        94.59        84.85        80.58        66.84 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       43.73        62.83       166.62        24.72        43.99        46.26 
TCGA-ET-A40R TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
       44.38        37.48        33.17        31.40        73.74        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
      112.80        39.95        33.63        81.83       106.36        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        13.28 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10       116.09         1.25        20.42        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        7.82         0.99        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A3YR 
       16.57        18.08         0.30         0.76        17.06        17.36 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
       15.16         6.58        22.49        19.04         1.35        21.60 
TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.68        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
       20.05        18.61        48.92        47.41        18.51        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
       21.83        31.10         8.22        25.64        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       27.19        11.24        31.82        27.85        24.69        22.29 
TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I 
        5.75         2.47         2.60         0.20       143.57        15.98 
TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 
       15.68       113.85        26.70        43.69        18.64        32.45 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ 
       87.39        84.72        35.28        33.24        33.40        40.37 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       21.83         9.50        36.10        32.45        30.21        23.93 
TCGA-QD-A8IV 
       12.89 

  DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE 
                        13.78                          0.16 
  DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE 
                        54.08                        169.32 
  DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE 
                       30.395                        30.610 
[1] "13.8 - 54.1 (30.4)" "0.2 - 169.3 (30.6)"
[1] "hr="     "3300000"
D96V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 42(XQ22.3) MUTATED         0        4         0        0         0
  DEL PEAK 42(XQ22.3) WILD-TYPE     282       46       111        2        46
                               vv
clus                            STAGE IVC
  DEL PEAK 42(XQ22.3) MUTATED           0
  DEL PEAK 42(XQ22.3) WILD-TYPE         6
D96V3, multiclass
           clus
vv          DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE
  STAGE I                             0                           282
  STAGE II                            4                            46
  STAGE III                           0                           111
  STAGE IV                            0                             2
  STAGE IVA                           0                            46
  STAGE IVC                           0                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 42(XQ22.3) MUTATED     0   4   0   0
  DEL PEAK 42(XQ22.3) WILD-TYPE 142 161 167  23
D96V4, multiclass
    clus
vv   DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE
  T1                           0                           142
  T2                           4                           161
  T3                           0                           167
  T4                           0                            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"
D96V5, binary
                               cls
clus                              0   1
  DEL PEAK 42(XQ22.3) MUTATED     4   0
  DEL PEAK 42(XQ22.3) WILD-TYPE 221 224
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 42(XQ22.3) MUTATED      4    0
  DEL PEAK 42(XQ22.3) WILD-TYPE  221  224
   clus
vv  DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE
  0                           4                           221
  1                           0                           224
[1] 2 2
[1] FALSE
D96V6, binary
                               cls
clus                              0   1
  DEL PEAK 42(XQ22.3) MUTATED     0   0
  DEL PEAK 42(XQ22.3) WILD-TYPE 278   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 42(XQ22.3) MUTATED      0    0
  DEL PEAK 42(XQ22.3) WILD-TYPE  278    9
D96V7, binary
                               cls
clus                              0   1
  DEL PEAK 42(XQ22.3) MUTATED     1   3
  DEL PEAK 42(XQ22.3) WILD-TYPE 364 131
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 42(XQ22.3) MUTATED      1    3
  DEL PEAK 42(XQ22.3) WILD-TYPE  364  131
        clus
vv       DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE
  FEMALE                           1                           364
  MALE                             3                           131
[1] 2 2
[1] FALSE
D96V8, binary
                               cls
clus                              0   1
  DEL PEAK 42(XQ22.3) MUTATED     0   4
  DEL PEAK 42(XQ22.3) WILD-TYPE 185 286
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 42(XQ22.3) MUTATED      0    4
  DEL PEAK 42(XQ22.3) WILD-TYPE  185  286
     clus
vv    DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE
  NO                            0                           185
  YES                           4                           286
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  DEL PEAK 42(XQ22.3) MUTATED                0
  DEL PEAK 42(XQ22.3) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 42(XQ22.3) MUTATED                                               3
  DEL PEAK 42(XQ22.3) WILD-TYPE                                           352
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 42(XQ22.3) MUTATED                                                                        1
  DEL PEAK 42(XQ22.3) WILD-TYPE                                                                     99
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 42(XQ22.3) MUTATED                                                                     0
  DEL PEAK 42(XQ22.3) WILD-TYPE                                                                  36
D96V9, multiclass
                                                                        clus
vv                                                                       DEL PEAK 42(XQ22.3) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       DEL PEAK 42(XQ22.3) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            99
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V10, binary
                               cls
clus                              0   1
  DEL PEAK 42(XQ22.3) MUTATED     2   1
  DEL PEAK 42(XQ22.3) WILD-TYPE 418  16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 42(XQ22.3) MUTATED      2    1
  DEL PEAK 42(XQ22.3) WILD-TYPE  418   16
     clus
vv    DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE
  NO                            2                           418
  YES                           1                            16
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 42(XQ22.3) MUTATED              0                       0    4
  DEL PEAK 42(XQ22.3) WILD-TYPE          132                      18  326
                               vv
clus                            VERY ADVANCED (T4B)
  DEL PEAK 42(XQ22.3) MUTATED                     0
  DEL PEAK 42(XQ22.3) WILD-TYPE                   1
D96V11, multiclass
                         clus
vv                        DEL PEAK 42(XQ22.3) MUTATED
  MINIMAL (T3)                                      0
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              4
  VERY ADVANCED (T4B)                               0
                         clus
vv                        DEL PEAK 42(XQ22.3) WILD-TYPE
  MINIMAL (T3)                                      132
  MODERATE/ADVANCED (T4A)                            18
  NONE                                              326
  VERY ADVANCED (T4B)                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 42(XQ22.3) MUTATED     3   0   0   1
  DEL PEAK 42(XQ22.3) WILD-TYPE 380  51   4  29
D96V12, multiclass
    clus
vv   DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE
  R0                           3                           380
  R1                           0                            51
  R2                           0                             4
  RX                           1                            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"
D96V13, continuous
D96V14, binary
                               cls
clus                              0   1
  DEL PEAK 42(XQ22.3) MUTATED     2   2
  DEL PEAK 42(XQ22.3) WILD-TYPE 223 262
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 42(XQ22.3) MUTATED      2    2
  DEL PEAK 42(XQ22.3) WILD-TYPE  223  262
            clus
vv           DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE
  MULTIFOCAL                           2                           223
  UNIFOCAL                             2                           262
[1] 2 2
[1] FALSE
D96V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 42(XQ22.3) MUTATED                                  0     0
  DEL PEAK 42(XQ22.3) WILD-TYPE                                1    52
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 42(XQ22.3) MUTATED                           0     2
  DEL PEAK 42(XQ22.3) WILD-TYPE                        27   326
D96V16, multiclass
[1] "Remove cluster labels:"      "DEL PEAK 42(XQ22.3) MUTATED"
clus
  DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE 
                            2                           406 
                   TCGA-4C-A93U                    TCGA-BJ-A0YZ 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A0Z2                    TCGA-BJ-A0Z3 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A0Z5                    TCGA-BJ-A0Z9 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A0ZA                    TCGA-BJ-A0ZB 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A0ZC                    TCGA-BJ-A0ZE 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A0ZG                    TCGA-BJ-A0ZH 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A0ZJ                    TCGA-BJ-A18Y 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A18Z                    TCGA-BJ-A191 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A192                    TCGA-BJ-A28R 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A28S                    TCGA-BJ-A28T 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A28V                    TCGA-BJ-A28W 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A28X                    TCGA-BJ-A28Z 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A290                    TCGA-BJ-A291 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A2N7                    TCGA-BJ-A2N8 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A2N9                    TCGA-BJ-A2NA 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A2P4                    TCGA-BJ-A3EZ 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A3F0                    TCGA-BJ-A3PR 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A3PT                    TCGA-BJ-A3PU 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A45C                    TCGA-BJ-A45D 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A45E                    TCGA-BJ-A45F 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A45G                    TCGA-BJ-A45H 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A45I                    TCGA-BJ-A45J 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A45K                    TCGA-BJ-A4O8 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A4O9                    TCGA-CE-A13K 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-CE-A27D                    TCGA-CE-A3MD 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-CE-A3ME                    TCGA-CE-A481 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-CE-A482                    TCGA-CE-A483 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-CE-A484                    TCGA-CE-A485 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DE-A0XZ                    TCGA-DE-A0Y2 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DE-A0Y3                    TCGA-DE-A2OL 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DE-A3KN                    TCGA-DE-A4M8 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DE-A4M9                    TCGA-DE-A4MA 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DE-A4MB                    TCGA-DE-A4MC 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DE-A4MD                    TCGA-DE-A69J 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DE-A69K                    TCGA-DE-A7U5 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A13L                    TCGA-DJ-A13M 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A13O                    TCGA-DJ-A13P 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A13R                    TCGA-DJ-A13S 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A13T                    TCGA-DJ-A13U 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A13W                    TCGA-DJ-A1QD 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A1QE                    TCGA-DJ-A1QF 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A1QG                    TCGA-DJ-A1QH 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A1QI                    TCGA-DJ-A1QM 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A1QO                    TCGA-DJ-A1QQ 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A2PN                    TCGA-DJ-A2PO 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A2PQ                    TCGA-DJ-A2PR 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A2PS                    TCGA-DJ-A2PT 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A2PU                    TCGA-DJ-A2PV 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A2PW                    TCGA-DJ-A2PX 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A2PY                    TCGA-DJ-A2PZ 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q0                    TCGA-DJ-A2Q1 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q2                    TCGA-DJ-A2Q3 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q4                    TCGA-DJ-A2Q5 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q6                    TCGA-DJ-A2Q7 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q9                    TCGA-DJ-A2QA 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A2QB                    TCGA-DJ-A3UK 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A3UM                    TCGA-DJ-A3UN 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A3UO                    TCGA-DJ-A3UQ 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A3UR                    TCGA-DJ-A3US 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A3UT                    TCGA-DJ-A3UU 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A3UW                    TCGA-DJ-A3UX 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A3UY                    TCGA-DJ-A3UZ 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A3V2                    TCGA-DJ-A3V3 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A3V4                    TCGA-DJ-A3V5 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A3V7                    TCGA-DJ-A3V8 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A3V9                    TCGA-DJ-A3VD 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A3VE                    TCGA-DJ-A3VF 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A3VG                    TCGA-DJ-A3VI 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A3VJ                    TCGA-DJ-A3VK 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A3VL                    TCGA-DJ-A3VM 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A4UL                    TCGA-DJ-A4UP 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A4UQ                    TCGA-DJ-A4UR 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A4UT                    TCGA-DJ-A4UW 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A4V0                    TCGA-DJ-A4V4 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A4V5                    TCGA-DO-A1JZ 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DO-A1K0                    TCGA-DO-A2HM 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-E3-A3DY                    TCGA-E3-A3DZ 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-E3-A3E0                    TCGA-E3-A3E1 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-E3-A3E2                    TCGA-E3-A3E3 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-E3-A3E5                    TCGA-E8-A242 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-E8-A2EA                    TCGA-E8-A3X7 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-E8-A413                    TCGA-E8-A414 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-E8-A415                    TCGA-E8-A416 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-E8-A417                    TCGA-E8-A418 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-E8-A419                    TCGA-E8-A432 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-E8-A433                    TCGA-E8-A434 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-E8-A436                    TCGA-E8-A437 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-E8-A438                    TCGA-E8-A44K 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-E8-A44M                    TCGA-EL-A3CL 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3CM                    TCGA-EL-A3CN 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3CO                    TCGA-EL-A3CP 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3CR                    TCGA-EL-A3CS 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3CT                    TCGA-EL-A3CU 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3CV                    TCGA-EL-A3CW 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3CX                    TCGA-EL-A3CY 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3CZ                    TCGA-EL-A3D0 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3D1                    TCGA-EL-A3D4 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3D5                    TCGA-EL-A3D6 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3GO                    TCGA-EL-A3GP 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3GQ                    TCGA-EL-A3GR 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3GS                    TCGA-EL-A3GU 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3GV                    TCGA-EL-A3GW 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3GX                    TCGA-EL-A3GY 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3GZ                    TCGA-EL-A3H1 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3H2                    TCGA-EL-A3H3 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3H4                    TCGA-EL-A3H5 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3H7                    TCGA-EL-A3H8 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3MW                    TCGA-EL-A3MX 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3MY                    TCGA-EL-A3MZ 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3N2                    TCGA-EL-A3N3 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3T0                    TCGA-EL-A3T1 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3T2                    TCGA-EL-A3T3 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3T6                    TCGA-EL-A3T7 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3T8                    TCGA-EL-A3T9 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3TA                    TCGA-EL-A3TB 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3ZG                    TCGA-EL-A3ZH 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3ZK                    TCGA-EL-A3ZL 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3ZN                    TCGA-EL-A3ZO 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3ZP                    TCGA-EL-A3ZQ 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3ZR                    TCGA-EL-A3ZS 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3ZT                    TCGA-EL-A4JV 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A4JW                    TCGA-EL-A4JX 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A4JZ                    TCGA-EL-A4K0 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A4K1                    TCGA-EL-A4K2 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A4K4                    TCGA-EL-A4K6 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A4K7                    TCGA-EL-A4K9 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A4KD                    TCGA-EL-A4KG 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A4KH                    TCGA-EL-A4KI 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EM-A22M                    TCGA-EM-A22O 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EM-A2OV                    TCGA-EM-A3AI 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A25G                    TCGA-ET-A25I 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A25J                    TCGA-ET-A25K 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A25L                    TCGA-ET-A25M 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A25N                    TCGA-ET-A25O 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A25P                    TCGA-ET-A25R 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A2MX                    TCGA-ET-A2MY 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A2MZ                    TCGA-ET-A2N0 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A2N1                    TCGA-ET-A2N3 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A2N4                    TCGA-ET-A2N5 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A39I                    TCGA-ET-A39J 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A39K                    TCGA-ET-A39M 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A39N                    TCGA-ET-A39O 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A39P                    TCGA-ET-A39R 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A39S                    TCGA-ET-A39T 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A3BN                    TCGA-ET-A3BO 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A3BP                    TCGA-ET-A3BQ 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A3BS                    TCGA-ET-A3BT 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A3BU                    TCGA-ET-A3BV 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A3BW                    TCGA-ET-A3BX 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A3DO                    TCGA-ET-A3DP 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A3DQ                    TCGA-ET-A3DR 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A3DS                    TCGA-ET-A3DT 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A3DU                    TCGA-ET-A3DV 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A3DW                    TCGA-ET-A40P 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A40Q                    TCGA-ET-A40R 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A40T                    TCGA-ET-A4KN 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A4KQ                    TCGA-FE-A22Z 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FE-A230                    TCGA-FE-A231 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FE-A232                    TCGA-FE-A233 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FE-A234                    TCGA-FE-A235 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FE-A236                    TCGA-FE-A237 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FE-A238                    TCGA-FE-A239 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FE-A23A                    TCGA-FE-A3PA 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FE-A3PB                    TCGA-FE-A3PC 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FE-A3PD                    TCGA-FK-A3S3 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FK-A3SB                    TCGA-FK-A3SD 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FK-A3SE                    TCGA-FK-A3SG 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FK-A3SH                    TCGA-FK-A4UB 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FY-A2QD                    TCGA-FY-A3BL 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FY-A3I4                    TCGA-FY-A3I5 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FY-A3NM                    TCGA-FY-A3ON 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FY-A3R6                    TCGA-FY-A3R7 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FY-A3R8                    TCGA-FY-A3R9 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FY-A3RA                    TCGA-FY-A3W9 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FY-A3WA                    TCGA-FY-A3YR 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FY-A40K                    TCGA-FY-A40L 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FY-A40M                    TCGA-FY-A40N 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FY-A4B0                    TCGA-FY-A4B3 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FY-A4B4                    TCGA-FY-A76V 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-GE-A2C6                    TCGA-H2-A26U 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-H2-A2K9                    TCGA-H2-A3RH 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-H2-A3RI                    TCGA-H2-A421 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-H2-A422                    TCGA-IM-A3EB 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-IM-A3ED                    TCGA-IM-A3U2 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-IM-A3U3                    TCGA-IM-A41Y 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-IM-A41Z                    TCGA-IM-A420 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-IM-A4EB                    TCGA-J8-A3NZ 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-J8-A3O0                    TCGA-J8-A3O1 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-J8-A3O2                    TCGA-J8-A3YD 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-J8-A3YE                    TCGA-J8-A3YF 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-J8-A3YG                    TCGA-J8-A3YH 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-J8-A42S                    TCGA-J8-A4HW 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-J8-A4HY                    TCGA-KS-A41F 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-KS-A41I                    TCGA-KS-A41J 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-KS-A41L                    TCGA-KS-A4I1 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-KS-A4I3                    TCGA-KS-A4I5 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-KS-A4I7                    TCGA-KS-A4I9 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-KS-A4IB                    TCGA-KS-A4IC 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-KS-A4ID                    TCGA-L6-A4EP 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-L6-A4EQ                    TCGA-L6-A4ET 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-L6-A4EU                    TCGA-MK-A4N6 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-MK-A4N7                    TCGA-MK-A4N9 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-MK-A84Z                    TCGA-QD-A8IV 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
D96V17, binary
                               cls
clus                              0   1
  DEL PEAK 42(XQ22.3) MUTATED     0   3
  DEL PEAK 42(XQ22.3) WILD-TYPE  38 356
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 42(XQ22.3) MUTATED      0    3
  DEL PEAK 42(XQ22.3) WILD-TYPE   38  356
                        clus
vv                       DEL PEAK 42(XQ22.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           3
                        clus
vv                       DEL PEAK 42(XQ22.3) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           356
[1] 2 2
[1] FALSE
