[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-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/11541741/THCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THCA-TP/11548102/transformed.cor.cli.txt"

nPatients in clinical file=497, in cluster file=501, common to both=495
[1] "Reduce the number of clustering variables from 110 to 98."
[1]  98 495
[1] "AMP PEAK  1(1P36.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE 
                             5                            490 
  AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE 
                             5                            490 
[1] "AMP PEAK  2(1P32.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE 
                            5                           490 
  AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE 
                            5                           490 
[1] "AMP PEAK  3(1P31.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE 
                            5                           490 
  AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE 
                            5                           490 
[1] "AMP PEAK  4(1Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE 
                           28                           467 
  AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE 
                           28                           467 
[1] "AMP PEAK  5(1Q43) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE 
                         28                         467 
  AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE 
                         28                         467 
[1] "AMP PEAK  6(2P16.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE 
                            3                           492 
  AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE 
                            3                           492 
[1] "AMP PEAK  9(2Q37.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(2Q37.2) MUTATED AMP PEAK  9(2Q37.2) WILD-TYPE 
                            3                           492 
  AMP PEAK  9(2Q37.2) MUTATED AMP PEAK  9(2Q37.2) WILD-TYPE 
                            3                           492 
[1] "AMP PEAK 10(3P22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(3P22.3) MUTATED AMP PEAK 10(3P22.3) WILD-TYPE 
                            4                           491 
  AMP PEAK 10(3P22.3) MUTATED AMP PEAK 10(3P22.3) WILD-TYPE 
                            4                           491 
[1] "AMP PEAK 11(3P14.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(3P14.1) MUTATED AMP PEAK 11(3P14.1) WILD-TYPE 
                            5                           490 
  AMP PEAK 11(3P14.1) MUTATED AMP PEAK 11(3P14.1) WILD-TYPE 
                            5                           490 
[1] "AMP PEAK 12(4P16.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(4P16.1) MUTATED AMP PEAK 12(4P16.1) WILD-TYPE 
                            7                           488 
  AMP PEAK 12(4P16.1) MUTATED AMP PEAK 12(4P16.1) WILD-TYPE 
                            7                           488 
[1] "AMP PEAK 13(4Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(4Q22.1) MUTATED AMP PEAK 13(4Q22.1) WILD-TYPE 
                            7                           488 
  AMP PEAK 13(4Q22.1) MUTATED AMP PEAK 13(4Q22.1) WILD-TYPE 
                            7                           488 
[1] "AMP PEAK 14(4Q28.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(4Q28.2) MUTATED AMP PEAK 14(4Q28.2) WILD-TYPE 
                            6                           489 
  AMP PEAK 14(4Q28.2) MUTATED AMP PEAK 14(4Q28.2) WILD-TYPE 
                            6                           489 
[1] "AMP PEAK 15(4Q31.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(4Q31.21) MUTATED AMP PEAK 15(4Q31.21) WILD-TYPE 
                            10                            485 
  AMP PEAK 15(4Q31.21) MUTATED AMP PEAK 15(4Q31.21) WILD-TYPE 
                            10                            485 
[1] "AMP PEAK 16(4Q32.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(4Q32.3) MUTATED AMP PEAK 16(4Q32.3) WILD-TYPE 
                            7                           488 
  AMP PEAK 16(4Q32.3) MUTATED AMP PEAK 16(4Q32.3) WILD-TYPE 
                            7                           488 
[1] "AMP PEAK 17(5P14.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(5P14.3) MUTATED AMP PEAK 17(5P14.3) WILD-TYPE 
                           22                           473 
  AMP PEAK 17(5P14.3) MUTATED AMP PEAK 17(5P14.3) WILD-TYPE 
                           22                           473 
[1] "AMP PEAK 18(5Q21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(5Q21.1) MUTATED AMP PEAK 18(5Q21.1) WILD-TYPE 
                           22                           473 
  AMP PEAK 18(5Q21.1) MUTATED AMP PEAK 18(5Q21.1) WILD-TYPE 
                           22                           473 
[1] "AMP PEAK 19(5Q21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(5Q21.1) MUTATED AMP PEAK 19(5Q21.1) WILD-TYPE 
                           19                           476 
  AMP PEAK 19(5Q21.1) MUTATED AMP PEAK 19(5Q21.1) WILD-TYPE 
                           19                           476 
[1] "AMP PEAK 20(5Q33.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(5Q33.1) MUTATED AMP PEAK 20(5Q33.1) WILD-TYPE 
                           20                           475 
  AMP PEAK 20(5Q33.1) MUTATED AMP PEAK 20(5Q33.1) WILD-TYPE 
                           20                           475 
[1] "AMP PEAK 21(5Q35.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(5Q35.2) MUTATED AMP PEAK 21(5Q35.2) WILD-TYPE 
                           19                           476 
  AMP PEAK 21(5Q35.2) MUTATED AMP PEAK 21(5Q35.2) WILD-TYPE 
                           19                           476 
[1] "AMP PEAK 22(6P22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(6P22.3) MUTATED AMP PEAK 22(6P22.3) WILD-TYPE 
                            3                           492 
  AMP PEAK 22(6P22.3) MUTATED AMP PEAK 22(6P22.3) WILD-TYPE 
                            3                           492 
[1] "AMP PEAK 23(6P22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(6P22.2) MUTATED AMP PEAK 23(6P22.2) WILD-TYPE 
                            4                           491 
  AMP PEAK 23(6P22.2) MUTATED AMP PEAK 23(6P22.2) WILD-TYPE 
                            4                           491 
[1] "AMP PEAK 24(6P21.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(6P21.31) MUTATED AMP PEAK 24(6P21.31) WILD-TYPE 
                             3                            492 
  AMP PEAK 24(6P21.31) MUTATED AMP PEAK 24(6P21.31) WILD-TYPE 
                             3                            492 
[1] "AMP PEAK 25(6P21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(6P21.2) MUTATED AMP PEAK 25(6P21.2) WILD-TYPE 
                            4                           491 
  AMP PEAK 25(6P21.2) MUTATED AMP PEAK 25(6P21.2) WILD-TYPE 
                            4                           491 
[1] "AMP PEAK 26(6P12.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(6P12.2) MUTATED AMP PEAK 26(6P12.2) WILD-TYPE 
                            3                           492 
  AMP PEAK 26(6P12.2) MUTATED AMP PEAK 26(6P12.2) WILD-TYPE 
                            3                           492 
[1] "AMP PEAK 27(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(6Q12) MUTATED AMP PEAK 27(6Q12) WILD-TYPE 
                          3                         492 
  AMP PEAK 27(6Q12) MUTATED AMP PEAK 27(6Q12) WILD-TYPE 
                          3                         492 
[1] "AMP PEAK 28(6Q27) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(6Q27) MUTATED AMP PEAK 28(6Q27) WILD-TYPE 
                          4                         491 
  AMP PEAK 28(6Q27) MUTATED AMP PEAK 28(6Q27) WILD-TYPE 
                          4                         491 
[1] "AMP PEAK 29(7Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(7Q11.21) MUTATED AMP PEAK 29(7Q11.21) WILD-TYPE 
                            19                            476 
  AMP PEAK 29(7Q11.21) MUTATED AMP PEAK 29(7Q11.21) WILD-TYPE 
                            19                            476 
[1] "AMP PEAK 30(7Q21.11) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 30(7Q21.11) MUTATED AMP PEAK 30(7Q21.11) WILD-TYPE 
                            20                            475 
  AMP PEAK 30(7Q21.11) MUTATED AMP PEAK 30(7Q21.11) WILD-TYPE 
                            20                            475 
[1] "AMP PEAK 31(7Q31.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 31(7Q31.1) MUTATED AMP PEAK 31(7Q31.1) WILD-TYPE 
                           21                           474 
  AMP PEAK 31(7Q31.1) MUTATED AMP PEAK 31(7Q31.1) WILD-TYPE 
                           21                           474 
[1] "AMP PEAK 32(7Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 32(7Q34) MUTATED AMP PEAK 32(7Q34) WILD-TYPE 
                         21                         474 
  AMP PEAK 32(7Q34) MUTATED AMP PEAK 32(7Q34) WILD-TYPE 
                         21                         474 
[1] "AMP PEAK 33(9Q22.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 33(9Q22.31) MUTATED AMP PEAK 33(9Q22.31) WILD-TYPE 
                             6                            489 
  AMP PEAK 33(9Q22.31) MUTATED AMP PEAK 33(9Q22.31) WILD-TYPE 
                             6                            489 
[1] "AMP PEAK 34(9Q31.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 34(9Q31.1) MUTATED AMP PEAK 34(9Q31.1) WILD-TYPE 
                            6                           489 
  AMP PEAK 34(9Q31.1) MUTATED AMP PEAK 34(9Q31.1) WILD-TYPE 
                            6                           489 
[1] "AMP PEAK 35(9Q34.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 35(9Q34.3) MUTATED AMP PEAK 35(9Q34.3) WILD-TYPE 
                            7                           488 
  AMP PEAK 35(9Q34.3) MUTATED AMP PEAK 35(9Q34.3) WILD-TYPE 
                            7                           488 
[1] "AMP PEAK 36(10Q24.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 36(10Q24.2) MUTATED AMP PEAK 36(10Q24.2) WILD-TYPE 
                             3                            492 
  AMP PEAK 36(10Q24.2) MUTATED AMP PEAK 36(10Q24.2) WILD-TYPE 
                             3                            492 
[1] "AMP PEAK 37(10Q25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 37(10Q25.1) MUTATED AMP PEAK 37(10Q25.1) WILD-TYPE 
                             4                            491 
  AMP PEAK 37(10Q25.1) MUTATED AMP PEAK 37(10Q25.1) WILD-TYPE 
                             4                            491 
[1] "AMP PEAK 38(11P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 38(11P13) MUTATED AMP PEAK 38(11P13) WILD-TYPE 
                           8                          487 
  AMP PEAK 38(11P13) MUTATED AMP PEAK 38(11P13) WILD-TYPE 
                           8                          487 
[1] "AMP PEAK 39(12P11.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 39(12P11.1) MUTATED AMP PEAK 39(12P11.1) WILD-TYPE 
                            16                            479 
  AMP PEAK 39(12P11.1) MUTATED AMP PEAK 39(12P11.1) WILD-TYPE 
                            16                            479 
[1] "AMP PEAK 40(12Q21.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 40(12Q21.31) MUTATED AMP PEAK 40(12Q21.31) WILD-TYPE 
                             17                             478 
  AMP PEAK 40(12Q21.31) MUTATED AMP PEAK 40(12Q21.31) WILD-TYPE 
                             17                             478 
[1] "AMP PEAK 41(12Q23.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 41(12Q23.1) MUTATED AMP PEAK 41(12Q23.1) WILD-TYPE 
                            17                            478 
  AMP PEAK 41(12Q23.1) MUTATED AMP PEAK 41(12Q23.1) WILD-TYPE 
                            17                            478 
[1] "AMP PEAK 42(13Q14.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 42(13Q14.2) MUTATED AMP PEAK 42(13Q14.2) WILD-TYPE 
                             6                            489 
  AMP PEAK 42(13Q14.2) MUTATED AMP PEAK 42(13Q14.2) WILD-TYPE 
                             6                            489 
[1] "AMP PEAK 43(13Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 43(13Q34) MUTATED AMP PEAK 43(13Q34) WILD-TYPE 
                           7                          488 
  AMP PEAK 43(13Q34) MUTATED AMP PEAK 43(13Q34) WILD-TYPE 
                           7                          488 
[1] "AMP PEAK 44(14Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 44(14Q12) MUTATED AMP PEAK 44(14Q12) WILD-TYPE 
                          13                          482 
  AMP PEAK 44(14Q12) MUTATED AMP PEAK 44(14Q12) WILD-TYPE 
                          13                          482 
[1] "AMP PEAK 45(14Q32.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 45(14Q32.31) MUTATED AMP PEAK 45(14Q32.31) WILD-TYPE 
                             13                             482 
  AMP PEAK 45(14Q32.31) MUTATED AMP PEAK 45(14Q32.31) WILD-TYPE 
                             13                             482 
[1] "AMP PEAK 48(18Q12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 48(18Q12.1) MUTATED AMP PEAK 48(18Q12.1) WILD-TYPE 
                             7                            488 
  AMP PEAK 48(18Q12.1) MUTATED AMP PEAK 48(18Q12.1) WILD-TYPE 
                             7                            488 
[1] "AMP PEAK 49(18Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 49(18Q22.1) MUTATED AMP PEAK 49(18Q22.1) WILD-TYPE 
                             7                            488 
  AMP PEAK 49(18Q22.1) MUTATED AMP PEAK 49(18Q22.1) WILD-TYPE 
                             7                            488 
[1] "AMP PEAK 50(18Q22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 50(18Q22.3) MUTATED AMP PEAK 50(18Q22.3) WILD-TYPE 
                             8                            487 
  AMP PEAK 50(18Q22.3) MUTATED AMP PEAK 50(18Q22.3) WILD-TYPE 
                             8                            487 
[1] "AMP PEAK 51(19P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 51(19P13.3) MUTATED AMP PEAK 51(19P13.3) WILD-TYPE 
                             8                            487 
  AMP PEAK 51(19P13.3) MUTATED AMP PEAK 51(19P13.3) WILD-TYPE 
                             8                            487 
[1] "AMP PEAK 52(20P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 52(20P13) MUTATED AMP PEAK 52(20P13) WILD-TYPE 
                          14                          481 
  AMP PEAK 52(20P13) MUTATED AMP PEAK 52(20P13) WILD-TYPE 
                          14                          481 
[1] "AMP PEAK 53(20Q13.11) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 53(20Q13.11) MUTATED AMP PEAK 53(20Q13.11) WILD-TYPE 
                             14                             481 
  AMP PEAK 53(20Q13.11) MUTATED AMP PEAK 53(20Q13.11) WILD-TYPE 
                             14                             481 
[1] "AMP PEAK 54(20Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 54(20Q13.2) MUTATED AMP PEAK 54(20Q13.2) WILD-TYPE 
                            14                            481 
  AMP PEAK 54(20Q13.2) MUTATED AMP PEAK 54(20Q13.2) WILD-TYPE 
                            14                            481 
[1] "AMP PEAK 55(20Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 55(20Q13.2) MUTATED AMP PEAK 55(20Q13.2) WILD-TYPE 
                            13                            482 
  AMP PEAK 55(20Q13.2) MUTATED AMP PEAK 55(20Q13.2) WILD-TYPE 
                            13                            482 
[1] "AMP PEAK 56(21Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 56(21Q21.3) MUTATED AMP PEAK 56(21Q21.3) WILD-TYPE 
                             6                            489 
  AMP PEAK 56(21Q21.3) MUTATED AMP PEAK 56(21Q21.3) WILD-TYPE 
                             6                            489 
[1] "AMP PEAK 57(22Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 57(22Q11.21) MUTATED AMP PEAK 57(22Q11.21) WILD-TYPE 
                              7                             488 
  AMP PEAK 57(22Q11.21) MUTATED AMP PEAK 57(22Q11.21) WILD-TYPE 
                              7                             488 
[1] "AMP PEAK 58(XP22.12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 58(XP22.12) MUTATED AMP PEAK 58(XP22.12) WILD-TYPE 
                            10                            485 
  AMP PEAK 58(XP22.12) MUTATED AMP PEAK 58(XP22.12) WILD-TYPE 
                            10                            485 
[1] "AMP PEAK 59(XP11.4) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 59(XP11.4) MUTATED AMP PEAK 59(XP11.4) WILD-TYPE 
                            9                           486 
  AMP PEAK 59(XP11.4) MUTATED AMP PEAK 59(XP11.4) WILD-TYPE 
                            9                           486 
[1] "AMP PEAK 60(XP11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 60(XP11.22) MUTATED AMP PEAK 60(XP11.22) WILD-TYPE 
                             8                            487 
  AMP PEAK 60(XP11.22) MUTATED AMP PEAK 60(XP11.22) WILD-TYPE 
                             8                            487 
[1] "AMP PEAK 61(XP11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 61(XP11.22) MUTATED AMP PEAK 61(XP11.22) WILD-TYPE 
                             8                            487 
  AMP PEAK 61(XP11.22) MUTATED AMP PEAK 61(XP11.22) WILD-TYPE 
                             8                            487 
[1] "AMP PEAK 62(XP11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 62(XP11.21) MUTATED AMP PEAK 62(XP11.21) WILD-TYPE 
                             9                            486 
  AMP PEAK 62(XP11.21) MUTATED AMP PEAK 62(XP11.21) WILD-TYPE 
                             9                            486 
[1] "AMP PEAK 63(XQ21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 63(XQ21.2) MUTATED AMP PEAK 63(XQ21.2) WILD-TYPE 
                            8                           487 
  AMP PEAK 63(XQ21.2) MUTATED AMP PEAK 63(XQ21.2) WILD-TYPE 
                            8                           487 
[1] "AMP PEAK 64(XQ22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 64(XQ22.3) MUTATED AMP PEAK 64(XQ22.3) WILD-TYPE 
                           15                           480 
  AMP PEAK 64(XQ22.3) MUTATED AMP PEAK 64(XQ22.3) WILD-TYPE 
                           15                           480 
[1] "AMP PEAK 65(XQ23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 65(XQ23) MUTATED AMP PEAK 65(XQ23) WILD-TYPE 
                          9                         486 
  AMP PEAK 65(XQ23) MUTATED AMP PEAK 65(XQ23) WILD-TYPE 
                          9                         486 
[1] "AMP PEAK 66(XQ24) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 66(XQ24) MUTATED AMP PEAK 66(XQ24) WILD-TYPE 
                          9                         486 
  AMP PEAK 66(XQ24) MUTATED AMP PEAK 66(XQ24) WILD-TYPE 
                          9                         486 
[1] "AMP PEAK 67(XQ24) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 67(XQ24) MUTATED AMP PEAK 67(XQ24) WILD-TYPE 
                          9                         486 
  AMP PEAK 67(XQ24) MUTATED AMP PEAK 67(XQ24) WILD-TYPE 
                          9                         486 
[1] "AMP PEAK 68(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 68(XQ28) MUTATED AMP PEAK 68(XQ28) WILD-TYPE 
                         10                         485 
  AMP PEAK 68(XQ28) MUTATED AMP PEAK 68(XQ28) WILD-TYPE 
                         10                         485 
[1] "DEL PEAK  1(1Q24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE 
                            3                           492 
  DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE 
                            3                           492 
[1] "DEL PEAK  2(1Q42.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE 
                             5                            490 
  DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE 
                             5                            490 
[1] "DEL PEAK  3(2P23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE 
                           12                           483 
  DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE 
                           12                           483 
[1] "DEL PEAK  4(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           10                           485 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           10                           485 
[1] "DEL PEAK  5(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           13                           482 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           13                           482 
[1] "DEL PEAK  7(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                            5                           490 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                            5                           490 
[1] "DEL PEAK  8(5P15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE 
                            4                           491 
  DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE 
                            4                           491 
[1] "DEL PEAK 11(6Q22.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                             7                            488 
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                             7                            488 
[1] "DEL PEAK 13(7Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE 
                          4                         491 
  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE 
                          4                         491 
[1] "DEL PEAK 14(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE 
                            4                           491 
  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE 
                            4                           491 
[1] "DEL PEAK 15(8P22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE 
                          4                         491 
  DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE 
                          4                         491 
[1] "DEL PEAK 16(8P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE 
                          4                         491 
  DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE 
                          4                         491 
[1] "DEL PEAK 17(8Q24.22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE 
                             7                            488 
  DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE 
                             7                            488 
[1] "DEL PEAK 18(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                           20                           475 
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                           20                           475 
[1] "DEL PEAK 19(9Q22.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE 
                            25                            470 
  DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE 
                            25                            470 
[1] "DEL PEAK 20(10P12.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE 
                              7                             488 
  DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE 
                              7                             488 
[1] "DEL PEAK 21(10Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE 
                            12                            483 
  DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE 
                            12                            483 
[1] "DEL PEAK 22(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE 
                             12                             483 
  DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE 
                             12                             483 
[1] "DEL PEAK 23(11P15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE 
                             7                            488 
  DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE 
                             7                            488 
[1] "DEL PEAK 24(13Q12.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE 
                             18                             477 
  DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE 
                             18                             477 
[1] "DEL PEAK 25(13Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE 
                            19                            476 
  DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE 
                            19                            476 
[1] "DEL PEAK 27(15Q25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE 
                             9                            486 
  DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE 
                             9                            486 
[1] "DEL PEAK 29(16Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE 
                             6                            489 
  DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE 
                             6                            489 
[1] "DEL PEAK 30(17P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE 
                             7                            488 
  DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE 
                             7                            488 
[1] "DEL PEAK 31(18Q12.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE 
                             4                            491 
  DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE 
                             4                            491 
[1] "DEL PEAK 32(19P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE 
                             7                            488 
  DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE 
                             7                            488 
[1] "DEL PEAK 33(19P13.12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE 
                              8                             487 
  DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE 
                              8                             487 
[1] "DEL PEAK 36(21Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE 
                             9                            486 
  DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE 
                             9                            486 
[1] "DEL PEAK 37(22Q12.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE 
                            88                            407 
  DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE 
                            88                            407 
[1] "DEL PEAK 38(22Q13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE 
                            87                            408 
  DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE 
                            87                            408 
[1] "DEL PEAK 39(22Q13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE 
                            87                            408 
  DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE 
                            87                            408 
[1] "DEL PEAK 40(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE 
                             88                             407 
  DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE 
                             88                             407 
[1] "DEL PEAK 41(XQ23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE 
                          4                         491 
  DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE 
                          4                         491 
[1] "DEL PEAK 42(XQ22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE 
                            4                           491 
  DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE 
                            4                           491 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "RADIATIONTHERAPY"                      
[14] "HISTOLOGICALTYPE"                      
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "RADIATIONEXPOSURE"                     
[17] "EXTRATHYROIDAL.EXTENSION"              
[18] "COMPLETENESS.OF.RESECTION"             
[19] "NUMBER.OF.LYMPH.NODES"                 
[20] "MULTIFOCALITY"                         
[21] "TUMOR.SIZE"                            
[22] "RACE"                                  
[23] "ETHNICITY"                             
[24] "BATCHNUMBER"                           

Input Data has 24 rows and 495 columns.

[1] "Batch" "24"   
[1] "Last Follow UP"
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
         754          419          554          497          448          251 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH 
         574          122          352          509          230          460 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
         538          710          630          626          147          246 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
         148          640           85          155          344          533 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
          37          919          696          559          504          623 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT 
         577          214          487          424          471          709 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
         567          175          197            1          105          193 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
         238          188          154          273          150          182 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
          16            3            6            7          346          325 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
           3           12            3          615          469         1109 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
         182          482          564          573          916          352 
TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M 
         913          764          130           98           84          525 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
         428         4194          103          265          771          408 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
         362          444          243          335         3042          563 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
         399          243          455          219           44          270 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
          31          181          307          243          162          258 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
         318           46          292          382          252          234 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
         168          267          256          247          284          206 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
         280          287          301          262          307          215 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
         315          378          330          483          459          944 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
         380          957          499          595         1105          998 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
         737          538         1308          345          650          388 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
         761          615          931          443          584          299 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
         647          623          363          697          639          577 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
         236          253          528          524          840          554 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
         328          334          430          447          542           95 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
         481          740         1670          655           71          945 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
         367         2019         1223         1922          922          427 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
          35          678           NA          596          414          434 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A432 
         420          428          434           92           NA          439 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
         447          429          455          234          629          419 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
         413           NA           NA         4731           NA         4831 
TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
          NA           NA           NA         4780         1154           NA 
TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 
        2461          127         1789           44         2260         1381 
TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR 
        1018         3296         1196           43          918         3128 
TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY 
        1989         3773         1532         1133         4494         3076 
TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 
        4258           NA           NA         1319         1176         1604 
TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ 
        4228         3989         3305           NA           NA           NA 
TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
         370         4484         3976         3941          988         3556 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
        2988         1256         2901           NA         2035         2519 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO 
        2353         2402          958         1531         1614         1441 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
        1597         1385         1465          215         1358         1393 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
         587         1398         1154          944          596          928 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
        1022          874         1251         1149          911          405 
TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
         361          265          817          553          636          376 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
         549          602          592         1649         1734         1645 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N 
         448          441          479          318          442          324 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
         357          339          433          500          544          401 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT 
         715          184           91          374          462          319 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
         400          674          421          600          535          367 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ 
         535          531          526          444          531          577 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
         477          430          597          407          254          500 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
         510          850          723          511          639          367 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 
         532          529          492          457          441          339 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
         223          381          281          423          238          350 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
         499          475          411          389         2149          514 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
         274          147          262          255          298          153 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
        1152          387           29         1444         1466          903 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
         984          450          375          450          824          559 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
         897         1644          672          373          489          888 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
         601           81         1771          418         2160         2434 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
        1988         2582         2998         1856         1786         1737 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
        1676         1799          859          178          127           74 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
         169          752         1165         1285           72          137 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
        2458         2106         1821         1323            9          547 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
         770         4026          752           98          218          146 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
         153           65          122           59         2243         1816 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
         961         1346          751         2075         3130         2031 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
        2474         1215           NA         2489         3235         2590 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
        2606         2396         1401          124           27          670 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
          28         1463         2773           38           35          542 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NN TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
          50           30           NA           46           23            1 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
         142          504          550            9           23          519 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 
         209          126          200          138           27           NA 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
          41           35           51          381          517          659 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED 
         379           91          610          566         1488         1442 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB 
         312          514          298          293           90          263 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
         524         1313          827          342          968          847 
TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY 
         751          678          175           75           79            6 
TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 
        4367          486          477         2637          183          378 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
         205          987         2658         2577         1073         1011 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
        1016         1228          664           22          506          987 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
         265          334          158 
Variable 1:'AGE':	nDistinctValues=73,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=407,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=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:'DCCUPLOADDAY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'HISTOLOGICAL.TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONEXPOSURE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'EXTRATHYROIDAL.EXTENSION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=30,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'MULTIFOCALITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'TUMOR.SIZE':	nDistinctValues=70,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 22:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 24:'BATCH.NUMBER':	nDistinctValues=26,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "NEOPLASM.DISEASESTAGE"                 
 [3] "PATHOLOGY.T.STAGE"                     
 [4] "PATHOLOGY.N.STAGE"                     
 [5] "PATHOLOGY.M.STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL.TYPE"                     
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "RADIATIONEXPOSURE"                     
[10] "EXTRATHYROIDAL.EXTENSION"              
[11] "COMPLETENESS.OF.RESECTION"             
[12] "NUMBER.OF.LYMPH.NODES"                 
[13] "MULTIFOCALITY"                         
[14] "TUMOR.SIZE"                            
[15] "RACE"                                  
[16] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 495 columns, 1 survival variables, and 16 non-survival variables.
AGE, nv=73, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, 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 
140 166 165  21 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
140 166 165  21 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
140 166 165  21 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
140 166 165  21 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
RADIATIONEXPOSURE, nv=2, binary=FALSE, numeric=FALSE
EXTRATHYROIDAL.EXTENSION, nv=4, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=30, binary=FALSE, numeric=TRUE
MULTIFOCALITY, nv=2, binary=FALSE, numeric=FALSE
TUMOR.SIZE, nv=70, 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 472  14
  AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE 
                             5                            486 
  AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE 
                             0                             14 
$`AMP PEAK  1(1P36.32) MUTATED`
TCGA-EL-A3GP TCGA-EL-A4JX TCGA-ET-A3BT TCGA-FY-A3NM TCGA-L6-A4EU 
        1.41        45.96        24.72         0.99         0.72 

$`AMP PEAK  1(1P36.32) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        5.52         8.78         8.42         8.12         9.34         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
        9.21         9.44         9.90         8.61        10.09         7.07 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       10.36        12.43        10.85        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        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 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.07        14.27         3.02        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        13.78        13.58        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        80.91         4.18 
TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 
       58.82         1.45        74.30        45.40        33.47       108.36 
TCGA-EL-A3GO TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       39.32        30.18       102.84        65.39       124.04        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       37.25       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        38.66        52.73       139.00       131.15       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        12.16       147.42       130.72 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       116.91        98.24        41.29        95.38 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       50.33        53.06        47.38        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JZ TCGA-EL-A4K0 
        7.07        44.65        45.80        19.30        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        12.36        18.05        19.79        19.46        54.21 
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        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        10.49        13.15        22.16        13.84        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       17.59        12.07        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 
       17.46        18.97        15.68        14.14        19.63        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        16.44        16.77        27.95        23.77        16.80 
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        11.15         7.33        12.53         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        16.41        15.62        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        9.80         5.03        37.87        12.72         0.95        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
       71.01        80.02        65.36        84.89        98.56        61.02 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       58.72        57.11        55.10        59.15        28.24         5.85 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        4.18         2.43         5.56        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       59.70        31.59        44.25        24.69        68.22       102.90 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77        81.34        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        46.06         4.08         0.89 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10        91.17         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       17.82         1.64         1.51         0.76         0.03         4.67 
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         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74        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        16.64        32.45         8.71        10.98         5.19 

  AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE 
                          0.72                           0.03 
  AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE 
                         45.96                         158.83 
  AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE 
                         1.410                         16.605 
[1] "0.7 - 46.0 (1.4)"   "0.0 - 158.8 (16.6)"
[1] "hr="     "3300000"
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     279       51       106        2        44
                                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                            279
  STAGE II                             0                             51
  STAGE III                            3                            106
  STAGE IV                             0                              2
  STAGE IVA                            1                             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  1(1P36.32) MUTATED     0   1   4   0
  AMP PEAK  1(1P36.32) WILD-TYPE 140 165 161  21
D1V4, multiclass
    clus
vv   AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE
  T1                            0                            140
  T2                            1                            165
  T3                            4                            161
  T4                            0                             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"
D1V5, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.32) MUTATED     2   3
  AMP PEAK  1(1P36.32) WILD-TYPE 221 219
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.32) MUTATED      2    3
  AMP PEAK  1(1P36.32) WILD-TYPE  221  219
   clus
vv  AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE
  0                            2                            221
  1                            3                            219
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK  1(1P36.32) MUTATED     2   0   3
  AMP PEAK  1(1P36.32) WILD-TYPE 271   9 209
D1V6, multiclass
    clus
vv   AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE
  M0                            2                            271
  M1                            0                              9
  MX                            3                            209
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.32) MUTATED     4   1
  AMP PEAK  1(1P36.32) WILD-TYPE 360 130
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.32) MUTATED      4    1
  AMP PEAK  1(1P36.32) WILD-TYPE  360  130
        clus
vv       AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE
  FEMALE                            4                            360
  MALE                              1                            130
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK  1(1P36.32) MUTATED                0
  AMP PEAK  1(1P36.32) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK  1(1P36.32) MUTATED                                               3
  AMP PEAK  1(1P36.32) WILD-TYPE                                           350
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK  1(1P36.32) MUTATED                                                                        0
  AMP PEAK  1(1P36.32) WILD-TYPE                                                                     98
                                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                                                                  33
D1V8, 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                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             98
  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"
D1V9, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.32) MUTATED     0   5
  AMP PEAK  1(1P36.32) WILD-TYPE  14 476
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.32) MUTATED      0    5
  AMP PEAK  1(1P36.32) WILD-TYPE   14  476
     clus
vv    AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE
  NO                             0                             14
  YES                            5                            476
[1] 2 2
[1] FALSE
D1V10, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.32) MUTATED     4   1
  AMP PEAK  1(1P36.32) WILD-TYPE 413  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.32) MUTATED      4    1
  AMP PEAK  1(1P36.32) WILD-TYPE  413   16
     clus
vv    AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE
  NO                             4                            413
  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          127                      16  326
                                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)                                       127
  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
  AMP PEAK  1(1P36.32) MUTATED     4   1   0   0
  AMP PEAK  1(1P36.32) WILD-TYPE 374  50   4  30
D1V12, multiclass
    clus
vv   AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE
  R0                            4                            374
  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 222 258
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.32) MUTATED      2    3
  AMP PEAK  1(1P36.32) WILD-TYPE  222  258
            clus
vv           AMP PEAK  1(1P36.32) MUTATED AMP PEAK  1(1P36.32) WILD-TYPE
  MULTIFOCAL                            2                            222
  UNIFOCAL                              3                            258
[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    49
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1P36.32) MUTATED                           3     2
  AMP PEAK  1(1P36.32) WILD-TYPE                        23   319
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                                                        49
  BLACK OR AFRICAN AMERICAN                                    23
  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"
D1V17, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.32) MUTATED     0   5
  AMP PEAK  1(1P36.32) WILD-TYPE  38 345
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.32) MUTATED      0    5
  AMP PEAK  1(1P36.32) WILD-TYPE   38  345
                        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                            345
[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 472  14
  AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE 
                            5                           486 
  AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE 
                            0                            14 
$`AMP PEAK  2(1P32.3) MUTATED`
TCGA-DO-A2HM TCGA-EM-A3O8 TCGA-ET-A3BT TCGA-ET-A40Q TCGA-FY-A3NM 
        2.33        12.53        24.72         7.17         0.99 

$`AMP PEAK  2(1P32.3) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        5.52         8.78         8.42         8.12         9.34         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
        9.21         9.44         9.90         8.61        10.09         7.07 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       10.36        12.43        10.85        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        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 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3DZ 
       15.81        24.33        54.90        21.53        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
        1.45        74.30        45.40        33.47       108.36        39.32 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        30.18       102.84        65.39       124.04        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       37.25       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        38.66        52.73       139.00       131.15       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        12.16       147.42       130.72 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       116.91        98.24        41.29        95.38 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       50.33        53.06        47.38        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       37.78        29.95        13.32        11.87         8.71        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        12.36        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       54.21        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        11.74        11.15        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       16.44        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
       12.30        15.19        10.49        13.15        22.16        13.84 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        17.59        12.07        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        17.46        18.97        15.68        14.14        19.63 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        16.44        16.77        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        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        11.15         7.33         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        16.41        15.62        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        9.80         5.03        37.87        12.72         0.95        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
       71.01        80.02        65.36        84.89        98.56        61.02 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       58.72        57.11        55.10        59.15        28.24         5.85 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        4.18         2.43         5.56        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40R 
       17.98        25.32       132.36        24.72         3.22         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        24.69        68.22       102.90        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       81.34        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        46.06         4.08         0.89        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10        91.17         1.25         1.15        17.82 
TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
        1.64         1.51         0.76         0.03         4.67        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         6.87         4.14 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58         4.54         0.89         1.35         1.15         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        10.26        16.90         9.80 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
        9.63         2.96         8.65        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 
       86.70         6.02        12.43         6.74        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 
        0.72        16.64        32.45         8.71        10.98         5.19 

  AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE 
                         0.99                          0.03 
  AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE 
                        24.72                        158.83 
  AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE 
                        7.170                        16.685 
[1] "1.0 - 24.7 (7.2)"   "0.0 - 158.8 (16.7)"
[1] "hr="    "450000"
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     278       51       108        2        43
                               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                           278
  STAGE II                            0                            51
  STAGE III                           1                           108
  STAGE IV                            0                             2
  STAGE IVA                           2                            43
  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 138 165 163  21
D2V4, multiclass
    clus
vv   AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE
  T1                           2                           138
  T2                           1                           165
  T3                           2                           163
  T4                           0                            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"
D2V5, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P32.3) MUTATED     2   3
  AMP PEAK  2(1P32.3) WILD-TYPE 221 219
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P32.3) MUTATED      2    3
  AMP PEAK  2(1P32.3) WILD-TYPE  221  219
   clus
vv  AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE
  0                           2                           221
  1                           3                           219
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK  2(1P32.3) MUTATED     0   0   5
  AMP PEAK  2(1P32.3) WILD-TYPE 273   9 207
D2V6, multiclass
    clus
vv   AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE
  M0                           0                           273
  M1                           0                             9
  MX                           5                           207
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P32.3) MUTATED     3   2
  AMP PEAK  2(1P32.3) WILD-TYPE 361 129
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P32.3) MUTATED      3    2
  AMP PEAK  2(1P32.3) WILD-TYPE  361  129
        clus
vv       AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE
  FEMALE                           3                           361
  MALE                             2                           129
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK  2(1P32.3) MUTATED                0
  AMP PEAK  2(1P32.3) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK  2(1P32.3) MUTATED                                               2
  AMP PEAK  2(1P32.3) WILD-TYPE                                           351
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK  2(1P32.3) MUTATED                                                                        1
  AMP PEAK  2(1P32.3) WILD-TYPE                                                                     97
                               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                                                                  33
D2V8, 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                                                                                     9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            97
  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"
D2V9, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P32.3) MUTATED     0   5
  AMP PEAK  2(1P32.3) WILD-TYPE  14 476
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P32.3) MUTATED      0    5
  AMP PEAK  2(1P32.3) WILD-TYPE   14  476
     clus
vv    AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE
  NO                            0                            14
  YES                           5                           476
[1] 2 2
[1] FALSE
D2V10, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P32.3) MUTATED     2   2
  AMP PEAK  2(1P32.3) WILD-TYPE 415  15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P32.3) MUTATED      2    2
  AMP PEAK  2(1P32.3) WILD-TYPE  415   15
     clus
vv    AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE
  NO                            2                           415
  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          128                      16  325
                               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)                                      128
  MODERATE/ADVANCED (T4A)                            16
  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  2(1P32.3) MUTATED     4   0   0   1
  AMP PEAK  2(1P32.3) WILD-TYPE 374  51   4  29
D2V12, multiclass
    clus
vv   AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE
  R0                           4                           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"
D2V13, continuous
D2V14, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P32.3) MUTATED     3   2
  AMP PEAK  2(1P32.3) WILD-TYPE 221 259
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P32.3) MUTATED      3    2
  AMP PEAK  2(1P32.3) WILD-TYPE  221  259
            clus
vv           AMP PEAK  2(1P32.3) MUTATED AMP PEAK  2(1P32.3) WILD-TYPE
  MULTIFOCAL                           3                           221
  UNIFOCAL                             2                           259
[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    49
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1P32.3) MUTATED                           0     4
  AMP PEAK  2(1P32.3) WILD-TYPE                        26   317
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                                                       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"
D2V17, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P32.3) MUTATED     0   4
  AMP PEAK  2(1P32.3) WILD-TYPE  38 346
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P32.3) MUTATED      0    4
  AMP PEAK  2(1P32.3) WILD-TYPE   38  346
                        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                           346
[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 472  14
  AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE 
                            5                           486 
  AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE 
                            0                            14 
$`AMP PEAK  3(1P31.1) MUTATED`
TCGA-DJ-A2PW TCGA-DO-A2HM TCGA-EM-A4FR TCGA-ET-A3BT TCGA-FY-A3NM 
        7.69         2.33         5.03        24.72         0.99 

$`AMP PEAK  3(1P31.1) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PX 
       10.45         1.51         9.60        12.56         8.28         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       24.33        54.90        21.53        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04         1.15        22.29 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        12.36        18.05        19.79        19.46        54.21 
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        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        10.49        13.15        22.16        13.84        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       17.59        12.07        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 
       17.46        18.97        15.68        14.14        19.63        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        16.44        16.77        27.95        23.77        16.80 
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        11.15         7.33        12.53         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        16.41        15.62        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        9.80        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
       80.02        65.36        84.89        98.56        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        2.43         5.56        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        24.69        68.22       102.90        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       81.34        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        46.06         4.08         0.89        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10        91.17         1.25         1.15        17.82 
TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
        1.64         1.51         0.76         0.03         4.67        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         6.87         4.14 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58         4.54         0.89         1.35         1.15         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        10.26        16.90         9.80 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
        9.63         2.96         8.65        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 
       86.70         6.02        12.43         6.74        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 
        0.72        16.64        32.45         8.71        10.98         5.19 

  AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE 
                         0.99                          0.03 
  AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE 
                        24.72                        158.83 
  AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE 
                        5.030                        16.685 
[1] "1.0 - 24.7 (5.0)"   "0.0 - 158.8 (16.7)"
[1] "hr="    "450000"
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     279       51       107        2        43
                               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                           279
  STAGE II                            0                            51
  STAGE III                           2                           107
  STAGE IV                            0                             2
  STAGE IVA                           2                            43
  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 139 165 162  21
D3V4, multiclass
    clus
vv   AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE
  T1                           1                           139
  T2                           1                           165
  T3                           3                           162
  T4                           0                            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"
D3V5, binary
                               cls
clus                              0   1
  AMP PEAK  3(1P31.1) MUTATED     1   4
  AMP PEAK  3(1P31.1) WILD-TYPE 222 218
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1P31.1) MUTATED      1    4
  AMP PEAK  3(1P31.1) WILD-TYPE  222  218
   clus
vv  AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE
  0                           1                           222
  1                           4                           218
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK  3(1P31.1) MUTATED     1   0   4
  AMP PEAK  3(1P31.1) WILD-TYPE 272   9 208
D3V6, multiclass
    clus
vv   AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE
  M0                           1                           272
  M1                           0                             9
  MX                           4                           208
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                               cls
clus                              0   1
  AMP PEAK  3(1P31.1) MUTATED     2   3
  AMP PEAK  3(1P31.1) WILD-TYPE 362 128
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1P31.1) MUTATED      2    3
  AMP PEAK  3(1P31.1) WILD-TYPE  362  128
        clus
vv       AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE
  FEMALE                           2                           362
  MALE                             3                           128
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK  3(1P31.1) MUTATED                1
  AMP PEAK  3(1P31.1) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK  3(1P31.1) MUTATED                                               3
  AMP PEAK  3(1P31.1) WILD-TYPE                                           350
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK  3(1P31.1) MUTATED                                                                        0
  AMP PEAK  3(1P31.1) WILD-TYPE                                                                     98
                               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                                                                  34
D3V8, 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                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            98
  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"
D3V9, binary
                               cls
clus                              0   1
  AMP PEAK  3(1P31.1) MUTATED     0   5
  AMP PEAK  3(1P31.1) WILD-TYPE  14 476
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1P31.1) MUTATED      0    5
  AMP PEAK  3(1P31.1) WILD-TYPE   14  476
     clus
vv    AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE
  NO                            0                            14
  YES                           5                           476
[1] 2 2
[1] FALSE
D3V10, binary
                               cls
clus                              0   1
  AMP PEAK  3(1P31.1) MUTATED     3   1
  AMP PEAK  3(1P31.1) WILD-TYPE 414  16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1P31.1) MUTATED      3    1
  AMP PEAK  3(1P31.1) WILD-TYPE  414   16
     clus
vv    AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE
  NO                            3                           414
  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          129                      16  324
                               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)                                      129
  MODERATE/ADVANCED (T4A)                            16
  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  3(1P31.1) MUTATED     4   0   0   1
  AMP PEAK  3(1P31.1) WILD-TYPE 374  51   4  29
D3V12, multiclass
    clus
vv   AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE
  R0                           4                           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"
D3V13, continuous
D3V14, binary
                               cls
clus                              0   1
  AMP PEAK  3(1P31.1) MUTATED     3   2
  AMP PEAK  3(1P31.1) WILD-TYPE 221 259
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1P31.1) MUTATED      3    2
  AMP PEAK  3(1P31.1) WILD-TYPE  221  259
            clus
vv           AMP PEAK  3(1P31.1) MUTATED AMP PEAK  3(1P31.1) WILD-TYPE
  MULTIFOCAL                           3                           221
  UNIFOCAL                             2                           259
[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    49
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(1P31.1) MUTATED                           0     4
  AMP PEAK  3(1P31.1) WILD-TYPE                        26   317
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                                                       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"
D3V17, binary
                               cls
clus                              0   1
  AMP PEAK  3(1P31.1) MUTATED     0   4
  AMP PEAK  3(1P31.1) WILD-TYPE  38 346
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1P31.1) MUTATED      0    4
  AMP PEAK  3(1P31.1) WILD-TYPE   38  346
                        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                           346
[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    25   2
  AMP PEAK  4(1Q31.2) WILD-TYPE 452  12
  AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE 
                           27                           464 
  AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE 
                            2                            12 
$`AMP PEAK  4(1Q31.2) MUTATED`
TCGA-BJ-A192 TCGA-BJ-A290 TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DJ-A13U 
        8.09        30.21        11.57        30.02        25.12        13.41 
TCGA-DO-A2HM TCGA-EL-A3GP TCGA-EL-A3GU TCGA-EL-A3H5 TCGA-EL-A3MZ TCGA-EL-A3T9 
        2.33         1.41       124.04        52.73        52.50         5.72 
TCGA-EL-A3ZO TCGA-EL-A4JX TCGA-EM-A3O3 TCGA-ET-A39P TCGA-ET-A3BT TCGA-FE-A231 
       47.38        45.96        14.50        58.72        24.72        31.59 
TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A40L TCGA-H2-A26U TCGA-IM-A3EB TCGA-IM-A3U2 
        0.99         1.51         6.58        17.00        48.92        10.26 
TCGA-J8-A3O1 TCGA-KS-A4IB TCGA-L6-A4EU 
       27.19        84.72         0.72 

$`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        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A28R 
       17.69        23.34        20.71        20.58         4.83         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
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        15.48        23.31        18.64         5.75 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
        6.48         0.03         3.45         6.35         7.82         6.18 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
        5.06         8.98         4.93         5.98         0.53         0.10 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
        0.20         0.23        11.38        10.68         0.10         0.39 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.10        20.22        15.42        36.46         5.98        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         4.27         3.22         2.76 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       17.26        14.07       137.88         3.39         8.71        25.35 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        5.52         8.78         8.42         8.12         9.34         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
        9.21         9.44         9.90         8.61        10.09         7.07 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       10.36        12.43        10.85        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        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 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3DZ 
       15.81        24.33        54.90        21.53        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
        1.45        74.30        45.40        33.47       108.36        39.32 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
       30.18       102.84        65.39        50.37        37.25       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        38.66 
TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3N2 
      139.00       131.15       108.66        57.63        17.52        12.16 
TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
      147.42       130.72       129.57        32.48       116.91        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
       41.29        95.38        66.90        82.82        77.36        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       31.50        50.33        53.06        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JZ TCGA-EL-A4K0 
        7.07        44.65        45.80        19.30        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        12.36        18.05        19.79        19.46        54.21 
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        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        10.49        13.15        22.16        13.84        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       17.59        12.07        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 
       17.46        18.97        15.68        14.14        19.63        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        16.44        16.77        27.95        23.77        16.80 
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-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       11.15         7.33        12.53         9.24        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        16.41        15.62        13.51        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39R 
       80.02        65.36        84.89        98.56        61.02        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        59.15        28.24         5.85         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
        5.56        38.30        42.25         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       69.24        59.87        43.50         0.30        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A232 
        2.14         4.01         1.94        73.74        59.70        44.25 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       102.90        66.77        81.34        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 
       46.06         4.08         0.89        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3R6 
       91.17         1.25         1.15        17.82         1.64         0.76 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
        0.03         4.67        16.57        18.08         0.30         0.76 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.06         6.87         4.14         4.54         0.89         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.15         1.68        12.53        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3ED TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       20.05        18.61        47.41        16.90         9.80         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O2 TCGA-J8-A3YD 
        2.96         8.65        17.23        43.17        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        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IC TCGA-KS-A4ID 
       12.43         6.74        32.45        87.39        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        40.37        21.83        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE 
                         0.72                          0.03 
  AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE 
                       124.04                        158.83 
  AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE 
                       24.720                        16.505 
[1] "0.7 - 124.0 (24.7)" "0.0 - 158.8 (16.5)"
[1] "hr=" "2.6"
D4V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK  4(1Q31.2) MUTATED         7        0        12        1         8
  AMP PEAK  4(1Q31.2) WILD-TYPE     273       51        97        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                           273
  STAGE II                            0                            51
  STAGE III                          12                            97
  STAGE IV                            1                             1
  STAGE IVA                           8                            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   4
  AMP PEAK  4(1Q31.2) WILD-TYPE 138 162 147  17
D4V4, multiclass
    clus
vv   AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE
  T1                           2                           138
  T2                           4                           162
  T3                          18                           147
  T4                           4                            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"
D4V5, binary
                               cls
clus                              0   1
  AMP PEAK  4(1Q31.2) MUTATED     5  21
  AMP PEAK  4(1Q31.2) WILD-TYPE 218 201
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(1Q31.2) MUTATED      5   21
  AMP PEAK  4(1Q31.2) WILD-TYPE  218  201
   clus
vv  AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE
  0                           5                           218
  1                          21                           201
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK  4(1Q31.2) MUTATED    13   0  15
  AMP PEAK  4(1Q31.2) WILD-TYPE 260   9 197
D4V6, multiclass
    clus
vv   AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE
  M0                          13                           260
  M1                           0                             9
  MX                          15                           197
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(1Q31.2) MUTATED    19   9
  AMP PEAK  4(1Q31.2) WILD-TYPE 345 122
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(1Q31.2) MUTATED     19    9
  AMP PEAK  4(1Q31.2) WILD-TYPE  345  122
        clus
vv       AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE
  FEMALE                          19                           345
  MALE                             9                           122
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK  4(1Q31.2) MUTATED                0
  AMP PEAK  4(1Q31.2) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK  4(1Q31.2) MUTATED                                              24
  AMP PEAK  4(1Q31.2) WILD-TYPE                                           329
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK  4(1Q31.2) MUTATED                                                                        0
  AMP PEAK  4(1Q31.2) WILD-TYPE                                                                     98
                               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                                                                  31
D4V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK  4(1Q31.2) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   24
  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                                                                                     9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    329
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V9, binary
                               cls
clus                              0   1
  AMP PEAK  4(1Q31.2) MUTATED     1  27
  AMP PEAK  4(1Q31.2) WILD-TYPE  13 454
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(1Q31.2) MUTATED      1   27
  AMP PEAK  4(1Q31.2) WILD-TYPE   13  454
     clus
vv    AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE
  NO                            1                            13
  YES                          27                           454
[1] 2 2
[1] FALSE
D4V10, binary
                               cls
clus                              0   1
  AMP PEAK  4(1Q31.2) MUTATED    25   1
  AMP PEAK  4(1Q31.2) WILD-TYPE 392  16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(1Q31.2) MUTATED     25    1
  AMP PEAK  4(1Q31.2) WILD-TYPE  392   16
     clus
vv    AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE
  NO                           25                           392
  YES                           1                            16
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK  4(1Q31.2) MUTATED             14                       3   10
  AMP PEAK  4(1Q31.2) WILD-TYPE          116                      13  318
                               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)                           3
  NONE                                             10
  VERY ADVANCED (T4B)                               1
                         clus
vv                        AMP PEAK  4(1Q31.2) WILD-TYPE
  MINIMAL (T3)                                      116
  MODERATE/ADVANCED (T4A)                            13
  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  4(1Q31.2) MUTATED    16   6   0   4
  AMP PEAK  4(1Q31.2) WILD-TYPE 362  45   4  26
D4V12, multiclass
    clus
vv   AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE
  R0                          16                           362
  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  19
  AMP PEAK  4(1Q31.2) WILD-TYPE 215 242
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(1Q31.2) MUTATED      9   19
  AMP PEAK  4(1Q31.2) WILD-TYPE  215  242
            clus
vv           AMP PEAK  4(1Q31.2) MUTATED AMP PEAK  4(1Q31.2) WILD-TYPE
  MULTIFOCAL                           9                           215
  UNIFOCAL                            19                           242
[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    48
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(1Q31.2) MUTATED                           4    21
  AMP PEAK  4(1Q31.2) WILD-TYPE                        22   300
D4V16, multiclass
                                  clus
vv                                 AMP PEAK  4(1Q31.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                     21
                                  clus
vv                                 AMP PEAK  4(1Q31.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       48
  BLACK OR AFRICAN AMERICAN                                   22
  WHITE                                                      300
[1] 4 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  19
  AMP PEAK  4(1Q31.2) WILD-TYPE  32 331
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(1Q31.2) MUTATED      6   19
  AMP PEAK  4(1Q31.2) WILD-TYPE   32  331
                        clus
vv                       AMP PEAK  4(1Q31.2) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                          19
                        clus
vv                       AMP PEAK  4(1Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                32
  NOT HISPANIC OR LATINO                           331
[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    24   3
  AMP PEAK  5(1Q43) WILD-TYPE 453  11
  AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE 
                         27                         464 
  AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE 
                          3                          11 
$`AMP PEAK  5(1Q43) MUTATED`
TCGA-BJ-A290 TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DJ-A13U TCGA-DJ-A1QE 
       30.21        11.57        30.02        25.12        13.41       100.01 
TCGA-DO-A2HM TCGA-EL-A3GP TCGA-EL-A3GU TCGA-EL-A3H5 TCGA-EL-A3MX TCGA-EL-A3MZ 
        2.33         1.41       124.04        52.73        57.63        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        58.72        24.72 
TCGA-FE-A231 TCGA-FY-A3NM TCGA-FY-A40L TCGA-H2-A26U TCGA-IM-A3EB TCGA-IM-A3U2 
       31.59         0.99         6.58        17.00        48.92        10.26 
TCGA-J8-A3O1 TCGA-KS-A4IB TCGA-L6-A4EU 
       27.19        84.72         0.72 

$`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        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
        1.22        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        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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         4.27         3.22 
TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        2.76        17.26        14.07       137.88         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QF 
       25.35        11.90        14.60         7.99        11.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        5.52         8.78         8.42         8.12         9.34         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
        9.21         9.44         9.90         8.61        10.09         7.07 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       10.36        12.43        10.85        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        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 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3DZ 
       15.81        24.33        54.90        21.53        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
        1.45        74.30        45.40        33.47       108.36        39.32 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
       30.18       102.84        65.39        50.37        37.25       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        38.66 
TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MY TCGA-EL-A3N2 TCGA-EL-A3N3 
      139.00       131.15       108.66        17.52        12.16       147.42 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      130.72       129.57        32.48       116.91        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
       95.38        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       50.33        53.06        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       44.65        45.80        19.30        37.94        31.04        19.59 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        33.60        28.73        41.13        37.78        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       13.32        11.87         8.71        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
       12.36        18.05        19.79        19.46        54.21        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        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       10.49        13.15        22.16        13.84        19.73        17.59 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       12.07        17.59        17.46        17.29        14.60        17.46 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       18.97        15.68        14.14        19.63        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       16.44        16.77        27.95        23.77        16.80        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        11.15 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33        12.53         9.24        13.91         7.82        11.51 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       16.41        15.62        13.51        12.79        70.65        16.90 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        9.01         4.83         8.61         8.38         9.80         5.03 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       37.87        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       29.49        54.05        22.09        12.26        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        98.56        61.02        57.11        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       59.15        28.24         5.85         4.18         2.43         5.56 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       38.30        42.25         2.37         4.50        80.81        69.24 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       59.87        43.50         0.30        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A232 TCGA-FE-A233 
        4.01         1.94        73.74        59.70        44.25        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       102.90        66.77        81.34        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        46.06 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.08         0.89        22.03         0.92        48.10        91.17 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25         1.15        17.82         1.64         1.51         0.76 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
        0.03         4.67        16.57        18.08         0.30         0.76 
TCGA-FY-A3WA TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
       17.06         6.87         4.14         4.54         0.89         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.15         1.68        12.53        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3ED TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       20.05        18.61        47.41        16.90         9.80         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O2 TCGA-J8-A3YD 
        2.96         8.65        17.23        43.17        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        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IC TCGA-KS-A4ID 
       12.43         6.74        32.45        87.39        35.28        33.24 
TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        40.37        21.83        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE 
                       0.72                        0.03 
  AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE 
                     124.04                      158.83 
  AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE 
                     27.190                      16.425 
[1] "0.7 - 124.0 (27.2)" "0.0 - 158.8 (16.4)"
[1] "hr=" "3.2"
D5V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK  5(1Q43) MUTATED         6        0        12        1         8
  AMP PEAK  5(1Q43) WILD-TYPE     274       51        97        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                         274
  STAGE II                          0                          51
  STAGE III                        12                          97
  STAGE IV                          1                           1
  STAGE IVA                         8                          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   5
  AMP PEAK  5(1Q43) WILD-TYPE 138 163 147  16
D5V4, multiclass
    clus
vv   AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE
  T1                         2                         138
  T2                         3                         163
  T3                        18                         147
  T4                         5                          16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
                             cls
clus                            0   1
  AMP PEAK  5(1Q43) MUTATED     6  21
  AMP PEAK  5(1Q43) WILD-TYPE 217 201
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(1Q43) MUTATED      6   21
  AMP PEAK  5(1Q43) WILD-TYPE  217  201
   clus
vv  AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE
  0                         6                         217
  1                        21                         201
[1] 2 2
[1] FALSE
                             vv
clus                           M0  M1  MX
  AMP PEAK  5(1Q43) MUTATED    13   1  14
  AMP PEAK  5(1Q43) WILD-TYPE 260   8 198
D5V6, multiclass
    clus
vv   AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE
  M0                        13                         260
  M1                         1                           8
  MX                        14                         198
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                             cls
clus                            0   1
  AMP PEAK  5(1Q43) MUTATED    20   8
  AMP PEAK  5(1Q43) WILD-TYPE 344 123
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(1Q43) MUTATED     20    8
  AMP PEAK  5(1Q43) WILD-TYPE  344  123
        clus
vv       AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE
  FEMALE                        20                         344
  MALE                           8                         123
[1] 2 2
[1] FALSE
                             vv
clus                          OTHER  SPECIFY
  AMP PEAK  5(1Q43) MUTATED                0
  AMP PEAK  5(1Q43) WILD-TYPE              9
                             vv
clus                          THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK  5(1Q43) MUTATED                                              24
  AMP PEAK  5(1Q43) WILD-TYPE                                           329
                             vv
clus                          THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK  5(1Q43) MUTATED                                                                        0
  AMP PEAK  5(1Q43) WILD-TYPE                                                                     98
                             vv
clus                          THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK  5(1Q43) MUTATED                                                                     4
  AMP PEAK  5(1Q43) WILD-TYPE                                                                  31
D5V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK  5(1Q43) MUTATED
  OTHER  SPECIFY                                                                                 0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                 24
  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                                                                                   9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  329
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          98
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, binary
                             cls
clus                            0   1
  AMP PEAK  5(1Q43) MUTATED     1  27
  AMP PEAK  5(1Q43) WILD-TYPE  13 454
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(1Q43) MUTATED      1   27
  AMP PEAK  5(1Q43) WILD-TYPE   13  454
     clus
vv    AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE
  NO                          1                          13
  YES                        27                         454
[1] 2 2
[1] FALSE
D5V10, binary
                             cls
clus                            0   1
  AMP PEAK  5(1Q43) MUTATED    25   1
  AMP PEAK  5(1Q43) WILD-TYPE 392  16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(1Q43) MUTATED     25    1
  AMP PEAK  5(1Q43) WILD-TYPE  392   16
     clus
vv    AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE
  NO                         25                         392
  YES                         1                          16
[1] 2 2
[1] FALSE
                             vv
clus                          MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK  5(1Q43) MUTATED             14                       3   10
  AMP PEAK  5(1Q43) WILD-TYPE          116                      13  318
                             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                         116
  MODERATE/ADVANCED (T4A)                         3                          13
  NONE                                           10                         318
  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    16   6   0   4
  AMP PEAK  5(1Q43) WILD-TYPE 362  45   4  26
D5V12, multiclass
    clus
vv   AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE
  R0                        16                         362
  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  20
  AMP PEAK  5(1Q43) WILD-TYPE 216 241
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(1Q43) MUTATED      8   20
  AMP PEAK  5(1Q43) WILD-TYPE  216  241
            clus
vv           AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE
  MULTIFOCAL                         8                         216
  UNIFOCAL                          20                         241
[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    48
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(1Q43) MUTATED                           4    21
  AMP PEAK  5(1Q43) WILD-TYPE                        22   300
D5V16, multiclass
                                  clus
vv                                 AMP PEAK  5(1Q43) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    1
  BLACK OR AFRICAN AMERICAN                                4
  WHITE                                                   21
                                  clus
vv                                 AMP PEAK  5(1Q43) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     48
  BLACK OR AFRICAN AMERICAN                                 22
  WHITE                                                    300
[1] 4 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  20
  AMP PEAK  5(1Q43) WILD-TYPE  33 330
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(1Q43) MUTATED      5   20
  AMP PEAK  5(1Q43) WILD-TYPE   33  330
                        clus
vv                       AMP PEAK  5(1Q43) MUTATED AMP PEAK  5(1Q43) WILD-TYPE
  HISPANIC OR LATINO                             5                          33
  NOT HISPANIC OR LATINO                        20                         330
[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 474  14
  AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE 
                            3                           488 
  AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE 
                            0                            14 
$`AMP PEAK  6(2P16.1) MUTATED`
TCGA-DJ-A4UQ TCGA-ET-A2MZ TCGA-ET-A39N 
       10.78        12.26        98.56 

$`AMP PEAK  6(2P16.1) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        5.52         8.78         8.42         8.12         9.34         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
        9.21         9.44         9.90         8.61        10.09         7.07 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       10.36        12.43        10.85        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        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 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
        1.45        74.30        45.40        33.47       108.36        39.32 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        30.18       102.84        65.39       124.04        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       37.25       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        38.66        52.73       139.00       131.15       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        12.16       147.42       130.72 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       116.91        98.24        41.29        95.38 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       50.33        53.06        47.38        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       37.78        29.95        13.32        11.87         8.71        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        12.36        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       54.21        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        11.74        11.15        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       16.44        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
       12.30        15.19        10.49        13.15        22.16        13.84 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        17.59        12.07        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        17.46        18.97        15.68        14.14        19.63 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        16.44        16.77        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        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        11.15         7.33        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       13.91         7.82        11.51        16.41        15.62        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        70.65        16.90         9.01         4.83         8.61 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
        8.38         9.80         5.03        37.87        12.72         0.95 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       47.47        48.20        29.69        32.35        14.79        12.33 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       14.79        27.09        18.38        29.49        54.05        22.09 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
       71.01        80.02        65.36        84.89        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        2.43         5.56        24.72        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       59.70        31.59        44.25        24.69        68.22       102.90 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77        81.34        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        46.06         4.08         0.89 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10        91.17         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       17.82         1.64         0.99         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
        4.67        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 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
        1.15         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        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90         9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74 
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         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE 
                        10.78                          0.03 
  AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE 
                        98.56                        158.83 
  AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE 
                       12.260                        16.605 
[1] "10.8 - 98.6 (12.3)" "0.0 - 158.8 (16.6)"
[1] "hr="     "9200000"
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     278       51       109        2        44
                               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                           278
  STAGE II                            0                            51
  STAGE III                           0                           109
  STAGE IV                            0                             2
  STAGE IVA                           1                            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  6(2P16.1) MUTATED     1   0   2   0
  AMP PEAK  6(2P16.1) WILD-TYPE 139 166 163  21
D6V4, multiclass
    clus
vv   AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE
  T1                           1                           139
  T2                           0                           166
  T3                           2                           163
  T4                           0                            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"
D6V5, binary
                               cls
clus                              0   1
  AMP PEAK  6(2P16.1) MUTATED     1   1
  AMP PEAK  6(2P16.1) WILD-TYPE 222 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(2P16.1) MUTATED      1    1
  AMP PEAK  6(2P16.1) WILD-TYPE  222  221
   clus
vv  AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE
  0                           1                           222
  1                           1                           221
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK  6(2P16.1) MUTATED     1   0   2
  AMP PEAK  6(2P16.1) WILD-TYPE 272   9 210
D6V6, multiclass
    clus
vv   AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE
  M0                           1                           272
  M1                           0                             9
  MX                           2                           210
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                               cls
clus                              0   1
  AMP PEAK  6(2P16.1) MUTATED     1   2
  AMP PEAK  6(2P16.1) WILD-TYPE 363 129
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(2P16.1) MUTATED      1    2
  AMP PEAK  6(2P16.1) WILD-TYPE  363  129
        clus
vv       AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE
  FEMALE                           1                           363
  MALE                             2                           129
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK  6(2P16.1) MUTATED                1
  AMP PEAK  6(2P16.1) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK  6(2P16.1) MUTATED                                               2
  AMP PEAK  6(2P16.1) WILD-TYPE                                           351
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK  6(2P16.1) MUTATED                                                                        0
  AMP PEAK  6(2P16.1) WILD-TYPE                                                                     98
                               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                                                                  35
D6V8, 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                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    351
  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"
D6V9, binary
                               cls
clus                              0   1
  AMP PEAK  6(2P16.1) MUTATED     0   3
  AMP PEAK  6(2P16.1) WILD-TYPE  14 478
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(2P16.1) MUTATED      0    3
  AMP PEAK  6(2P16.1) WILD-TYPE   14  478
     clus
vv    AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE
  NO                            0                            14
  YES                           3                           478
[1] 2 2
[1] FALSE
D6V10, binary
                               cls
clus                              0   1
  AMP PEAK  6(2P16.1) MUTATED     3   0
  AMP PEAK  6(2P16.1) WILD-TYPE 414  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(2P16.1) MUTATED      3    0
  AMP PEAK  6(2P16.1) WILD-TYPE  414   17
     clus
vv    AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE
  NO                            3                           414
  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          129                      16  326
                               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)                                      129
  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
  AMP PEAK  6(2P16.1) MUTATED     2   0   0   1
  AMP PEAK  6(2P16.1) WILD-TYPE 376  51   4  29
D6V12, multiclass
    clus
vv   AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE
  R0                           2                           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"
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                           389 
                   TCGA-BJ-A0Z0                    TCGA-BJ-A0Z3 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A0Z9                    TCGA-BJ-A0ZA 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A0ZB                    TCGA-BJ-A0ZH 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A0ZJ                    TCGA-BJ-A18Y 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A18Z                    TCGA-BJ-A190 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A191                    TCGA-BJ-A28R 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A28T                    TCGA-BJ-A28W 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A28X                    TCGA-BJ-A28Z 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A290                    TCGA-BJ-A291 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A2N8                    TCGA-BJ-A2N9 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A2NA                    TCGA-BJ-A3EZ 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A3PR                    TCGA-BJ-A3PU 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A45C                    TCGA-BJ-A45D 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A45E                    TCGA-BJ-A45G 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A45I                    TCGA-BJ-A45J 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A45K                    TCGA-BJ-A4O8 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-BJ-A4O9                    TCGA-CE-A13K 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-CE-A3MD                    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-A13P                    TCGA-DJ-A13R 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A13T                    TCGA-DJ-A13U 
"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-A3VJ                    TCGA-DJ-A3VL 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A4UL                    TCGA-DJ-A4UR 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A4UW                    TCGA-DJ-A4V2 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DJ-A4V5                    TCGA-DO-A1K0 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-DO-A2HM                    TCGA-E3-A3DY 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-E3-A3DZ                    TCGA-E3-A3E0 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-E3-A3E1                    TCGA-E3-A3E2 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-E3-A3E3                    TCGA-E3-A3E5 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-E8-A242                    TCGA-E8-A2EA 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-E8-A2JQ                    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-A3ZN 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A3ZO                    TCGA-EL-A3ZP 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A3ZS                    TCGA-EL-A4JV 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A4JW                    TCGA-EL-A4JX 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A4JZ                    TCGA-EL-A4K0 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A4K1                    TCGA-EL-A4K2 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A4K4                    TCGA-EL-A4K6 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A4K7                    TCGA-EL-A4KD 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EL-A4KG                    TCGA-EL-A4KI 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A1CS                    TCGA-EM-A1CT 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A1CU                    TCGA-EM-A1CV 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A1CW                    TCGA-EM-A1YA 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A1YB                    TCGA-EM-A1YC 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A1YD                    TCGA-EM-A1YE 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A22I                    TCGA-EM-A22J 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A22K                    TCGA-EM-A22L 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A22M                    TCGA-EM-A22N 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A22O                    TCGA-EM-A22P 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A22Q                    TCGA-EM-A2CK 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A2CN                    TCGA-EM-A2CP 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A2CQ                    TCGA-EM-A2CS 
"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-A2OW 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A2OX                    TCGA-EM-A2OY 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A2OZ                    TCGA-EM-A2P0 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A2P1                    TCGA-EM-A2P2 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A2P3                    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-A3FL                    TCGA-EM-A3FM 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A3FN                    TCGA-EM-A3FO 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A3FP                    TCGA-EM-A3FQ 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A3FR                    TCGA-EM-A3O3 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A3O7                    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-A3SY                    TCGA-EM-A3SZ 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A4FF                    TCGA-EM-A4FH 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A4FK                    TCGA-EM-A4FM 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A4FN                    TCGA-EM-A4FO 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A4FQ                    TCGA-EM-A4FR 
"AMP PEAK  6(2P16.1) WILD-TYPE" "AMP PEAK  6(2P16.1) WILD-TYPE" 
                   TCGA-EM-A4FU                    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 223 259
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(2P16.1) MUTATED      1    2
  AMP PEAK  6(2P16.1) WILD-TYPE  223  259
            clus
vv           AMP PEAK  6(2P16.1) MUTATED AMP PEAK  6(2P16.1) WILD-TYPE
  MULTIFOCAL                           1                           223
  UNIFOCAL                             2                           259
[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    48
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(2P16.1) MUTATED                           0     2
  AMP PEAK  6(2P16.1) WILD-TYPE                        26   319
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                                                       48
  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"
D6V17, binary
                               cls
clus                              0   1
  AMP PEAK  6(2P16.1) MUTATED     0   3
  AMP PEAK  6(2P16.1) WILD-TYPE  38 347
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(2P16.1) MUTATED      0    3
  AMP PEAK  6(2P16.1) WILD-TYPE   38  347
                        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                           347
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  9(2Q37.2) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  9(2Q37.2) MUTATED     3   0
  AMP PEAK  9(2Q37.2) WILD-TYPE 474  14
  AMP PEAK  9(2Q37.2) MUTATED AMP PEAK  9(2Q37.2) WILD-TYPE 
                            3                           488 
  AMP PEAK  9(2Q37.2) MUTATED AMP PEAK  9(2Q37.2) WILD-TYPE 
                            0                            14 
$`AMP PEAK  9(2Q37.2) MUTATED`
TCGA-BJ-A290 TCGA-DJ-A13M TCGA-FK-A3SD 
       30.21        17.26         0.89 

$`AMP PEAK  9(2Q37.2) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
        1.22        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        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A13O TCGA-DJ-A13P 
       25.12         4.27         3.22         2.76        14.07       137.88 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
        3.39         8.71        25.35        13.41        11.90        14.60 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        7.99        11.01       100.01        18.51        13.12         7.99 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96         7.20         1.45         8.88         1.02         5.95 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS 
       10.09         7.99         5.33         8.48        10.45         1.51 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY 
        9.60        12.56         8.28         7.69         5.52         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.42         8.12         9.34         6.77         9.21         9.44 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
        9.90         8.61        10.09         7.07        10.36        12.43 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        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        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04         1.15        22.29 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        12.36        18.05        19.79        19.46        54.21 
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        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        10.49        13.15        22.16        13.84        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       17.59        12.07        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 
       17.46        18.97        15.68        14.14        19.63        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        16.44        16.77        27.95        23.77        16.80 
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        11.15         7.33        12.53         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        16.41        15.62        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        9.80         5.03        37.87        12.72         0.95        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
       71.01        80.02        65.36        84.89        98.56        61.02 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       58.72        57.11        55.10        59.15        28.24         5.85 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
        4.18         2.43         5.56        24.72        38.30        42.25 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
        2.37         4.50        80.81        69.24        59.87        43.50 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
        0.30        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        59.70        31.59        44.25        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      102.90        66.77        81.34        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        46.06         4.08 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10        91.17         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       17.82         1.64         0.99         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
        4.67        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 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
        1.15         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        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90         9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74 
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         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  AMP PEAK  9(2Q37.2) MUTATED AMP PEAK  9(2Q37.2) WILD-TYPE 
                         0.89                          0.03 
  AMP PEAK  9(2Q37.2) MUTATED AMP PEAK  9(2Q37.2) WILD-TYPE 
                        30.21                        158.83 
  AMP PEAK  9(2Q37.2) MUTATED AMP PEAK  9(2Q37.2) WILD-TYPE 
                        17.26                         16.57 
[1] "0.9 - 30.2 (17.3)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "1200000"
D7V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK  9(2Q37.2) MUTATED         2        0         1        0         0
  AMP PEAK  9(2Q37.2) WILD-TYPE     278       51       108        2        45
                               vv
clus                            STAGE IVC
  AMP PEAK  9(2Q37.2) MUTATED           0
  AMP PEAK  9(2Q37.2) WILD-TYPE         6
D7V3, multiclass
           clus
vv          AMP PEAK  9(2Q37.2) MUTATED AMP PEAK  9(2Q37.2) WILD-TYPE
  STAGE I                             2                           278
  STAGE II                            0                            51
  STAGE III                           1                           108
  STAGE IV                            0                             2
  STAGE IVA                           0                            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  9(2Q37.2) MUTATED     2   0   1   0
  AMP PEAK  9(2Q37.2) WILD-TYPE 138 166 164  21
D7V4, multiclass
    clus
vv   AMP PEAK  9(2Q37.2) MUTATED AMP PEAK  9(2Q37.2) WILD-TYPE
  T1                           2                           138
  T2                           0                           166
  T3                           1                           164
  T4                           0                            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"
D7V5, binary
                               cls
clus                              0   1
  AMP PEAK  9(2Q37.2) MUTATED     2   1
  AMP PEAK  9(2Q37.2) WILD-TYPE 221 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(2Q37.2) MUTATED      2    1
  AMP PEAK  9(2Q37.2) WILD-TYPE  221  221
   clus
vv  AMP PEAK  9(2Q37.2) MUTATED AMP PEAK  9(2Q37.2) WILD-TYPE
  0                           2                           221
  1                           1                           221
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK  9(2Q37.2) MUTATED     3   0   0
  AMP PEAK  9(2Q37.2) WILD-TYPE 270   9 212
D7V6, multiclass
    clus
vv   AMP PEAK  9(2Q37.2) MUTATED AMP PEAK  9(2Q37.2) WILD-TYPE
  M0                           3                           270
  M1                           0                             9
  MX                           0                           212
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                               cls
clus                              0   1
  AMP PEAK  9(2Q37.2) MUTATED     2   1
  AMP PEAK  9(2Q37.2) WILD-TYPE 362 130
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(2Q37.2) MUTATED      2    1
  AMP PEAK  9(2Q37.2) WILD-TYPE  362  130
        clus
vv       AMP PEAK  9(2Q37.2) MUTATED AMP PEAK  9(2Q37.2) WILD-TYPE
  FEMALE                           2                           362
  MALE                             1                           130
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK  9(2Q37.2) MUTATED                0
  AMP PEAK  9(2Q37.2) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK  9(2Q37.2) MUTATED                                               1
  AMP PEAK  9(2Q37.2) WILD-TYPE                                           352
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK  9(2Q37.2) MUTATED                                                                        1
  AMP PEAK  9(2Q37.2) WILD-TYPE                                                                     97
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK  9(2Q37.2) MUTATED                                                                     1
  AMP PEAK  9(2Q37.2) WILD-TYPE                                                                  34
D7V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK  9(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  9(2Q37.2) WILD-TYPE
  OTHER  SPECIFY                                                                                     9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            97
  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"
D7V9, binary
                               cls
clus                              0   1
  AMP PEAK  9(2Q37.2) MUTATED     0   3
  AMP PEAK  9(2Q37.2) WILD-TYPE  14 478
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(2Q37.2) MUTATED      0    3
  AMP PEAK  9(2Q37.2) WILD-TYPE   14  478
     clus
vv    AMP PEAK  9(2Q37.2) MUTATED AMP PEAK  9(2Q37.2) WILD-TYPE
  NO                            0                            14
  YES                           3                           478
[1] 2 2
[1] FALSE
D7V10, binary
                               cls
clus                              0   1
  AMP PEAK  9(2Q37.2) MUTATED     2   0
  AMP PEAK  9(2Q37.2) WILD-TYPE 415  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(2Q37.2) MUTATED      2    0
  AMP PEAK  9(2Q37.2) WILD-TYPE  415   17
     clus
vv    AMP PEAK  9(2Q37.2) MUTATED AMP PEAK  9(2Q37.2) WILD-TYPE
  NO                            2                           415
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK  9(2Q37.2) MUTATED              1                       0    1
  AMP PEAK  9(2Q37.2) WILD-TYPE          129                      16  327
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK  9(2Q37.2) MUTATED                     0
  AMP PEAK  9(2Q37.2) WILD-TYPE                   1
D7V11, multiclass
[1] "Remove cluster labels:"      "AMP PEAK  9(2Q37.2) MUTATED"
clus
  AMP PEAK  9(2Q37.2) MUTATED AMP PEAK  9(2Q37.2) WILD-TYPE 
                            2                           473 
                   TCGA-BJ-A0YZ                    TCGA-BJ-A0Z0 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0Z2                    TCGA-BJ-A0Z3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0Z9                    TCGA-BJ-A0ZA 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0ZB                    TCGA-BJ-A0ZC 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0ZE                    TCGA-BJ-A0ZG 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0ZH                    TCGA-BJ-A0ZJ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A18Y                    TCGA-BJ-A18Z 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A190                    TCGA-BJ-A191 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A192                    TCGA-BJ-A28X 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A28Z                    TCGA-BJ-A2N7 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A2N9                    TCGA-BJ-A2NA 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A3EZ                    TCGA-BJ-A3F0 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A3PR                    TCGA-BJ-A3PU 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A45C                    TCGA-BJ-A45D 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A45G                    TCGA-BJ-A45H 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A45I                    TCGA-BJ-A45K 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A4O8                    TCGA-BJ-A4O9 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A13K                    TCGA-CE-A27D 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A3MD                    TCGA-CE-A3ME 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A481                    TCGA-CE-A482 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A483                    TCGA-CE-A484 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A485                    TCGA-DE-A0XZ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A0Y2                    TCGA-DE-A2OL 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A3KN                    TCGA-DE-A4M8 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A4M9                    TCGA-DE-A4MA 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A4MB                    TCGA-DE-A4MC 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A4MD                    TCGA-DE-A69J 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A69K                    TCGA-DJ-A13O 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13P                    TCGA-DJ-A13R 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13S                    TCGA-DJ-A13T 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13U                    TCGA-DJ-A13V 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13W                    TCGA-DJ-A13X 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QD                    TCGA-DJ-A1QE 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QF                    TCGA-DJ-A1QG 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QH                    TCGA-DJ-A1QI 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QL                    TCGA-DJ-A1QM 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QN                    TCGA-DJ-A1QO 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QQ                    TCGA-DJ-A2PN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PO                    TCGA-DJ-A2PP 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PQ                    TCGA-DJ-A2PR 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PS                    TCGA-DJ-A2PT 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PU                    TCGA-DJ-A2PV 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PW                    TCGA-DJ-A2PX 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PY                    TCGA-DJ-A2PZ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q0                    TCGA-DJ-A2Q1 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q2                    TCGA-DJ-A2Q3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q4                    TCGA-DJ-A2Q5 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q6                    TCGA-DJ-A2Q7 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q8                    TCGA-DJ-A2Q9 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2QA                    TCGA-DJ-A2QB 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2QC                    TCGA-DJ-A3UK 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UM                    TCGA-DJ-A3UN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UO                    TCGA-DJ-A3UP 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UQ                    TCGA-DJ-A3UR 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3US                    TCGA-DJ-A3UT 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UU                    TCGA-DJ-A3UW 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UX                    TCGA-DJ-A3UY 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UZ                    TCGA-DJ-A3V0 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V2                    TCGA-DJ-A3V3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V4                    TCGA-DJ-A3V5 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V7                    TCGA-DJ-A3V8 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V9                    TCGA-DJ-A3VA 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VB                    TCGA-DJ-A3VD 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VE                    TCGA-DJ-A3VF 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VG                    TCGA-DJ-A3VJ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VL                    TCGA-DJ-A3VM 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4UL                    TCGA-DJ-A4UQ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4UR                    TCGA-DJ-A4UT 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4UW                    TCGA-DJ-A4V0 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4V2                    TCGA-DJ-A4V4 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4V5                    TCGA-DO-A1JZ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DO-A1K0                    TCGA-DO-A2HM 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E3-A3DY                    TCGA-E3-A3DZ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E3-A3E0                    TCGA-E3-A3E1 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E3-A3E2                    TCGA-E3-A3E3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E3-A3E5                    TCGA-E8-A242 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A2EA                    TCGA-E8-A2JQ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A3X7                    TCGA-E8-A413 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A414                    TCGA-E8-A415 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A416                    TCGA-E8-A417 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A418                    TCGA-E8-A419 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A432                    TCGA-E8-A433 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A434                    TCGA-E8-A436 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A437                    TCGA-E8-A438 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A44K                    TCGA-E8-A44M 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CL                    TCGA-EL-A3CM 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CN                    TCGA-EL-A3CO 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CP                    TCGA-EL-A3CR 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CS                    TCGA-EL-A3CT 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CU                    TCGA-EL-A3CV 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CW                    TCGA-EL-A3CX 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CY                    TCGA-EL-A3CZ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3D0                    TCGA-EL-A3D1 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3D4                    TCGA-EL-A3D5 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3D6                    TCGA-EL-A3GO 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GP                    TCGA-EL-A3GQ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GR                    TCGA-EL-A3GS 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GU                    TCGA-EL-A3GV 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GW                    TCGA-EL-A3GX 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GY                    TCGA-EL-A3GZ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3H1                    TCGA-EL-A3H2 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3H3                    TCGA-EL-A3H4 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3H5                    TCGA-EL-A3H7 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3H8                    TCGA-EL-A3MW 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3MX                    TCGA-EL-A3MY 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3MZ                    TCGA-EL-A3N2 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3N3                    TCGA-EL-A3T0 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3T1                    TCGA-EL-A3T2 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3T3                    TCGA-EL-A3T6 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3T7                    TCGA-EL-A3T8 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3T9                    TCGA-EL-A3TA 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3TB                    TCGA-EL-A3ZG 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZH                    TCGA-EL-A3ZK 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZL                    TCGA-EL-A3ZN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZO                    TCGA-EL-A3ZP 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZQ                    TCGA-EL-A3ZR 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZS                    TCGA-EL-A3ZT 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4JV                    TCGA-EL-A4JW 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4JX                    TCGA-EL-A4JZ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4K0                    TCGA-EL-A4K1 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4K2                    TCGA-EL-A4K4 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4K6                    TCGA-EL-A4K7 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4K9                    TCGA-EL-A4KD 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4KG                    TCGA-EL-A4KH 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4KI                    TCGA-EM-A1CS 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1CT                    TCGA-EM-A1CU 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1CV                    TCGA-EM-A1CW 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1YA                    TCGA-EM-A1YB 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1YC                    TCGA-EM-A1YD 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1YE                    TCGA-EM-A22I 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22J                    TCGA-EM-A22K 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22L                    TCGA-EM-A22M 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22N                    TCGA-EM-A22O 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22P                    TCGA-EM-A22Q 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CJ                    TCGA-EM-A2CK 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CL                    TCGA-EM-A2CN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CO                    TCGA-EM-A2CP 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CQ                    TCGA-EM-A2CS 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CT                    TCGA-EM-A2CU 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2OV                    TCGA-EM-A2OW 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2OX                    TCGA-EM-A2OY 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2OZ                    TCGA-EM-A2P0 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2P1                    TCGA-EM-A2P2 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2P3                    TCGA-EM-A3AI 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AJ                    TCGA-EM-A3AK 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AL                    TCGA-EM-A3AN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AO                    TCGA-EM-A3AP 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AQ                    TCGA-EM-A3AR 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FJ                    TCGA-EM-A3FK 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FL                    TCGA-EM-A3FM 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FN                    TCGA-EM-A3FO 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FP                    TCGA-EM-A3FQ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FR                    TCGA-EM-A3O3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3O6                    TCGA-EM-A3O7 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3O8                    TCGA-EM-A3O9 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3OA                    TCGA-EM-A3OB 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3ST                    TCGA-EM-A3SU 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3SX                    TCGA-EM-A3SY 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3SZ                    TCGA-EM-A4FF 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FH                    TCGA-EM-A4FK 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FM                    TCGA-EM-A4FN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FO                    TCGA-EM-A4FQ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FR                    TCGA-EM-A4FU 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FV                    TCGA-EM-A4G1 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25G                    TCGA-ET-A25I 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25J                    TCGA-ET-A25K 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25L                    TCGA-ET-A25M 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25N                    TCGA-ET-A25O 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25P                    TCGA-ET-A25R 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A2MX                    TCGA-ET-A2MY 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A2MZ                    TCGA-ET-A2N0 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A2N1                    TCGA-ET-A2N3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A2N4                    TCGA-ET-A2N5 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39I                    TCGA-ET-A39J 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39K                    TCGA-ET-A39L 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39M                    TCGA-ET-A39N 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39O                    TCGA-ET-A39P 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39R                    TCGA-ET-A39S 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39T                    TCGA-ET-A3BN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BO                    TCGA-ET-A3BP 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BQ                    TCGA-ET-A3BS 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BT                    TCGA-ET-A3BU 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BV                    TCGA-ET-A3BW 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BX                    TCGA-ET-A3DO 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3DP                    TCGA-ET-A3DQ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3DR                    TCGA-ET-A3DS 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3DT                    TCGA-ET-A3DU 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3DV                    TCGA-ET-A3DW 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A40P                    TCGA-ET-A40Q 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A40R                    TCGA-ET-A40S 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A40T                    TCGA-ET-A4KN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A4KQ                    TCGA-FE-A22Z 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A230                    TCGA-FE-A231 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A232                    TCGA-FE-A233 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A234                    TCGA-FE-A235 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A236                    TCGA-FE-A237 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A238                    TCGA-FE-A239 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A23A                    TCGA-FE-A3PA 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A3PB                    TCGA-FE-A3PC 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A3PD                    TCGA-FK-A3S3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FK-A3SB                    TCGA-FK-A3SE 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FK-A3SG                    TCGA-FK-A3SH 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FK-A4UB                    TCGA-FY-A2QD 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3BL                    TCGA-FY-A3I4 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3I5                    TCGA-FY-A3NM 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3NN                    TCGA-FY-A3ON 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3R6                    TCGA-FY-A3R7 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3R8                    TCGA-FY-A3R9 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3RA                    TCGA-FY-A3TY 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3W9                    TCGA-FY-A3WA 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3YR                    TCGA-FY-A40K 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A40L                    TCGA-FY-A40M 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A40N                    TCGA-FY-A4B0 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A4B3                    TCGA-FY-A4B4 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A76V                    TCGA-GE-A2C6 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-H2-A26U                    TCGA-H2-A2K9 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-H2-A3RH                    TCGA-H2-A3RI 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-H2-A421                    TCGA-H2-A422 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A3EB                    TCGA-IM-A3ED 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A3U2                    TCGA-IM-A3U3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A41Y                    TCGA-IM-A41Z 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A420                    TCGA-IM-A4EB 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3NZ                    TCGA-J8-A3O0 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3O1                    TCGA-J8-A3O2 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3YD                    TCGA-J8-A3YE 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3YF                    TCGA-J8-A3YG 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3YH                    TCGA-J8-A42S 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A4HW                    TCGA-J8-A4HY 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A41F                    TCGA-KS-A41I 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A41J                    TCGA-KS-A41L 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4I1                    TCGA-KS-A4I5 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4I7                    TCGA-KS-A4I9 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4IB                    TCGA-KS-A4IC 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4ID                    TCGA-L6-A4EP 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-L6-A4EQ                    TCGA-L6-A4ET 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-L6-A4EU                    TCGA-MK-A4N7 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-QD-A8IV 
"AMP PEAK  9(2Q37.2) WILD-TYPE" 
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  9(2Q37.2) MUTATED     2   0   0   0
  AMP PEAK  9(2Q37.2) WILD-TYPE 376  51   4  30
D7V12, multiclass
[1] "Remove cluster labels:"      "AMP PEAK  9(2Q37.2) MUTATED"
clus
  AMP PEAK  9(2Q37.2) MUTATED AMP PEAK  9(2Q37.2) WILD-TYPE 
                            2                           461 
                   TCGA-BJ-A0YZ                    TCGA-BJ-A0Z0 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0Z2                    TCGA-BJ-A0Z3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0Z9                    TCGA-BJ-A0ZA 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0ZB                    TCGA-BJ-A0ZC 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0ZE                    TCGA-BJ-A0ZG 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0ZH                    TCGA-BJ-A0ZJ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A18Y                    TCGA-BJ-A18Z 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A190                    TCGA-BJ-A191 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A192                    TCGA-BJ-A28X 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A2N7                    TCGA-BJ-A2N9 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A2NA                    TCGA-BJ-A2P4 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A3EZ                    TCGA-BJ-A3F0 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A3PR                    TCGA-BJ-A3PU 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A45I                    TCGA-BJ-A4O8 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A13K                    TCGA-CE-A27D 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A3MD                    TCGA-CE-A3ME 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A481                    TCGA-CE-A482 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A483                    TCGA-CE-A484 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A485                    TCGA-DE-A0XZ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A0Y2                    TCGA-DE-A0Y3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A2OL                    TCGA-DE-A3KN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A4M8                    TCGA-DE-A4M9 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A4MA                    TCGA-DE-A4MB 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A4MC                    TCGA-DE-A4MD 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A69J                    TCGA-DE-A69K 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A7U5                    TCGA-DJ-A13O 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13P                    TCGA-DJ-A13R 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13S                    TCGA-DJ-A13T 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13U                    TCGA-DJ-A13V 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13W                    TCGA-DJ-A13X 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QD                    TCGA-DJ-A1QE 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QF                    TCGA-DJ-A1QG 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QH                    TCGA-DJ-A1QI 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QL                    TCGA-DJ-A1QM 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QN                    TCGA-DJ-A1QO 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QQ                    TCGA-DJ-A2PN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PO                    TCGA-DJ-A2PP 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PQ                    TCGA-DJ-A2PR 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PS                    TCGA-DJ-A2PT 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PU                    TCGA-DJ-A2PV 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PW                    TCGA-DJ-A2PX 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PY                    TCGA-DJ-A2PZ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q0                    TCGA-DJ-A2Q1 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q2                    TCGA-DJ-A2Q3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q4                    TCGA-DJ-A2Q5 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q6                    TCGA-DJ-A2Q7 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q8                    TCGA-DJ-A2Q9 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2QA                    TCGA-DJ-A2QB 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2QC                    TCGA-DJ-A3UK 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UM                    TCGA-DJ-A3UN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UO                    TCGA-DJ-A3UP 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UQ                    TCGA-DJ-A3UR 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3US                    TCGA-DJ-A3UT 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UU                    TCGA-DJ-A3UW 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UX                    TCGA-DJ-A3UY 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UZ                    TCGA-DJ-A3V0 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V2                    TCGA-DJ-A3V3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V4                    TCGA-DJ-A3V5 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V7                    TCGA-DJ-A3V8 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V9                    TCGA-DJ-A3VA 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VB                    TCGA-DJ-A3VD 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VE                    TCGA-DJ-A3VF 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VG                    TCGA-DJ-A3VJ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VL                    TCGA-DJ-A3VM 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4UL                    TCGA-DJ-A4UQ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4UR                    TCGA-DJ-A4UT 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4UW                    TCGA-DJ-A4V0 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4V2                    TCGA-DJ-A4V4 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4V5                    TCGA-DO-A1JZ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DO-A1K0                    TCGA-DO-A2HM 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E3-A3DY                    TCGA-E3-A3DZ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E3-A3E0                    TCGA-E3-A3E1 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E3-A3E2                    TCGA-E3-A3E3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E3-A3E5                    TCGA-E8-A242 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A2EA                    TCGA-E8-A3X7 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A413                    TCGA-E8-A414 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A415                    TCGA-E8-A416 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A417                    TCGA-E8-A418 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A419                    TCGA-E8-A432 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A433                    TCGA-E8-A434 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A436                    TCGA-E8-A437 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A438                    TCGA-E8-A44K 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A44M                    TCGA-EL-A3CL 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CM                    TCGA-EL-A3CN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CO                    TCGA-EL-A3CP 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CR                    TCGA-EL-A3CS 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CT                    TCGA-EL-A3CU 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CV                    TCGA-EL-A3CW 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CX                    TCGA-EL-A3CY 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CZ                    TCGA-EL-A3D0 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3D1                    TCGA-EL-A3D4 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3D5                    TCGA-EL-A3D6 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GO                    TCGA-EL-A3GP 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GQ                    TCGA-EL-A3GR 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GS                    TCGA-EL-A3GU 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GV                    TCGA-EL-A3GW 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GX                    TCGA-EL-A3GY 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GZ                    TCGA-EL-A3H1 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3H2                    TCGA-EL-A3H3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3H4                    TCGA-EL-A3H5 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3H7                    TCGA-EL-A3H8 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3MW                    TCGA-EL-A3MX 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3MY                    TCGA-EL-A3MZ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3N2                    TCGA-EL-A3N3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3T0                    TCGA-EL-A3T1 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3T2                    TCGA-EL-A3T3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3T6                    TCGA-EL-A3T7 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3T8                    TCGA-EL-A3T9 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3TA                    TCGA-EL-A3TB 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZG                    TCGA-EL-A3ZH 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZK                    TCGA-EL-A3ZL 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZN                    TCGA-EL-A3ZO 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZP                    TCGA-EL-A3ZQ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZR                    TCGA-EL-A3ZS 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZT                    TCGA-EL-A4JV 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4JW                    TCGA-EL-A4JX 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4JZ                    TCGA-EL-A4K0 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4K1                    TCGA-EL-A4K2 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4K4                    TCGA-EL-A4K6 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4K7                    TCGA-EL-A4K9 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4KD                    TCGA-EL-A4KG 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4KH                    TCGA-EL-A4KI 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1CS                    TCGA-EM-A1CW 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1YA                    TCGA-EM-A1YB 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1YC                    TCGA-EM-A1YD 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1YE                    TCGA-EM-A22I 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22J                    TCGA-EM-A22K 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22L                    TCGA-EM-A22M 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22N                    TCGA-EM-A22O 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22P                    TCGA-EM-A22Q 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CJ                    TCGA-EM-A2CK 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CL                    TCGA-EM-A2CN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CO                    TCGA-EM-A2CP 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CQ                    TCGA-EM-A2CS 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CT                    TCGA-EM-A2CU 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2OV                    TCGA-EM-A2OW 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2OX                    TCGA-EM-A2OY 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2OZ                    TCGA-EM-A2P0 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2P1                    TCGA-EM-A2P2 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2P3                    TCGA-EM-A3AI 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AJ                    TCGA-EM-A3AK 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AL                    TCGA-EM-A3AN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AO                    TCGA-EM-A3AP 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AQ                    TCGA-EM-A3AR 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FJ                    TCGA-EM-A3FK 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FL                    TCGA-EM-A3FM 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FN                    TCGA-EM-A3FO 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FP                    TCGA-EM-A3FQ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FR                    TCGA-EM-A3O3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3O6                    TCGA-EM-A3O7 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3O8                    TCGA-EM-A3O9 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3OA                    TCGA-EM-A3OB 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3ST                    TCGA-EM-A3SU 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3SX                    TCGA-EM-A3SY 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3SZ                    TCGA-EM-A4FF 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FH                    TCGA-EM-A4FK 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FM                    TCGA-EM-A4FN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FO                    TCGA-EM-A4FQ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FR                    TCGA-EM-A4FU 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FV                    TCGA-EM-A4G1 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25G                    TCGA-ET-A25I 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25J                    TCGA-ET-A25K 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25L                    TCGA-ET-A25M 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25N                    TCGA-ET-A25O 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25P                    TCGA-ET-A25R 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A2MX                    TCGA-ET-A2MY 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A2MZ                    TCGA-ET-A2N0 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A2N1                    TCGA-ET-A2N3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A2N4                    TCGA-ET-A2N5 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39I                    TCGA-ET-A39J 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39K                    TCGA-ET-A39L 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39M                    TCGA-ET-A39N 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39O                    TCGA-ET-A39P 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39R                    TCGA-ET-A39S 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39T                    TCGA-ET-A3BN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BO                    TCGA-ET-A3BP 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BQ                    TCGA-ET-A3BS 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BT                    TCGA-ET-A3BU 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BV                    TCGA-ET-A3BW 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BX                    TCGA-ET-A3DO 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3DP                    TCGA-ET-A3DQ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3DR                    TCGA-ET-A3DS 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3DT                    TCGA-ET-A3DU 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3DV                    TCGA-ET-A3DW 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A40P                    TCGA-ET-A40Q 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A40R                    TCGA-ET-A40S 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A40T                    TCGA-ET-A4KN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A4KQ                    TCGA-FE-A22Z 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A230                    TCGA-FE-A231 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A232                    TCGA-FE-A233 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A234                    TCGA-FE-A235 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A236                    TCGA-FE-A237 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A238                    TCGA-FE-A239 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A23A                    TCGA-FE-A3PA 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A3PB                    TCGA-FE-A3PC 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A3PD                    TCGA-FK-A3S3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FK-A3SB                    TCGA-FK-A3SE 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FK-A3SG                    TCGA-FK-A3SH 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FK-A4UB                    TCGA-FY-A3BL 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3I4                    TCGA-FY-A3I5 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3NM                    TCGA-FY-A3NN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3ON                    TCGA-FY-A3R6 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3R8                    TCGA-FY-A3R9 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3RA                    TCGA-FY-A3TY 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3W9                    TCGA-FY-A3WA 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3YR                    TCGA-FY-A40K 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A40L                    TCGA-FY-A40M 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A40N                    TCGA-FY-A4B0 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A4B3                    TCGA-FY-A4B4 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A76V                    TCGA-GE-A2C6 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-H2-A422                    TCGA-IM-A3EB 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A3ED                    TCGA-IM-A3U2 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A3U3                    TCGA-IM-A41Y 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A41Z                    TCGA-IM-A420 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A4EB                    TCGA-J8-A3NZ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3O0                    TCGA-J8-A3O1 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3O2                    TCGA-J8-A3YD 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3YE                    TCGA-J8-A3YF 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3YG                    TCGA-J8-A3YH 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A42S                    TCGA-J8-A4HW 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A4HY                    TCGA-KS-A41F 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A41I                    TCGA-KS-A41J 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A41L                    TCGA-KS-A4I1 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4I3                    TCGA-KS-A4I5 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4I7                    TCGA-KS-A4I9 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4IB                    TCGA-KS-A4IC 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4ID                    TCGA-L6-A4EP 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-L6-A4EQ                    TCGA-L6-A4ET 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-L6-A4EU                    TCGA-MK-A4N6 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-MK-A4N7                    TCGA-MK-A4N9 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-QD-A8IV 
"AMP PEAK  9(2Q37.2) WILD-TYPE" 
D7V13, continuous
[1] "Remove cluster labels:"      "AMP PEAK  9(2Q37.2) MUTATED"
clus
  AMP PEAK  9(2Q37.2) MUTATED AMP PEAK  9(2Q37.2) WILD-TYPE 
                            2                           389 
                   TCGA-BJ-A0Z0                    TCGA-BJ-A0Z3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0Z9                    TCGA-BJ-A0ZA 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0ZB                    TCGA-BJ-A0ZH 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0ZJ                    TCGA-BJ-A18Y 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A18Z                    TCGA-BJ-A190 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A191                    TCGA-BJ-A28R 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A28T                    TCGA-BJ-A28W 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A28X                    TCGA-BJ-A28Z 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A291                    TCGA-BJ-A2N8 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A2N9                    TCGA-BJ-A2NA 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A3EZ                    TCGA-BJ-A3PR 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A3PU                    TCGA-BJ-A45C 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A45D                    TCGA-BJ-A45E 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A45G                    TCGA-BJ-A45I 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A45J                    TCGA-BJ-A45K 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A4O8                    TCGA-BJ-A4O9 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A13K                    TCGA-CE-A3MD 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A0XZ                    TCGA-DE-A0Y2 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A0Y3                    TCGA-DE-A3KN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A4M8                    TCGA-DE-A4MA 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A4MB                    TCGA-DE-A4MC 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A4MD                    TCGA-DE-A69K 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A7U5                    TCGA-DJ-A13O 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13P                    TCGA-DJ-A13R 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13T                    TCGA-DJ-A13U 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13V                    TCGA-DJ-A13W 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13X                    TCGA-DJ-A1QG 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QH                    TCGA-DJ-A1QM 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PO                    TCGA-DJ-A2PP 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PQ                    TCGA-DJ-A2PR 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PS                    TCGA-DJ-A2PT 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PU                    TCGA-DJ-A2PV 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PW                    TCGA-DJ-A2PX 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PY                    TCGA-DJ-A2PZ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q0                    TCGA-DJ-A2Q1 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q2                    TCGA-DJ-A2Q3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q4                    TCGA-DJ-A2Q5 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q6                    TCGA-DJ-A2Q7 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q8                    TCGA-DJ-A2Q9 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2QA                    TCGA-DJ-A2QB 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UK                    TCGA-DJ-A3UM 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UN                    TCGA-DJ-A3UO 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UP                    TCGA-DJ-A3UQ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UR                    TCGA-DJ-A3UU 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UW                    TCGA-DJ-A3UX 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UZ                    TCGA-DJ-A3V0 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V2                    TCGA-DJ-A3V3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V4                    TCGA-DJ-A3V5 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V7                    TCGA-DJ-A3V8 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V9                    TCGA-DJ-A3VA 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VB                    TCGA-DJ-A3VD 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VF                    TCGA-DJ-A3VG 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VJ                    TCGA-DJ-A3VL 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4UL                    TCGA-DJ-A4UQ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4UR                    TCGA-DJ-A4UW 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4V2                    TCGA-DJ-A4V5 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DO-A1K0                    TCGA-DO-A2HM 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E3-A3DY                    TCGA-E3-A3DZ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E3-A3E0                    TCGA-E3-A3E1 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E3-A3E2                    TCGA-E3-A3E3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E3-A3E5                    TCGA-E8-A242 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A2EA                    TCGA-E8-A2JQ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A414                    TCGA-E8-A415 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A417                    TCGA-E8-A419 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A433                    TCGA-E8-A436 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E8-A438                    TCGA-E8-A44K 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CM                    TCGA-EL-A3CN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CO                    TCGA-EL-A3CR 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CS                    TCGA-EL-A3CT 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CU                    TCGA-EL-A3CV 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CW                    TCGA-EL-A3CX 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CY                    TCGA-EL-A3CZ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3D0                    TCGA-EL-A3D1 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3D4                    TCGA-EL-A3D5 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3D6                    TCGA-EL-A3GO 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GP                    TCGA-EL-A3GQ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GS                    TCGA-EL-A3GU 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GV                    TCGA-EL-A3GX 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3H3                    TCGA-EL-A3H4 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3H5                    TCGA-EL-A3H7 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3H8                    TCGA-EL-A3MW 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3MX                    TCGA-EL-A3MZ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3N2                    TCGA-EL-A3T0 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3T1                    TCGA-EL-A3T2 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3TB                    TCGA-EL-A3ZH 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZK                    TCGA-EL-A3ZL 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZN                    TCGA-EL-A3ZO 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZP                    TCGA-EL-A3ZS 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4JV                    TCGA-EL-A4JW 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4JX                    TCGA-EL-A4JZ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4K0                    TCGA-EL-A4K1 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4K2                    TCGA-EL-A4K4 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4K6                    TCGA-EL-A4K7 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4KD                    TCGA-EL-A4KG 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4KI                    TCGA-EM-A1CS 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1CT                    TCGA-EM-A1CU 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1CV                    TCGA-EM-A1CW 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1YA                    TCGA-EM-A1YB 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1YC                    TCGA-EM-A1YD 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1YE                    TCGA-EM-A22I 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22J                    TCGA-EM-A22K 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22L                    TCGA-EM-A22M 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22N                    TCGA-EM-A22O 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22P                    TCGA-EM-A22Q 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CK                    TCGA-EM-A2CN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CP                    TCGA-EM-A2CQ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CS                    TCGA-EM-A2CT 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CU                    TCGA-EM-A2OV 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2OW                    TCGA-EM-A2OX 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2OY                    TCGA-EM-A2OZ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2P0                    TCGA-EM-A2P1 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2P2                    TCGA-EM-A2P3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AJ                    TCGA-EM-A3AK 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AL                    TCGA-EM-A3AN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AO                    TCGA-EM-A3AQ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AR                    TCGA-EM-A3FJ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FK                    TCGA-EM-A3FL 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FM                    TCGA-EM-A3FN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FO                    TCGA-EM-A3FP 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FQ                    TCGA-EM-A3FR 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3O3                    TCGA-EM-A3O7 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3O8                    TCGA-EM-A3O9 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3OA                    TCGA-EM-A3OB 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3ST                    TCGA-EM-A3SU 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3SX                    TCGA-EM-A3SY 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3SZ                    TCGA-EM-A4FF 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FH                    TCGA-EM-A4FK 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FM                    TCGA-EM-A4FN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FO                    TCGA-EM-A4FQ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FR                    TCGA-EM-A4FU 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FV                    TCGA-EM-A4G1 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25G                    TCGA-ET-A25I 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25J                    TCGA-ET-A25K 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25L                    TCGA-ET-A25M 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25N                    TCGA-ET-A25O 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25P                    TCGA-ET-A2MX 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A2MZ                    TCGA-ET-A2N0 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A2N1                    TCGA-ET-A2N4 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39K                    TCGA-ET-A39L 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39O                    TCGA-ET-A39P 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39R                    TCGA-ET-A39S 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39T                    TCGA-ET-A3BO 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BP                    TCGA-ET-A3BQ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BS                    TCGA-ET-A3BT 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BU                    TCGA-ET-A3BV 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BX                    TCGA-ET-A3DQ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3DR                    TCGA-ET-A3DS 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3DT                    TCGA-ET-A3DU 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3DV                    TCGA-ET-A3DW 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A40P                    TCGA-ET-A40Q 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A40R                    TCGA-ET-A40S 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A40T                    TCGA-ET-A4KN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A22Z                    TCGA-FE-A230 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A231                    TCGA-FE-A232 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A233                    TCGA-FE-A234 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A235                    TCGA-FE-A236 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A237                    TCGA-FE-A238 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A239                    TCGA-FE-A23A 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A3PB                    TCGA-FE-A3PC 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A3PD                    TCGA-FK-A3S3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FK-A3SB                    TCGA-FK-A3SE 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FK-A3SG                    TCGA-FK-A3SH 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FK-A4UB                    TCGA-FY-A2QD 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3I4                    TCGA-FY-A3I5 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3NM                    TCGA-FY-A3NN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3ON                    TCGA-FY-A3R6 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3R7                    TCGA-FY-A3R9 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3TY                    TCGA-FY-A3W9 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3YR                    TCGA-FY-A40K 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A40L                    TCGA-FY-A40M 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A40N                    TCGA-FY-A4B3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A4B4                    TCGA-GE-A2C6 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-H2-A26U                    TCGA-H2-A2K9 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-H2-A3RH                    TCGA-H2-A3RI 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-H2-A421                    TCGA-H2-A422 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A3EB                    TCGA-IM-A3ED 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A3U2                    TCGA-IM-A3U3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A41Y                    TCGA-IM-A41Z 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A420                    TCGA-IM-A4EB 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3NZ                    TCGA-J8-A3O0 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3O1                    TCGA-J8-A3O2 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3YD                    TCGA-J8-A3YE 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3YF                    TCGA-J8-A3YG 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3YH                    TCGA-J8-A42S 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A4HW                    TCGA-J8-A4HY 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A41F                    TCGA-KS-A41I 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A41J                    TCGA-KS-A41L 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4I1                    TCGA-KS-A4I3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4I5                    TCGA-KS-A4I7 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4I9                    TCGA-KS-A4IB 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4IC                    TCGA-KS-A4ID 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-L6-A4EP                    TCGA-L6-A4EQ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-L6-A4EU                    TCGA-MK-A4N6 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-MK-A4N7                    TCGA-MK-A4N9 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-QD-A8IV 
"AMP PEAK  9(2Q37.2) WILD-TYPE" 
D7V14, binary
                               cls
clus                              0   1
  AMP PEAK  9(2Q37.2) MUTATED     1   2
  AMP PEAK  9(2Q37.2) WILD-TYPE 223 259
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(2Q37.2) MUTATED      1    2
  AMP PEAK  9(2Q37.2) WILD-TYPE  223  259
            clus
vv           AMP PEAK  9(2Q37.2) MUTATED AMP PEAK  9(2Q37.2) WILD-TYPE
  MULTIFOCAL                           1                           223
  UNIFOCAL                             2                           259
[1] 2 2
[1] FALSE
D7V15, continuous
[1] "Remove cluster labels:"      "AMP PEAK  9(2Q37.2) MUTATED"
clus
  AMP PEAK  9(2Q37.2) MUTATED AMP PEAK  9(2Q37.2) WILD-TYPE 
                            2                           395 
                   TCGA-BJ-A0Z2                    TCGA-BJ-A0Z3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0Z9                    TCGA-BJ-A0ZA 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0ZB                    TCGA-BJ-A0ZC 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0ZE                    TCGA-BJ-A0ZG 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A0ZH                    TCGA-BJ-A0ZJ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A18Y                    TCGA-BJ-A18Z 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A190                    TCGA-BJ-A191 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A192                    TCGA-BJ-A28R 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A28S                    TCGA-BJ-A28T 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A28V                    TCGA-BJ-A28W 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A28Z                    TCGA-BJ-A291 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A2N8                    TCGA-BJ-A2N9 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A2P4                    TCGA-BJ-A3PU 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A45C                    TCGA-BJ-A45D 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A45E                    TCGA-BJ-A45F 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A45G                    TCGA-BJ-A45H 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A45I                    TCGA-BJ-A45J 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A45K                    TCGA-BJ-A4O8 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-BJ-A4O9                    TCGA-CE-A13K 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A27D                    TCGA-CE-A3MD 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A3ME                    TCGA-CE-A481 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A482                    TCGA-CE-A483 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-CE-A484                    TCGA-CE-A485 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A0XZ                    TCGA-DE-A0Y2 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A0Y3                    TCGA-DE-A2OL 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A3KN                    TCGA-DE-A4M8 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A4M9                    TCGA-DE-A4MA 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A4MB                    TCGA-DE-A4MC 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A4MD                    TCGA-DE-A69J 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DE-A69K                    TCGA-DE-A7U5 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13O                    TCGA-DJ-A13R 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13S                    TCGA-DJ-A13U 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13V                    TCGA-DJ-A13W 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A13X                    TCGA-DJ-A1QD 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QE                    TCGA-DJ-A1QF 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QG                    TCGA-DJ-A1QH 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QI                    TCGA-DJ-A1QL 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QM                    TCGA-DJ-A1QN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A1QO                    TCGA-DJ-A1QQ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PN                    TCGA-DJ-A2PO 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PP                    TCGA-DJ-A2PQ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PR                    TCGA-DJ-A2PS 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PT                    TCGA-DJ-A2PU 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PV                    TCGA-DJ-A2PW 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2PY                    TCGA-DJ-A2PZ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q0                    TCGA-DJ-A2Q1 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q2                    TCGA-DJ-A2Q3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q4                    TCGA-DJ-A2Q5 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q6                    TCGA-DJ-A2Q7 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2Q8                    TCGA-DJ-A2Q9 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A2QA                    TCGA-DJ-A2QC 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UK                    TCGA-DJ-A3UM 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UN                    TCGA-DJ-A3UO 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UP                    TCGA-DJ-A3UQ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UR                    TCGA-DJ-A3US 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UT                    TCGA-DJ-A3UU 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UW                    TCGA-DJ-A3UX 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3UY                    TCGA-DJ-A3V0 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V2                    TCGA-DJ-A3V3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V4                    TCGA-DJ-A3V5 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3V7                    TCGA-DJ-A3V8 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VA                    TCGA-DJ-A3VB 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VD                    TCGA-DJ-A3VE 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VF                    TCGA-DJ-A3VG 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VJ                    TCGA-DJ-A3VL 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A3VM                    TCGA-DJ-A4UL 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4UQ                    TCGA-DJ-A4UT 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4V0                    TCGA-DJ-A4V2 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DJ-A4V4                    TCGA-DJ-A4V5 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DO-A1JZ                    TCGA-DO-A1K0 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-DO-A2HM                    TCGA-E3-A3DY 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E3-A3DZ                    TCGA-E3-A3E0 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E3-A3E1                    TCGA-E3-A3E2 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-E3-A3E3                    TCGA-E8-A419 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CN                    TCGA-EL-A3CO 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CR                    TCGA-EL-A3CS 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CT                    TCGA-EL-A3CU 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CV                    TCGA-EL-A3CW 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CX                    TCGA-EL-A3CY 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3CZ                    TCGA-EL-A3D0 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3D1                    TCGA-EL-A3D4 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3D5                    TCGA-EL-A3D6 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GO                    TCGA-EL-A3GP 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GQ                    TCGA-EL-A3GR 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GS                    TCGA-EL-A3GU 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GV                    TCGA-EL-A3GW 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GX                    TCGA-EL-A3GY 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3GZ                    TCGA-EL-A3H2 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3H3                    TCGA-EL-A3H4 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3H5                    TCGA-EL-A3H7 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3H8                    TCGA-EL-A3MW 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3MX                    TCGA-EL-A3MY 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3MZ                    TCGA-EL-A3N2 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3N3                    TCGA-EL-A3T1 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3T2                    TCGA-EL-A3T3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3T6                    TCGA-EL-A3T7 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3T8                    TCGA-EL-A3T9 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3TA                    TCGA-EL-A3TB 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZG                    TCGA-EL-A3ZH 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZK                    TCGA-EL-A3ZL 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZN                    TCGA-EL-A3ZO 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZP                    TCGA-EL-A3ZQ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZR                    TCGA-EL-A3ZS 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A3ZT                    TCGA-EL-A4JV 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4JW                    TCGA-EL-A4JX 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4JZ                    TCGA-EL-A4K0 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4K1                    TCGA-EL-A4K2 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4K4                    TCGA-EL-A4K6 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4K7                    TCGA-EL-A4K9 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4KD                    TCGA-EL-A4KG 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EL-A4KH                    TCGA-EL-A4KI 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1CS                    TCGA-EM-A1CT 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1CU                    TCGA-EM-A1CV 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1CW                    TCGA-EM-A1YA 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1YB                    TCGA-EM-A1YC 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A1YD                    TCGA-EM-A1YE 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22I                    TCGA-EM-A22J 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22K                    TCGA-EM-A22L 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22N                    TCGA-EM-A22O 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A22P                    TCGA-EM-A22Q 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CJ                    TCGA-EM-A2CK 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CL                    TCGA-EM-A2CN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CO                    TCGA-EM-A2CP 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CQ                    TCGA-EM-A2CS 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2CT                    TCGA-EM-A2CU 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2OW                    TCGA-EM-A2OX 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2OY                    TCGA-EM-A2P0 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2P1                    TCGA-EM-A2P2 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A2P3                    TCGA-EM-A3AI 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AJ                    TCGA-EM-A3AK 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AL                    TCGA-EM-A3AN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AO                    TCGA-EM-A3AP 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3AQ                    TCGA-EM-A3AR 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FJ                    TCGA-EM-A3FM 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FN                    TCGA-EM-A3FO 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3FP                    TCGA-EM-A3FR 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3O3                    TCGA-EM-A3O6 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3O7                    TCGA-EM-A3O8 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3O9                    TCGA-EM-A3OA 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3OB                    TCGA-EM-A3ST 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3SU                    TCGA-EM-A3SX 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A3SY                    TCGA-EM-A3SZ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FF                    TCGA-EM-A4FH 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FK                    TCGA-EM-A4FM 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FN                    TCGA-EM-A4FQ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FR                    TCGA-EM-A4FU 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-EM-A4FV                    TCGA-EM-A4G1 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25G                    TCGA-ET-A25I 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25J                    TCGA-ET-A25K 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25L                    TCGA-ET-A25M 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25N                    TCGA-ET-A25O 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A25P                    TCGA-ET-A25R 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A2MY                    TCGA-ET-A2MZ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A2N0                    TCGA-ET-A2N5 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39J                    TCGA-ET-A39M 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39N                    TCGA-ET-A39O 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A39P                    TCGA-ET-A39T 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BN                    TCGA-ET-A3BO 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BP                    TCGA-ET-A3BQ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BS                    TCGA-ET-A3BT 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BU                    TCGA-ET-A3BV 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3BW                    TCGA-ET-A3BX 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3DO                    TCGA-ET-A3DS 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A3DT                    TCGA-ET-A40P 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A40Q                    TCGA-ET-A40R 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A40S                    TCGA-ET-A4KN 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-ET-A4KQ                    TCGA-FE-A22Z 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A230                    TCGA-FE-A232 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A233                    TCGA-FE-A234 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A235                    TCGA-FE-A236 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A237                    TCGA-FE-A238 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A239                    TCGA-FE-A23A 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A3PA                    TCGA-FE-A3PB 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FE-A3PC                    TCGA-FE-A3PD 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A2QD                    TCGA-FY-A3I4 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3I5                    TCGA-FY-A3ON 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3R8                    TCGA-FY-A3TY 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A3W9                    TCGA-FY-A3YR 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A40K                    TCGA-FY-A40L 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A40M                    TCGA-FY-A40N 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-FY-A4B3                    TCGA-FY-A76V 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-GE-A2C6                    TCGA-H2-A421 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A3EB                    TCGA-IM-A3ED 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A3U2                    TCGA-IM-A3U3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A41Y                    TCGA-IM-A41Z 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-IM-A420                    TCGA-IM-A4EB 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3O0                    TCGA-J8-A3YD 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-J8-A3YG                    TCGA-KS-A41F 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A41I                    TCGA-KS-A41J 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A41L                    TCGA-KS-A4I3 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4I5                    TCGA-KS-A4I7 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4I9                    TCGA-KS-A4IB 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-KS-A4IC                    TCGA-KS-A4ID 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-L6-A4EP                    TCGA-L6-A4EQ 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-L6-A4ET                    TCGA-L6-A4EU 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-MK-A4N6                    TCGA-MK-A4N7 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-MK-A4N9                    TCGA-MK-A84Z 
"AMP PEAK  9(2Q37.2) WILD-TYPE" "AMP PEAK  9(2Q37.2) WILD-TYPE" 
                   TCGA-QD-A8IV 
"AMP PEAK  9(2Q37.2) WILD-TYPE" 
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  9(2Q37.2) MUTATED                                  0     0
  AMP PEAK  9(2Q37.2) WILD-TYPE                                1    49
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(2Q37.2) MUTATED                           0     3
  AMP PEAK  9(2Q37.2) WILD-TYPE                        26   318
D7V16, multiclass
                                  clus
vv                                 AMP PEAK  9(2Q37.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      3
                                  clus
vv                                 AMP PEAK  9(2Q37.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       49
  BLACK OR AFRICAN AMERICAN                                   26
  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"
D7V17, binary
                               cls
clus                              0   1
  AMP PEAK  9(2Q37.2) MUTATED     0   3
  AMP PEAK  9(2Q37.2) WILD-TYPE  38 347
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(2Q37.2) MUTATED      0    3
  AMP PEAK  9(2Q37.2) WILD-TYPE   38  347
                        clus
vv                       AMP PEAK  9(2Q37.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           3
                        clus
vv                       AMP PEAK  9(2Q37.2) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           347
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK 10(3P22.3) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(3P22.3) MUTATED     3   1
  AMP PEAK 10(3P22.3) WILD-TYPE 474  13
  AMP PEAK 10(3P22.3) MUTATED AMP PEAK 10(3P22.3) WILD-TYPE 
                            4                           487 
  AMP PEAK 10(3P22.3) MUTATED AMP PEAK 10(3P22.3) WILD-TYPE 
                            1                            13 
$`AMP PEAK 10(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 10(3P22.3) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       24.79        18.21        16.34        14.73         8.25        18.87 
TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ 
        4.01        11.57        16.73         7.56        15.12        17.69 
TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       23.34        20.71        20.58         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
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        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
        1.45        74.30        45.40        33.47       108.36        39.32 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        30.18       102.84        65.39       124.04        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       37.25       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        38.66        52.73       139.00       131.15       108.66 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        12.36        18.05        19.79        19.46        54.21 
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        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT 
       13.18        23.51         2.99        12.30        15.19        10.49 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        13.84        19.73        17.59        12.07 
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        17.46        18.97 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        19.63        13.38         8.35        16.44 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       16.77        27.95        23.77        16.80        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        11.15 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33        12.53         9.24        13.91         7.82        11.51 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       16.41        15.62        13.51        12.79        70.65        16.90 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        9.01         4.83         8.61         8.38         9.80         5.03 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       37.87        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       29.49        54.05        22.09        12.26        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       65.36        84.89        98.56        61.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        59.15        28.24         5.85         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        24.69        68.22       102.90        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       81.34        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        46.06         4.08         0.89        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10        91.17         1.25         1.15        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        1.64         0.99         1.51         0.76         0.03         4.67 
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         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74        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         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  AMP PEAK 10(3P22.3) MUTATED AMP PEAK 10(3P22.3) WILD-TYPE 
                         6.05                          0.03 
  AMP PEAK 10(3P22.3) MUTATED AMP PEAK 10(3P22.3) WILD-TYPE 
                        57.63                        158.83 
  AMP PEAK 10(3P22.3) MUTATED AMP PEAK 10(3P22.3) WILD-TYPE 
                       12.215                        16.640 
[1] "6.0 - 57.6 (12.2)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "9"  
D8V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 10(3P22.3) MUTATED         1        2         0        0         0
  AMP PEAK 10(3P22.3) WILD-TYPE     279       49       109        2        45
                               vv
clus                            STAGE IVC
  AMP PEAK 10(3P22.3) MUTATED           1
  AMP PEAK 10(3P22.3) WILD-TYPE         5
D8V3, multiclass
           clus
vv          AMP PEAK 10(3P22.3) MUTATED AMP PEAK 10(3P22.3) WILD-TYPE
  STAGE I                             1                           279
  STAGE II                            2                            49
  STAGE III                           0                           109
  STAGE IV                            0                             2
  STAGE IVA                           0                            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
  AMP PEAK 10(3P22.3) MUTATED     1   2   0   1
  AMP PEAK 10(3P22.3) WILD-TYPE 139 164 165  20
D8V4, multiclass
    clus
vv   AMP PEAK 10(3P22.3) MUTATED AMP PEAK 10(3P22.3) WILD-TYPE
  T1                           1                           139
  T2                           2                           164
  T3                           0                           165
  T4                           1                            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"
D8V5, binary
                               cls
clus                              0   1
  AMP PEAK 10(3P22.3) MUTATED     2   1
  AMP PEAK 10(3P22.3) WILD-TYPE 221 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(3P22.3) MUTATED      2    1
  AMP PEAK 10(3P22.3) WILD-TYPE  221  221
   clus
vv  AMP PEAK 10(3P22.3) MUTATED AMP PEAK 10(3P22.3) WILD-TYPE
  0                           2                           221
  1                           1                           221
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK 10(3P22.3) MUTATED     0   1   3
  AMP PEAK 10(3P22.3) WILD-TYPE 273   8 209
D8V6, multiclass
    clus
vv   AMP PEAK 10(3P22.3) MUTATED AMP PEAK 10(3P22.3) WILD-TYPE
  M0                           0                           273
  M1                           1                             8
  MX                           3                           209
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                               cls
clus                              0   1
  AMP PEAK 10(3P22.3) MUTATED     3   1
  AMP PEAK 10(3P22.3) WILD-TYPE 361 130
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(3P22.3) MUTATED      3    1
  AMP PEAK 10(3P22.3) WILD-TYPE  361  130
        clus
vv       AMP PEAK 10(3P22.3) MUTATED AMP PEAK 10(3P22.3) WILD-TYPE
  FEMALE                           3                           361
  MALE                             1                           130
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 10(3P22.3) MUTATED                0
  AMP PEAK 10(3P22.3) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 10(3P22.3) MUTATED                                               2
  AMP PEAK 10(3P22.3) WILD-TYPE                                           351
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 10(3P22.3) MUTATED                                                                        2
  AMP PEAK 10(3P22.3) WILD-TYPE                                                                     96
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 10(3P22.3) MUTATED                                                                     0
  AMP PEAK 10(3P22.3) WILD-TYPE                                                                  35
D8V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 10(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 10(3P22.3) WILD-TYPE
  OTHER  SPECIFY                                                                                     9
  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"
D8V9, binary
                               cls
clus                              0   1
  AMP PEAK 10(3P22.3) MUTATED     0   4
  AMP PEAK 10(3P22.3) WILD-TYPE  14 477
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(3P22.3) MUTATED      0    4
  AMP PEAK 10(3P22.3) WILD-TYPE   14  477
     clus
vv    AMP PEAK 10(3P22.3) MUTATED AMP PEAK 10(3P22.3) WILD-TYPE
  NO                            0                            14
  YES                           4                           477
[1] 2 2
[1] FALSE
D8V10, binary
                               cls
clus                              0   1
  AMP PEAK 10(3P22.3) MUTATED     3   0
  AMP PEAK 10(3P22.3) WILD-TYPE 414  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(3P22.3) MUTATED      3    0
  AMP PEAK 10(3P22.3) WILD-TYPE  414   17
     clus
vv    AMP PEAK 10(3P22.3) MUTATED AMP PEAK 10(3P22.3) WILD-TYPE
  NO                            3                           414
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 10(3P22.3) MUTATED              0                       0    4
  AMP PEAK 10(3P22.3) WILD-TYPE          130                      16  324
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 10(3P22.3) MUTATED                     0
  AMP PEAK 10(3P22.3) WILD-TYPE                   1
D8V11, multiclass
                         clus
vv                        AMP PEAK 10(3P22.3) MUTATED
  MINIMAL (T3)                                      0
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              4
  VERY ADVANCED (T4B)                               0
                         clus
vv                        AMP PEAK 10(3P22.3) WILD-TYPE
  MINIMAL (T3)                                      130
  MODERATE/ADVANCED (T4A)                            16
  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 10(3P22.3) MUTATED     2   0   0   2
  AMP PEAK 10(3P22.3) WILD-TYPE 376  51   4  28
D8V12, multiclass
    clus
vv   AMP PEAK 10(3P22.3) MUTATED AMP PEAK 10(3P22.3) WILD-TYPE
  R0                           2                           376
  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 10(3P22.3) MUTATED     1   3
  AMP PEAK 10(3P22.3) WILD-TYPE 223 258
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(3P22.3) MUTATED      1    3
  AMP PEAK 10(3P22.3) WILD-TYPE  223  258
            clus
vv           AMP PEAK 10(3P22.3) MUTATED AMP PEAK 10(3P22.3) WILD-TYPE
  MULTIFOCAL                           1                           223
  UNIFOCAL                             3                           258
[1] 2 2
[1] FALSE
D8V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 10(3P22.3) MUTATED                                  0     0
  AMP PEAK 10(3P22.3) WILD-TYPE                                1    49
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(3P22.3) MUTATED                           0     1
  AMP PEAK 10(3P22.3) WILD-TYPE                        26   320
D8V16, multiclass
[1] "Remove cluster labels:"      "AMP PEAK 10(3P22.3) MUTATED"
clus
  AMP PEAK 10(3P22.3) MUTATED AMP PEAK 10(3P22.3) WILD-TYPE 
                            1                           396 
                   TCGA-BJ-A0YZ                    TCGA-BJ-A0Z2 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A0Z3                    TCGA-BJ-A0Z5 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A0Z9                    TCGA-BJ-A0ZA 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A0ZB                    TCGA-BJ-A0ZC 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A0ZE                    TCGA-BJ-A0ZG 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A0ZH                    TCGA-BJ-A0ZJ 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A18Y                    TCGA-BJ-A18Z 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A190                    TCGA-BJ-A191 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A192                    TCGA-BJ-A28R 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A28S                    TCGA-BJ-A28T 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A28V                    TCGA-BJ-A28W 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A28X                    TCGA-BJ-A28Z 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A290                    TCGA-BJ-A291 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A2N7                    TCGA-BJ-A2N8 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A2N9                    TCGA-BJ-A2NA 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A2P4                    TCGA-BJ-A3EZ 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A3F0                    TCGA-BJ-A3PR 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A3PT                    TCGA-BJ-A3PU 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A45C                    TCGA-BJ-A45D 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A45E                    TCGA-BJ-A45F 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A45G                    TCGA-BJ-A45H 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A45I                    TCGA-BJ-A45J 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A45K                    TCGA-BJ-A4O8 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-BJ-A4O9                    TCGA-CE-A13K 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-CE-A27D                    TCGA-CE-A3MD 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-CE-A3ME                    TCGA-CE-A481 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-CE-A482                    TCGA-CE-A483 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-CE-A484                    TCGA-CE-A485 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DE-A0XZ                    TCGA-DE-A0Y2 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DE-A0Y3                    TCGA-DE-A2OL 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DE-A3KN                    TCGA-DE-A4M8 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DE-A4M9                    TCGA-DE-A4MA 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DE-A4MB                    TCGA-DE-A4MC 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DE-A4MD                    TCGA-DE-A69J 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DE-A69K                    TCGA-DE-A7U5 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A13M                    TCGA-DJ-A13O 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A13P                    TCGA-DJ-A13R 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A13S                    TCGA-DJ-A13T 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A13U                    TCGA-DJ-A13W 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A1QD                    TCGA-DJ-A1QE 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A1QF                    TCGA-DJ-A1QG 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A1QH                    TCGA-DJ-A1QI 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A1QM                    TCGA-DJ-A1QO 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A1QQ                    TCGA-DJ-A2PN 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PO                    TCGA-DJ-A2PQ 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PR                    TCGA-DJ-A2PT 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PU                    TCGA-DJ-A2PV 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PW                    TCGA-DJ-A2PX 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PY                    TCGA-DJ-A2PZ 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q0                    TCGA-DJ-A2Q1 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q2                    TCGA-DJ-A2Q3 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q4                    TCGA-DJ-A2Q5 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q6                    TCGA-DJ-A2Q7 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q9                    TCGA-DJ-A2QA 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A2QB                    TCGA-DJ-A3UK 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UM                    TCGA-DJ-A3UN 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UO                    TCGA-DJ-A3UQ 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UR                    TCGA-DJ-A3US 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UT                    TCGA-DJ-A3UU 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UW                    TCGA-DJ-A3UX 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UY                    TCGA-DJ-A3UZ 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A3V2                    TCGA-DJ-A3V3 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A3V4                    TCGA-DJ-A3V5 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A3V7                    TCGA-DJ-A3V8 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A3V9                    TCGA-DJ-A3VD 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A3VE                    TCGA-DJ-A3VF 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A3VG                    TCGA-DJ-A3VJ 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A3VL                    TCGA-DJ-A3VM 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A4UL                    TCGA-DJ-A4UQ 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A4UR                    TCGA-DJ-A4UT 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A4UW                    TCGA-DJ-A4V0 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DJ-A4V4                    TCGA-DJ-A4V5 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DO-A1JZ                    TCGA-DO-A1K0 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-DO-A2HM                    TCGA-E3-A3DY 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-E3-A3DZ                    TCGA-E3-A3E0 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-E3-A3E1                    TCGA-E3-A3E2 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-E3-A3E3                    TCGA-E3-A3E5 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-E8-A242                    TCGA-E8-A2EA 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-E8-A2JQ                    TCGA-E8-A3X7 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-E8-A413                    TCGA-E8-A414 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-E8-A415                    TCGA-E8-A416 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-E8-A417                    TCGA-E8-A418 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-E8-A419                    TCGA-E8-A432 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-E8-A433                    TCGA-E8-A434 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-E8-A436                    TCGA-E8-A437 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-E8-A438                    TCGA-E8-A44K 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-E8-A44M                    TCGA-EL-A3CL 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3CM                    TCGA-EL-A3CN 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3CO                    TCGA-EL-A3CP 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3CR                    TCGA-EL-A3CS 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3CT                    TCGA-EL-A3CU 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3CV                    TCGA-EL-A3CW 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3CX                    TCGA-EL-A3CY 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3CZ                    TCGA-EL-A3D0 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3D1                    TCGA-EL-A3D4 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3D5                    TCGA-EL-A3D6 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3GO                    TCGA-EL-A3GP 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3GQ                    TCGA-EL-A3GR 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3GS                    TCGA-EL-A3GU 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3GV                    TCGA-EL-A3GW 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3GX                    TCGA-EL-A3GY 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3GZ                    TCGA-EL-A3H1 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3H2                    TCGA-EL-A3H3 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3H4                    TCGA-EL-A3H5 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3H7                    TCGA-EL-A3H8 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3MW                    TCGA-EL-A3MY 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3MZ                    TCGA-EL-A3N2 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3N3                    TCGA-EL-A3T0 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3T1                    TCGA-EL-A3T2 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3T3                    TCGA-EL-A3T6 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3T7                    TCGA-EL-A3T8 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3T9                    TCGA-EL-A3TA 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3TB                    TCGA-EL-A3ZG 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZH                    TCGA-EL-A3ZK 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZL                    TCGA-EL-A3ZN 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZO                    TCGA-EL-A3ZP 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZQ                    TCGA-EL-A3ZR 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZS                    TCGA-EL-A3ZT 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A4JV                    TCGA-EL-A4JW 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A4JX                    TCGA-EL-A4JZ 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A4K0                    TCGA-EL-A4K1 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A4K2                    TCGA-EL-A4K4 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A4K6                    TCGA-EL-A4K7 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A4K9                    TCGA-EL-A4KD 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A4KG                    TCGA-EL-A4KH 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-EL-A4KI                    TCGA-ET-A25G 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-ET-A25I                    TCGA-ET-A25J 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-ET-A25K                    TCGA-ET-A25L 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-ET-A25M                    TCGA-ET-A25N 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-ET-A25O                    TCGA-ET-A25P 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-ET-A25R                    TCGA-ET-A2MX 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-ET-A2MY                    TCGA-ET-A2MZ 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-ET-A2N0                    TCGA-ET-A2N1 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-ET-A2N3                    TCGA-ET-A2N4 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-ET-A2N5                    TCGA-ET-A39I 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-ET-A39J                    TCGA-ET-A39K 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-ET-A39M                    TCGA-ET-A39N 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-ET-A39O                    TCGA-ET-A39P 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-ET-A39R                    TCGA-ET-A39S 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-ET-A39T                    TCGA-ET-A3BN 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-ET-A3BO                    TCGA-ET-A3BQ 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-ET-A3BS                    TCGA-ET-A3BT 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-ET-A3BU                    TCGA-ET-A3BV 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-ET-A3BW                    TCGA-ET-A3DO 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-ET-A3DP                    TCGA-ET-A3DQ 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-ET-A3DR                    TCGA-ET-A3DS 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-ET-A3DT                    TCGA-ET-A3DU 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-ET-A3DV                    TCGA-ET-A3DW 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-ET-A40P                    TCGA-ET-A40Q 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-ET-A40R                    TCGA-ET-A40S 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-ET-A40T                    TCGA-ET-A4KN 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-ET-A4KQ                    TCGA-FE-A22Z 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-FE-A230                    TCGA-FE-A231 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-FE-A232                    TCGA-FE-A233 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-FE-A234                    TCGA-FE-A235 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-FE-A236                    TCGA-FE-A237 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-FE-A238                    TCGA-FE-A239 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-FE-A23A                    TCGA-FE-A3PA 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-FE-A3PB                    TCGA-FE-A3PC 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-FE-A3PD                    TCGA-FK-A3S3 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-FK-A3SB                    TCGA-FK-A3SD 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-FK-A3SE                    TCGA-FK-A3SG 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-FK-A3SH                    TCGA-FK-A4UB 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-FY-A2QD                    TCGA-FY-A3BL 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-FY-A3I4                    TCGA-FY-A3I5 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-FY-A3NM                    TCGA-FY-A3ON 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-FY-A3R6                    TCGA-FY-A3R7 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-FY-A3R8                    TCGA-FY-A3R9 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-FY-A3RA                    TCGA-FY-A3W9 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-FY-A3WA                    TCGA-FY-A3YR 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-FY-A40K                    TCGA-FY-A40L 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-FY-A40M                    TCGA-FY-A40N 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-FY-A4B0                    TCGA-FY-A4B3 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-FY-A4B4                    TCGA-FY-A76V 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-GE-A2C6                    TCGA-H2-A26U 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-H2-A2K9                    TCGA-H2-A3RH 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-H2-A3RI                    TCGA-H2-A421 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-H2-A422                    TCGA-IM-A3EB 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-IM-A3ED                    TCGA-IM-A3U2 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-IM-A3U3                    TCGA-IM-A41Y 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-IM-A41Z                    TCGA-IM-A420 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-IM-A4EB                    TCGA-J8-A3NZ 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-J8-A3O0                    TCGA-J8-A3O1 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-J8-A3O2                    TCGA-J8-A3YD 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-J8-A3YE                    TCGA-J8-A3YF 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-J8-A3YG                    TCGA-J8-A3YH 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-J8-A42S                    TCGA-J8-A4HW 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-J8-A4HY                    TCGA-KS-A41F 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-KS-A41I                    TCGA-KS-A41J 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-KS-A41L                    TCGA-KS-A4I1 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-KS-A4I3                    TCGA-KS-A4I5 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-KS-A4I7                    TCGA-KS-A4I9 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-KS-A4IB                    TCGA-KS-A4IC 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-KS-A4ID                    TCGA-L6-A4EP 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-L6-A4EQ                    TCGA-L6-A4ET 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-L6-A4EU                    TCGA-MK-A4N6 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-MK-A4N7                    TCGA-MK-A4N9 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
                   TCGA-MK-A84Z                    TCGA-QD-A8IV 
"AMP PEAK 10(3P22.3) WILD-TYPE" "AMP PEAK 10(3P22.3) WILD-TYPE" 
D8V17, binary
                               cls
clus                              0   1
  AMP PEAK 10(3P22.3) MUTATED     0   2
  AMP PEAK 10(3P22.3) WILD-TYPE  38 348
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(3P22.3) MUTATED      0    2
  AMP PEAK 10(3P22.3) WILD-TYPE   38  348
                        clus
vv                       AMP PEAK 10(3P22.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           2
                        clus
vv                       AMP PEAK 10(3P22.3) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           348
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK 11(3P14.1) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 11(3P14.1) MUTATED     4   1
  AMP PEAK 11(3P14.1) WILD-TYPE 473  13
  AMP PEAK 11(3P14.1) MUTATED AMP PEAK 11(3P14.1) WILD-TYPE 
                            5                           486 
  AMP PEAK 11(3P14.1) MUTATED AMP PEAK 11(3P14.1) WILD-TYPE 
                            1                            13 
$`AMP PEAK 11(3P14.1) MUTATED`
TCGA-DJ-A2PR TCGA-DJ-A3UY TCGA-EL-A3MX TCGA-EM-A22N TCGA-EM-A2CO 
       10.45        21.37        57.63        10.65         6.05 

$`AMP PEAK 11(3P14.1) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       17.69        43.00        11.34        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04         1.15        22.29 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       108.66        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       52.50        12.16       147.42       130.72       129.57        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      116.91        98.24        41.29        95.38         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN 
       82.82        77.36        78.97        31.50        50.33        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        52.50        45.53        48.16         7.07        44.65 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       45.80        19.30        45.96        37.94        31.04        19.59 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        33.60        28.73        41.13        37.78        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       13.32        11.87         8.71        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
       12.36        18.05        19.79        19.46        54.21        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 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         2.99        12.30        15.19        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        13.84        19.73        17.59        12.07        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        17.46        18.97        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR 
       14.14        19.63        13.38         8.35        16.44        16.77 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        16.80        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        11.15         7.33 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
       12.53         9.24        13.91         7.82        11.51        16.41 
TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       15.62        13.51        12.79        70.65        16.90         9.01 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        4.83         8.61         8.38         9.80         5.03        37.87 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       12.72         0.95        47.47        48.20        29.69        32.35 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       14.79        12.33        14.79        27.09        18.38        29.49 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       54.05        22.09        12.26        16.08        29.19        19.76 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        58.22        13.74        71.01        80.02        65.36 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       84.89        98.56        61.02        58.72        57.11        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       59.15        28.24         5.85         4.18         2.43         5.56 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       24.72        38.30        42.25         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       69.24        59.87        43.50         0.30        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       102.90        66.77        81.34 
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        46.06         4.08         0.89        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 
       48.10        91.17         1.25         1.15        17.82         1.64 
TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
        0.99         1.51         0.76         0.03         4.67        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         6.87         4.14 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58         4.54         0.89         1.35         1.15         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        10.26        16.90         9.80 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
        9.63         2.96         8.65        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 
       86.70         6.02        12.43         6.74        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 
        0.72        16.64        32.45         8.71        10.98         5.19 

  AMP PEAK 11(3P14.1) MUTATED AMP PEAK 11(3P14.1) WILD-TYPE 
                         6.05                          0.03 
  AMP PEAK 11(3P14.1) MUTATED AMP PEAK 11(3P14.1) WILD-TYPE 
                        57.63                        158.83 
  AMP PEAK 11(3P14.1) MUTATED AMP PEAK 11(3P14.1) WILD-TYPE 
                       10.650                        16.605 
[1] "6.0 - 57.6 (10.7)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "8.3"
D9V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 11(3P14.1) MUTATED         3        1         0        0         0
  AMP PEAK 11(3P14.1) WILD-TYPE     277       50       109        2        45
                               vv
clus                            STAGE IVC
  AMP PEAK 11(3P14.1) MUTATED           1
  AMP PEAK 11(3P14.1) WILD-TYPE         5
D9V3, multiclass
           clus
vv          AMP PEAK 11(3P14.1) MUTATED AMP PEAK 11(3P14.1) WILD-TYPE
  STAGE I                             3                           277
  STAGE II                            1                            50
  STAGE III                           0                           109
  STAGE IV                            0                             2
  STAGE IVA                           0                            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
  AMP PEAK 11(3P14.1) MUTATED     2   1   1   1
  AMP PEAK 11(3P14.1) WILD-TYPE 138 165 164  20
D9V4, multiclass
    clus
vv   AMP PEAK 11(3P14.1) MUTATED AMP PEAK 11(3P14.1) WILD-TYPE
  T1                           2                           138
  T2                           1                           165
  T3                           1                           164
  T4                           1                            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"
D9V5, binary
                               cls
clus                              0   1
  AMP PEAK 11(3P14.1) MUTATED     2   2
  AMP PEAK 11(3P14.1) WILD-TYPE 221 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(3P14.1) MUTATED      2    2
  AMP PEAK 11(3P14.1) WILD-TYPE  221  220
   clus
vv  AMP PEAK 11(3P14.1) MUTATED AMP PEAK 11(3P14.1) WILD-TYPE
  0                           2                           221
  1                           2                           220
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK 11(3P14.1) MUTATED     2   1   2
  AMP PEAK 11(3P14.1) WILD-TYPE 271   8 210
D9V6, multiclass
    clus
vv   AMP PEAK 11(3P14.1) MUTATED AMP PEAK 11(3P14.1) WILD-TYPE
  M0                           2                           271
  M1                           1                             8
  MX                           2                           210
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                               cls
clus                              0   1
  AMP PEAK 11(3P14.1) MUTATED     4   1
  AMP PEAK 11(3P14.1) WILD-TYPE 360 130
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(3P14.1) MUTATED      4    1
  AMP PEAK 11(3P14.1) WILD-TYPE  360  130
        clus
vv       AMP PEAK 11(3P14.1) MUTATED AMP PEAK 11(3P14.1) WILD-TYPE
  FEMALE                           4                           360
  MALE                             1                           130
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 11(3P14.1) MUTATED                0
  AMP PEAK 11(3P14.1) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 11(3P14.1) MUTATED                                               3
  AMP PEAK 11(3P14.1) WILD-TYPE                                           350
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 11(3P14.1) MUTATED                                                                        2
  AMP PEAK 11(3P14.1) WILD-TYPE                                                                     96
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 11(3P14.1) MUTATED                                                                     0
  AMP PEAK 11(3P14.1) WILD-TYPE                                                                  35
D9V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 11(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 11(3P14.1) WILD-TYPE
  OTHER  SPECIFY                                                                                     9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    350
  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"
D9V9, binary
                               cls
clus                              0   1
  AMP PEAK 11(3P14.1) MUTATED     0   5
  AMP PEAK 11(3P14.1) WILD-TYPE  14 476
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(3P14.1) MUTATED      0    5
  AMP PEAK 11(3P14.1) WILD-TYPE   14  476
     clus
vv    AMP PEAK 11(3P14.1) MUTATED AMP PEAK 11(3P14.1) WILD-TYPE
  NO                            0                            14
  YES                           5                           476
[1] 2 2
[1] FALSE
D9V10, binary
                               cls
clus                              0   1
  AMP PEAK 11(3P14.1) MUTATED     4   1
  AMP PEAK 11(3P14.1) WILD-TYPE 413  16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(3P14.1) MUTATED      4    1
  AMP PEAK 11(3P14.1) WILD-TYPE  413   16
     clus
vv    AMP PEAK 11(3P14.1) MUTATED AMP PEAK 11(3P14.1) WILD-TYPE
  NO                            4                           413
  YES                           1                            16
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 11(3P14.1) MUTATED              1                       0    4
  AMP PEAK 11(3P14.1) WILD-TYPE          129                      16  324
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 11(3P14.1) MUTATED                     0
  AMP PEAK 11(3P14.1) WILD-TYPE                   1
D9V11, multiclass
                         clus
vv                        AMP PEAK 11(3P14.1) MUTATED
  MINIMAL (T3)                                      1
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              4
  VERY ADVANCED (T4B)                               0
                         clus
vv                        AMP PEAK 11(3P14.1) WILD-TYPE
  MINIMAL (T3)                                      129
  MODERATE/ADVANCED (T4A)                            16
  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 11(3P14.1) MUTATED     3   0   0   2
  AMP PEAK 11(3P14.1) WILD-TYPE 375  51   4  28
D9V12, multiclass
    clus
vv   AMP PEAK 11(3P14.1) MUTATED AMP PEAK 11(3P14.1) WILD-TYPE
  R0                           3                           375
  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 11(3P14.1) MUTATED     2   3
  AMP PEAK 11(3P14.1) WILD-TYPE 222 258
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(3P14.1) MUTATED      2    3
  AMP PEAK 11(3P14.1) WILD-TYPE  222  258
            clus
vv           AMP PEAK 11(3P14.1) MUTATED AMP PEAK 11(3P14.1) WILD-TYPE
  MULTIFOCAL                           2                           222
  UNIFOCAL                             3                           258
[1] 2 2
[1] FALSE
D9V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 11(3P14.1) MUTATED                                  0     1
  AMP PEAK 11(3P14.1) WILD-TYPE                                1    48
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(3P14.1) MUTATED                           0     2
  AMP PEAK 11(3P14.1) WILD-TYPE                        26   319
D9V16, multiclass
                                  clus
vv                                 AMP PEAK 11(3P14.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      2
                                  clus
vv                                 AMP PEAK 11(3P14.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       48
  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"
D9V17, binary
                               cls
clus                              0   1
  AMP PEAK 11(3P14.1) MUTATED     0   3
  AMP PEAK 11(3P14.1) WILD-TYPE  38 347
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(3P14.1) MUTATED      0    3
  AMP PEAK 11(3P14.1) WILD-TYPE   38  347
                        clus
vv                       AMP PEAK 11(3P14.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           3
                        clus
vv                       AMP PEAK 11(3P14.1) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           347
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 12(4P16.1) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 12(4P16.1) MUTATED     6   1
  AMP PEAK 12(4P16.1) WILD-TYPE 471  13
  AMP PEAK 12(4P16.1) MUTATED AMP PEAK 12(4P16.1) WILD-TYPE 
                            7                           484 
  AMP PEAK 12(4P16.1) MUTATED AMP PEAK 12(4P16.1) WILD-TYPE 
                            1                            13 
$`AMP PEAK 12(4P16.1) MUTATED`
TCGA-BJ-A0Z0 TCGA-DJ-A1QQ TCGA-EM-A1YD TCGA-EM-A22N TCGA-FE-A239 TCGA-FY-A3I5 
       13.78         5.95        57.01        10.65        33.63         1.64 
TCGA-FY-A3NM 
        0.99 

$`AMP PEAK 12(4P16.1) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       24.79        18.21        16.34        14.73         8.25        18.87 
TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ 
        4.01        11.57        16.73         7.56        15.12        17.69 
TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       23.34        20.71        20.58         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
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        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS 
       10.09         7.99         5.33         8.48        10.45         1.51 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY 
        9.60        12.56         8.28         7.69         5.52         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.42         8.12         9.34         6.77         9.21         9.44 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
        9.90         8.61        10.09         7.07        10.36        12.43 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        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        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04         1.15        22.29 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        12.36        18.05        19.79        19.46        54.21 
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 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT 
       23.51         6.05         2.99        12.30        15.19        10.49 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        13.84        19.73        17.59        12.07 
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        17.46        18.97 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        19.63        13.38         8.35        16.44 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       16.77        27.95        23.77        16.80        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        11.15 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33        12.53         9.24        13.91         7.82        11.51 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       16.41        15.62        13.51        12.79        70.65        16.90 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        9.01         4.83         8.61         8.38         9.80         5.03 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       37.87        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       29.49        54.05        22.09        12.26        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       65.36        84.89        98.56        61.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        59.15        28.24         5.85         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        24.69        68.22       102.90        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       81.34        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        46.06         4.08         0.89        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON 
       48.10        91.17         1.25         1.15        17.82         1.51 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        0.76         0.03         4.67        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         6.87         4.14         6.58         4.54 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
        0.89         1.35         1.15         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        10.26        16.90         9.80         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        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        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       12.43         6.74        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         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

  AMP PEAK 12(4P16.1) MUTATED AMP PEAK 12(4P16.1) WILD-TYPE 
                         0.99                          0.03 
  AMP PEAK 12(4P16.1) MUTATED AMP PEAK 12(4P16.1) WILD-TYPE 
                        57.01                        158.83 
  AMP PEAK 12(4P16.1) MUTATED AMP PEAK 12(4P16.1) WILD-TYPE 
                       10.650                        16.685 
[1] "1.0 - 57.0 (10.7)"  "0.0 - 158.8 (16.7)"
[1] "hr=" "7.4"
D10V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 12(4P16.1) MUTATED         2        2         3        0         0
  AMP PEAK 12(4P16.1) WILD-TYPE     278       49       106        2        45
                               vv
clus                            STAGE IVC
  AMP PEAK 12(4P16.1) MUTATED           0
  AMP PEAK 12(4P16.1) WILD-TYPE         6
D10V3, multiclass
           clus
vv          AMP PEAK 12(4P16.1) MUTATED AMP PEAK 12(4P16.1) WILD-TYPE
  STAGE I                             2                           278
  STAGE II                            2                            49
  STAGE III                           3                           106
  STAGE IV                            0                             2
  STAGE IVA                           0                            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 12(4P16.1) MUTATED     1   2   4   0
  AMP PEAK 12(4P16.1) WILD-TYPE 139 164 161  21
D10V4, multiclass
    clus
vv   AMP PEAK 12(4P16.1) MUTATED AMP PEAK 12(4P16.1) WILD-TYPE
  T1                           1                           139
  T2                           2                           164
  T3                           4                           161
  T4                           0                            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"
D10V5, binary
                               cls
clus                              0   1
  AMP PEAK 12(4P16.1) MUTATED     7   0
  AMP PEAK 12(4P16.1) WILD-TYPE 216 222
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(4P16.1) MUTATED      7    0
  AMP PEAK 12(4P16.1) WILD-TYPE  216  222
   clus
vv  AMP PEAK 12(4P16.1) MUTATED AMP PEAK 12(4P16.1) WILD-TYPE
  0                           7                           216
  1                           0                           222
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK 12(4P16.1) MUTATED     1   0   6
  AMP PEAK 12(4P16.1) WILD-TYPE 272   9 206
D10V6, multiclass
    clus
vv   AMP PEAK 12(4P16.1) MUTATED AMP PEAK 12(4P16.1) WILD-TYPE
  M0                           1                           272
  M1                           0                             9
  MX                           6                           206
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                               cls
clus                              0   1
  AMP PEAK 12(4P16.1) MUTATED     4   3
  AMP PEAK 12(4P16.1) WILD-TYPE 360 128
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(4P16.1) MUTATED      4    3
  AMP PEAK 12(4P16.1) WILD-TYPE  360  128
        clus
vv       AMP PEAK 12(4P16.1) MUTATED AMP PEAK 12(4P16.1) WILD-TYPE
  FEMALE                           4                           360
  MALE                             3                           128
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 12(4P16.1) MUTATED                0
  AMP PEAK 12(4P16.1) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 12(4P16.1) MUTATED                                               4
  AMP PEAK 12(4P16.1) WILD-TYPE                                           349
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 12(4P16.1) MUTATED                                                                        3
  AMP PEAK 12(4P16.1) WILD-TYPE                                                                     95
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 12(4P16.1) MUTATED                                                                     0
  AMP PEAK 12(4P16.1) WILD-TYPE                                                                  35
D10V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 12(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 12(4P16.1) WILD-TYPE
  OTHER  SPECIFY                                                                                     9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    349
  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"
D10V9, binary
                               cls
clus                              0   1
  AMP PEAK 12(4P16.1) MUTATED     1   6
  AMP PEAK 12(4P16.1) WILD-TYPE  13 475
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(4P16.1) MUTATED      1    6
  AMP PEAK 12(4P16.1) WILD-TYPE   13  475
     clus
vv    AMP PEAK 12(4P16.1) MUTATED AMP PEAK 12(4P16.1) WILD-TYPE
  NO                            1                            13
  YES                           6                           475
[1] 2 2
[1] FALSE
D10V10, binary
                               cls
clus                              0   1
  AMP PEAK 12(4P16.1) MUTATED     5   0
  AMP PEAK 12(4P16.1) WILD-TYPE 412  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(4P16.1) MUTATED      5    0
  AMP PEAK 12(4P16.1) WILD-TYPE  412   17
     clus
vv    AMP PEAK 12(4P16.1) MUTATED AMP PEAK 12(4P16.1) WILD-TYPE
  NO                            5                           412
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 12(4P16.1) MUTATED              2                       0    5
  AMP PEAK 12(4P16.1) WILD-TYPE          128                      16  323
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 12(4P16.1) MUTATED                     0
  AMP PEAK 12(4P16.1) WILD-TYPE                   1
D10V11, multiclass
                         clus
vv                        AMP PEAK 12(4P16.1) MUTATED
  MINIMAL (T3)                                      2
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              5
  VERY ADVANCED (T4B)                               0
                         clus
vv                        AMP PEAK 12(4P16.1) WILD-TYPE
  MINIMAL (T3)                                      128
  MODERATE/ADVANCED (T4A)                            16
  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 12(4P16.1) MUTATED     6   0   0   1
  AMP PEAK 12(4P16.1) WILD-TYPE 372  51   4  29
D10V12, multiclass
    clus
vv   AMP PEAK 12(4P16.1) MUTATED AMP PEAK 12(4P16.1) WILD-TYPE
  R0                           6                           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"
D10V13, continuous
D10V14, binary
                               cls
clus                              0   1
  AMP PEAK 12(4P16.1) MUTATED     5   2
  AMP PEAK 12(4P16.1) WILD-TYPE 219 259
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(4P16.1) MUTATED      5    2
  AMP PEAK 12(4P16.1) WILD-TYPE  219  259
            clus
vv           AMP PEAK 12(4P16.1) MUTATED AMP PEAK 12(4P16.1) WILD-TYPE
  MULTIFOCAL                           5                           219
  UNIFOCAL                             2                           259
[1] 2 2
[1] FALSE
D10V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 12(4P16.1) MUTATED                                  0     1
  AMP PEAK 12(4P16.1) WILD-TYPE                                1    48
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(4P16.1) MUTATED                           0     3
  AMP PEAK 12(4P16.1) WILD-TYPE                        26   318
D10V16, multiclass
                                  clus
vv                                 AMP PEAK 12(4P16.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      3
                                  clus
vv                                 AMP PEAK 12(4P16.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       48
  BLACK OR AFRICAN AMERICAN                                   26
  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"
D10V17, binary
                               cls
clus                              0   1
  AMP PEAK 12(4P16.1) MUTATED     0   5
  AMP PEAK 12(4P16.1) WILD-TYPE  38 345
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(4P16.1) MUTATED      0    5
  AMP PEAK 12(4P16.1) WILD-TYPE   38  345
                        clus
vv                       AMP PEAK 12(4P16.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           5
                        clus
vv                       AMP PEAK 12(4P16.1) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           345
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 13(4Q22.1) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 13(4Q22.1) MUTATED     6   1
  AMP PEAK 13(4Q22.1) WILD-TYPE 471  13
  AMP PEAK 13(4Q22.1) MUTATED AMP PEAK 13(4Q22.1) WILD-TYPE 
                            7                           484 
  AMP PEAK 13(4Q22.1) MUTATED AMP PEAK 13(4Q22.1) WILD-TYPE 
                            1                            13 
$`AMP PEAK 13(4Q22.1) MUTATED`
TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22N TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3NM 
       57.01        14.73        10.65        33.63         1.64         0.99 
TCGA-J8-A3YD 
       31.82 

$`AMP PEAK 13(4Q22.1) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        5.52         8.78         8.42         8.12         9.34         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
        9.21         9.44         9.90         8.61        10.09         7.07 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       10.36        12.43        10.85        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        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 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.07        14.27         3.02        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        13.78        13.58        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        80.91         4.18 
TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 
       58.82         1.45        74.30        45.40        33.47       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
       39.32         1.41        30.18       102.84        65.39       124.04 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        37.25       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        38.66        52.73       139.00       131.15 
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        12.16       147.42 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      130.72       129.57        32.48       116.91        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
       95.38         5.72        66.90        82.82        77.36        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       31.50        50.33        53.06        47.38        52.50        45.53 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       48.16         7.07        44.65        45.80        19.30        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        19.59        30.51        33.60        28.73 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        37.78        29.95        13.32        11.87         8.71 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        12.36        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YE TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       19.46        54.21        54.08        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        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       10.49        13.15        22.16        13.84        19.73        17.59 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       12.07        17.59        17.46        17.29        14.60        17.46 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       18.97        15.68        14.14        19.63        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       16.44        16.77        27.95        23.77        16.80        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 
       11.15         7.33        12.53         9.24        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        16.41        15.62        13.51        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
       80.02        65.36        84.89        98.56        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        2.43         5.56        24.72        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       59.70        31.59        44.25        24.69        68.22       102.90 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       66.77        81.34        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        46.06         4.08         0.89        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10        91.17         1.25         1.15        17.82 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
        1.51         0.76         0.03         4.67        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         6.87         4.14         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
        4.54         0.89         1.35         1.15         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        10.26        16.90         9.80         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        17.23        43.17        27.19        11.24 
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        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       12.43         6.74        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         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

  AMP PEAK 13(4Q22.1) MUTATED AMP PEAK 13(4Q22.1) WILD-TYPE 
                         0.99                          0.03 
  AMP PEAK 13(4Q22.1) MUTATED AMP PEAK 13(4Q22.1) WILD-TYPE 
                        57.01                        158.83 
  AMP PEAK 13(4Q22.1) MUTATED AMP PEAK 13(4Q22.1) WILD-TYPE 
                       14.730                        16.605 
[1] "1.0 - 57.0 (14.7)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "6.5"
D11V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 13(4Q22.1) MUTATED         1        1         5        0         0
  AMP PEAK 13(4Q22.1) WILD-TYPE     279       50       104        2        45
                               vv
clus                            STAGE IVC
  AMP PEAK 13(4Q22.1) MUTATED           0
  AMP PEAK 13(4Q22.1) WILD-TYPE         6
D11V3, multiclass
           clus
vv          AMP PEAK 13(4Q22.1) MUTATED AMP PEAK 13(4Q22.1) WILD-TYPE
  STAGE I                             1                           279
  STAGE II                            1                            50
  STAGE III                           5                           104
  STAGE IV                            0                             2
  STAGE IVA                           0                            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 13(4Q22.1) MUTATED     2   1   4   0
  AMP PEAK 13(4Q22.1) WILD-TYPE 138 165 161  21
D11V4, multiclass
    clus
vv   AMP PEAK 13(4Q22.1) MUTATED AMP PEAK 13(4Q22.1) WILD-TYPE
  T1                           2                           138
  T2                           1                           165
  T3                           4                           161
  T4                           0                            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"
D11V5, binary
                               cls
clus                              0   1
  AMP PEAK 13(4Q22.1) MUTATED     6   1
  AMP PEAK 13(4Q22.1) WILD-TYPE 217 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(4Q22.1) MUTATED      6    1
  AMP PEAK 13(4Q22.1) WILD-TYPE  217  221
   clus
vv  AMP PEAK 13(4Q22.1) MUTATED AMP PEAK 13(4Q22.1) WILD-TYPE
  0                           6                           217
  1                           1                           221
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK 13(4Q22.1) MUTATED     1   0   6
  AMP PEAK 13(4Q22.1) WILD-TYPE 272   9 206
D11V6, multiclass
    clus
vv   AMP PEAK 13(4Q22.1) MUTATED AMP PEAK 13(4Q22.1) WILD-TYPE
  M0                           1                           272
  M1                           0                             9
  MX                           6                           206
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                               cls
clus                              0   1
  AMP PEAK 13(4Q22.1) MUTATED     6   1
  AMP PEAK 13(4Q22.1) WILD-TYPE 358 130
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(4Q22.1) MUTATED      6    1
  AMP PEAK 13(4Q22.1) WILD-TYPE  358  130
        clus
vv       AMP PEAK 13(4Q22.1) MUTATED AMP PEAK 13(4Q22.1) WILD-TYPE
  FEMALE                           6                           358
  MALE                             1                           130
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 13(4Q22.1) MUTATED                0
  AMP PEAK 13(4Q22.1) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 13(4Q22.1) MUTATED                                               4
  AMP PEAK 13(4Q22.1) WILD-TYPE                                           349
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 13(4Q22.1) MUTATED                                                                        3
  AMP PEAK 13(4Q22.1) WILD-TYPE                                                                     95
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 13(4Q22.1) MUTATED                                                                     0
  AMP PEAK 13(4Q22.1) WILD-TYPE                                                                  35
D11V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 13(4Q22.1) 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 13(4Q22.1) WILD-TYPE
  OTHER  SPECIFY                                                                                     9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    349
  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"
D11V9, binary
                               cls
clus                              0   1
  AMP PEAK 13(4Q22.1) MUTATED     1   6
  AMP PEAK 13(4Q22.1) WILD-TYPE  13 475
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(4Q22.1) MUTATED      1    6
  AMP PEAK 13(4Q22.1) WILD-TYPE   13  475
     clus
vv    AMP PEAK 13(4Q22.1) MUTATED AMP PEAK 13(4Q22.1) WILD-TYPE
  NO                            1                            13
  YES                           6                           475
[1] 2 2
[1] FALSE
D11V10, binary
                               cls
clus                              0   1
  AMP PEAK 13(4Q22.1) MUTATED     5   0
  AMP PEAK 13(4Q22.1) WILD-TYPE 412  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(4Q22.1) MUTATED      5    0
  AMP PEAK 13(4Q22.1) WILD-TYPE  412   17
     clus
vv    AMP PEAK 13(4Q22.1) MUTATED AMP PEAK 13(4Q22.1) WILD-TYPE
  NO                            5                           412
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 13(4Q22.1) MUTATED              2                       0    5
  AMP PEAK 13(4Q22.1) WILD-TYPE          128                      16  323
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 13(4Q22.1) MUTATED                     0
  AMP PEAK 13(4Q22.1) WILD-TYPE                   1
D11V11, multiclass
                         clus
vv                        AMP PEAK 13(4Q22.1) MUTATED
  MINIMAL (T3)                                      2
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              5
  VERY ADVANCED (T4B)                               0
                         clus
vv                        AMP PEAK 13(4Q22.1) WILD-TYPE
  MINIMAL (T3)                                      128
  MODERATE/ADVANCED (T4A)                            16
  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 13(4Q22.1) MUTATED     5   1   0   1
  AMP PEAK 13(4Q22.1) WILD-TYPE 373  50   4  29
D11V12, multiclass
    clus
vv   AMP PEAK 13(4Q22.1) MUTATED AMP PEAK 13(4Q22.1) WILD-TYPE
  R0                           5                           373
  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"
D11V13, continuous
D11V14, binary
                               cls
clus                              0   1
  AMP PEAK 13(4Q22.1) MUTATED     5   2
  AMP PEAK 13(4Q22.1) WILD-TYPE 219 259
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(4Q22.1) MUTATED      5    2
  AMP PEAK 13(4Q22.1) WILD-TYPE  219  259
            clus
vv           AMP PEAK 13(4Q22.1) MUTATED AMP PEAK 13(4Q22.1) WILD-TYPE
  MULTIFOCAL                           5                           219
  UNIFOCAL                             2                           259
[1] 2 2
[1] FALSE
D11V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 13(4Q22.1) MUTATED                                  0     0
  AMP PEAK 13(4Q22.1) WILD-TYPE                                1    49
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(4Q22.1) MUTATED                           0     4
  AMP PEAK 13(4Q22.1) WILD-TYPE                        26   317
D11V16, multiclass
                                  clus
vv                                 AMP PEAK 13(4Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      4
                                  clus
vv                                 AMP PEAK 13(4Q22.1) 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"
D11V17, binary
                               cls
clus                              0   1
  AMP PEAK 13(4Q22.1) MUTATED     0   3
  AMP PEAK 13(4Q22.1) WILD-TYPE  38 347
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(4Q22.1) MUTATED      0    3
  AMP PEAK 13(4Q22.1) WILD-TYPE   38  347
                        clus
vv                       AMP PEAK 13(4Q22.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           3
                        clus
vv                       AMP PEAK 13(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           347
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 14(4Q28.2) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 14(4Q28.2) MUTATED     5   1
  AMP PEAK 14(4Q28.2) WILD-TYPE 472  13
  AMP PEAK 14(4Q28.2) MUTATED AMP PEAK 14(4Q28.2) WILD-TYPE 
                            6                           485 
  AMP PEAK 14(4Q28.2) MUTATED AMP PEAK 14(4Q28.2) WILD-TYPE 
                            1                            13 
$`AMP PEAK 14(4Q28.2) MUTATED`
TCGA-DJ-A1QQ TCGA-EM-A1YD TCGA-EM-A22N TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3NM 
        5.95        57.01        10.65        33.63         1.64         0.99 

$`AMP PEAK 14(4Q28.2) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        1.02        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
        1.45        74.30        45.40        33.47       108.36        39.32 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        30.18       102.84        65.39       124.04        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       37.25       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        38.66        52.73       139.00       131.15       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        12.16       147.42       130.72 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       116.91        98.24        41.29        95.38 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       50.33        53.06        47.38        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       37.78        29.95        13.32        11.87         8.71        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        12.36        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       54.21        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        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       10.49        13.15        22.16        13.84        19.73        17.59 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       12.07        17.59        17.46        17.29        14.60        17.46 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       18.97        15.68        14.14        19.63        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       16.44        16.77        27.95        23.77        16.80        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 
       11.15         7.33        12.53         9.24        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        16.41        15.62        13.51        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
       80.02        65.36        84.89        98.56        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        2.43         5.56        24.72        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       59.70        31.59        44.25        24.69        68.22       102.90 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       66.77        81.34        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        46.06         4.08         0.89        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10        91.17         1.25         1.15        17.82 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
        1.51         0.76         0.03         4.67        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         6.87         4.14         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
        4.54         0.89         1.35         1.15         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        10.26        16.90         9.80         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        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        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        12.43         6.74        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         0.72 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       16.64        32.45         8.71        10.98         5.19 

  AMP PEAK 14(4Q28.2) MUTATED AMP PEAK 14(4Q28.2) WILD-TYPE 
                         0.99                          0.03 
  AMP PEAK 14(4Q28.2) MUTATED AMP PEAK 14(4Q28.2) WILD-TYPE 
                        57.01                        158.83 
  AMP PEAK 14(4Q28.2) MUTATED AMP PEAK 14(4Q28.2) WILD-TYPE 
                         8.30                         16.64 
[1] "1.0 - 57.0 (8.3)"   "0.0 - 158.8 (16.6)"
[1] "hr=" "7.7"
D12V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 14(4Q28.2) MUTATED         2        1         3        0         0
  AMP PEAK 14(4Q28.2) WILD-TYPE     278       50       106        2        45
                               vv
clus                            STAGE IVC
  AMP PEAK 14(4Q28.2) MUTATED           0
  AMP PEAK 14(4Q28.2) WILD-TYPE         6
D12V3, multiclass
           clus
vv          AMP PEAK 14(4Q28.2) MUTATED AMP PEAK 14(4Q28.2) WILD-TYPE
  STAGE I                             2                           278
  STAGE II                            1                            50
  STAGE III                           3                           106
  STAGE IV                            0                             2
  STAGE IVA                           0                            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 14(4Q28.2) MUTATED     1   1   4   0
  AMP PEAK 14(4Q28.2) WILD-TYPE 139 165 161  21
D12V4, multiclass
    clus
vv   AMP PEAK 14(4Q28.2) MUTATED AMP PEAK 14(4Q28.2) WILD-TYPE
  T1                           1                           139
  T2                           1                           165
  T3                           4                           161
  T4                           0                            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"
D12V5, binary
                               cls
clus                              0   1
  AMP PEAK 14(4Q28.2) MUTATED     6   0
  AMP PEAK 14(4Q28.2) WILD-TYPE 217 222
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(4Q28.2) MUTATED      6    0
  AMP PEAK 14(4Q28.2) WILD-TYPE  217  222
   clus
vv  AMP PEAK 14(4Q28.2) MUTATED AMP PEAK 14(4Q28.2) WILD-TYPE
  0                           6                           217
  1                           0                           222
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK 14(4Q28.2) MUTATED     1   0   5
  AMP PEAK 14(4Q28.2) WILD-TYPE 272   9 207
D12V6, multiclass
    clus
vv   AMP PEAK 14(4Q28.2) MUTATED AMP PEAK 14(4Q28.2) WILD-TYPE
  M0                           1                           272
  M1                           0                             9
  MX                           5                           207
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                               cls
clus                              0   1
  AMP PEAK 14(4Q28.2) MUTATED     4   2
  AMP PEAK 14(4Q28.2) WILD-TYPE 360 129
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(4Q28.2) MUTATED      4    2
  AMP PEAK 14(4Q28.2) WILD-TYPE  360  129
        clus
vv       AMP PEAK 14(4Q28.2) MUTATED AMP PEAK 14(4Q28.2) WILD-TYPE
  FEMALE                           4                           360
  MALE                             2                           129
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 14(4Q28.2) MUTATED                0
  AMP PEAK 14(4Q28.2) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 14(4Q28.2) MUTATED                                               3
  AMP PEAK 14(4Q28.2) WILD-TYPE                                           350
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 14(4Q28.2) MUTATED                                                                        3
  AMP PEAK 14(4Q28.2) WILD-TYPE                                                                     95
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 14(4Q28.2) MUTATED                                                                     0
  AMP PEAK 14(4Q28.2) WILD-TYPE                                                                  35
D12V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 14(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 14(4Q28.2) WILD-TYPE
  OTHER  SPECIFY                                                                                     9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    350
  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"
D12V9, binary
                               cls
clus                              0   1
  AMP PEAK 14(4Q28.2) MUTATED     1   5
  AMP PEAK 14(4Q28.2) WILD-TYPE  13 476
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(4Q28.2) MUTATED      1    5
  AMP PEAK 14(4Q28.2) WILD-TYPE   13  476
     clus
vv    AMP PEAK 14(4Q28.2) MUTATED AMP PEAK 14(4Q28.2) WILD-TYPE
  NO                            1                            13
  YES                           5                           476
[1] 2 2
[1] FALSE
D12V10, binary
                               cls
clus                              0   1
  AMP PEAK 14(4Q28.2) MUTATED     5   0
  AMP PEAK 14(4Q28.2) WILD-TYPE 412  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(4Q28.2) MUTATED      5    0
  AMP PEAK 14(4Q28.2) WILD-TYPE  412   17
     clus
vv    AMP PEAK 14(4Q28.2) MUTATED AMP PEAK 14(4Q28.2) WILD-TYPE
  NO                            5                           412
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 14(4Q28.2) MUTATED              2                       0    4
  AMP PEAK 14(4Q28.2) WILD-TYPE          128                      16  324
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 14(4Q28.2) MUTATED                     0
  AMP PEAK 14(4Q28.2) WILD-TYPE                   1
D12V11, multiclass
                         clus
vv                        AMP PEAK 14(4Q28.2) MUTATED
  MINIMAL (T3)                                      2
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              4
  VERY ADVANCED (T4B)                               0
                         clus
vv                        AMP PEAK 14(4Q28.2) WILD-TYPE
  MINIMAL (T3)                                      128
  MODERATE/ADVANCED (T4A)                            16
  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 14(4Q28.2) MUTATED     5   0   0   1
  AMP PEAK 14(4Q28.2) WILD-TYPE 373  51   4  29
D12V12, multiclass
    clus
vv   AMP PEAK 14(4Q28.2) MUTATED AMP PEAK 14(4Q28.2) WILD-TYPE
  R0                           5                           373
  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"
D12V13, continuous
D12V14, binary
                               cls
clus                              0   1
  AMP PEAK 14(4Q28.2) MUTATED     5   1
  AMP PEAK 14(4Q28.2) WILD-TYPE 219 260
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(4Q28.2) MUTATED      5    1
  AMP PEAK 14(4Q28.2) WILD-TYPE  219  260
            clus
vv           AMP PEAK 14(4Q28.2) MUTATED AMP PEAK 14(4Q28.2) WILD-TYPE
  MULTIFOCAL                           5                           219
  UNIFOCAL                             1                           260
[1] 2 2
[1] FALSE
D12V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 14(4Q28.2) MUTATED                                  0     1
  AMP PEAK 14(4Q28.2) WILD-TYPE                                1    48
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(4Q28.2) MUTATED                           0     3
  AMP PEAK 14(4Q28.2) WILD-TYPE                        26   318
D12V16, multiclass
                                  clus
vv                                 AMP PEAK 14(4Q28.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      3
                                  clus
vv                                 AMP PEAK 14(4Q28.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       48
  BLACK OR AFRICAN AMERICAN                                   26
  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"
D12V17, binary
                               cls
clus                              0   1
  AMP PEAK 14(4Q28.2) MUTATED     0   4
  AMP PEAK 14(4Q28.2) WILD-TYPE  38 346
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(4Q28.2) MUTATED      0    4
  AMP PEAK 14(4Q28.2) WILD-TYPE   38  346
                        clus
vv                       AMP PEAK 14(4Q28.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           4
                        clus
vv                       AMP PEAK 14(4Q28.2) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           346
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 15(4Q31.21) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(4Q31.21) MUTATED     9   1
  AMP PEAK 15(4Q31.21) WILD-TYPE 468  13
  AMP PEAK 15(4Q31.21) MUTATED AMP PEAK 15(4Q31.21) WILD-TYPE 
                            10                            481 
  AMP PEAK 15(4Q31.21) MUTATED AMP PEAK 15(4Q31.21) WILD-TYPE 
                             1                             13 
$`AMP PEAK 15(4Q31.21) MUTATED`
TCGA-DJ-A3V2 TCGA-DJ-A3V7 TCGA-EL-A3T1 TCGA-EM-A1YD TCGA-EM-A22N TCGA-ET-A39P 
       20.22         9.83       129.57        57.01        10.65        58.72 
TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A76V 
       33.63         1.64         0.99         1.68 

$`AMP PEAK 15(4Q31.21) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        5.52         8.78         8.42         8.12         9.34         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
        9.21         9.44         9.90         8.61        10.09         7.07 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       10.36        12.43        10.85        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        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 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       25.02        30.61        14.56        19.20        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04         1.15        22.29 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      116.91        98.24        41.29        95.38         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN 
       82.82        77.36        78.97        31.50        50.33        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        52.50        45.53        48.16         7.07        44.65 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       45.80        19.30        45.96        37.94        31.04        19.59 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        33.60        28.73        41.13        37.78        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       13.32        11.87         8.71        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YE 
       12.36        18.05        19.79        19.46        54.21        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        11.74 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.15        14.24        16.44        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
        6.05         2.99        12.30        15.19        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        13.84        19.73        17.59        12.07        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        17.46        18.97        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR 
       14.14        19.63        13.38         8.35        16.44        16.77 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        16.80        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        11.15         7.33 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
       12.53         9.24        13.91         7.82        11.51        16.41 
TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       15.62        13.51        12.79        70.65        16.90         9.01 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        4.83         8.61         8.38         9.80         5.03        37.87 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       12.72         0.95        47.47        48.20        29.69        32.35 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       14.79        12.33        14.79        27.09        18.38        29.49 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       54.05        22.09        12.26        16.08        29.19        19.76 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        58.22        13.74        71.01        80.02        65.36 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89        98.56        61.02        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24         5.85         4.18         2.43         5.56        24.72 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       38.30        42.25         2.37         4.50        80.81        69.24 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       59.87        43.50         0.30        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        4.01         1.94        73.74        59.70        31.59        44.25 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       102.90        66.77        81.34        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        46.06 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.08         0.89        22.03         0.92        48.10        91.17 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        1.25         1.15        17.82         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
        4.67        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 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.15        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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74        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         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  AMP PEAK 15(4Q31.21) MUTATED AMP PEAK 15(4Q31.21) WILD-TYPE 
                          0.99                           0.03 
  AMP PEAK 15(4Q31.21) MUTATED AMP PEAK 15(4Q31.21) WILD-TYPE 
                        129.57                         158.83 
  AMP PEAK 15(4Q31.21) MUTATED AMP PEAK 15(4Q31.21) WILD-TYPE 
                        15.435                         16.570 
[1] "1.0 - 129.6 (15.4)" "0.0 - 158.8 (16.6)"
[1] "hr=" "2.4"
D13V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 15(4Q31.21) MUTATED         3        2         5        0         0
  AMP PEAK 15(4Q31.21) WILD-TYPE     277       49       104        2        45
                                vv
clus                             STAGE IVC
  AMP PEAK 15(4Q31.21) MUTATED           0
  AMP PEAK 15(4Q31.21) WILD-TYPE         6
D13V3, multiclass
           clus
vv          AMP PEAK 15(4Q31.21) MUTATED AMP PEAK 15(4Q31.21) WILD-TYPE
  STAGE I                              3                            277
  STAGE II                             2                             49
  STAGE III                            5                            104
  STAGE IV                             0                              2
  STAGE IVA                            0                             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 15(4Q31.21) MUTATED     1   4   5   0
  AMP PEAK 15(4Q31.21) WILD-TYPE 139 162 160  21
D13V4, multiclass
    clus
vv   AMP PEAK 15(4Q31.21) MUTATED AMP PEAK 15(4Q31.21) WILD-TYPE
  T1                            1                            139
  T2                            4                            162
  T3                            5                            160
  T4                            0                             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"
D13V5, binary
                                cls
clus                               0   1
  AMP PEAK 15(4Q31.21) MUTATED     8   1
  AMP PEAK 15(4Q31.21) WILD-TYPE 215 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(4Q31.21) MUTATED      8    1
  AMP PEAK 15(4Q31.21) WILD-TYPE  215  221
   clus
vv  AMP PEAK 15(4Q31.21) MUTATED AMP PEAK 15(4Q31.21) WILD-TYPE
  0                            8                            215
  1                            1                            221
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 15(4Q31.21) MUTATED     3   0   7
  AMP PEAK 15(4Q31.21) WILD-TYPE 270   9 205
D13V6, multiclass
    clus
vv   AMP PEAK 15(4Q31.21) MUTATED AMP PEAK 15(4Q31.21) WILD-TYPE
  M0                            3                            270
  M1                            0                              9
  MX                            7                            205
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                                cls
clus                               0   1
  AMP PEAK 15(4Q31.21) MUTATED     8   2
  AMP PEAK 15(4Q31.21) WILD-TYPE 356 129
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(4Q31.21) MUTATED      8    2
  AMP PEAK 15(4Q31.21) WILD-TYPE  356  129
        clus
vv       AMP PEAK 15(4Q31.21) MUTATED AMP PEAK 15(4Q31.21) WILD-TYPE
  FEMALE                            8                            356
  MALE                              2                            129
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 15(4Q31.21) MUTATED                0
  AMP PEAK 15(4Q31.21) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 15(4Q31.21) MUTATED                                               6
  AMP PEAK 15(4Q31.21) WILD-TYPE                                           347
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 15(4Q31.21) MUTATED                                                                        3
  AMP PEAK 15(4Q31.21) WILD-TYPE                                                                     95
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 15(4Q31.21) MUTATED                                                                     1
  AMP PEAK 15(4Q31.21) WILD-TYPE                                                                  34
D13V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 15(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 15(4Q31.21) WILD-TYPE
  OTHER  SPECIFY                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     347
  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"
D13V9, binary
                                cls
clus                               0   1
  AMP PEAK 15(4Q31.21) MUTATED     1   9
  AMP PEAK 15(4Q31.21) WILD-TYPE  13 472
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(4Q31.21) MUTATED      1    9
  AMP PEAK 15(4Q31.21) WILD-TYPE   13  472
     clus
vv    AMP PEAK 15(4Q31.21) MUTATED AMP PEAK 15(4Q31.21) WILD-TYPE
  NO                             1                             13
  YES                            9                            472
[1] 2 2
[1] FALSE
D13V10, binary
                                cls
clus                               0   1
  AMP PEAK 15(4Q31.21) MUTATED     9   0
  AMP PEAK 15(4Q31.21) WILD-TYPE 408  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(4Q31.21) MUTATED      9    0
  AMP PEAK 15(4Q31.21) WILD-TYPE  408   17
     clus
vv    AMP PEAK 15(4Q31.21) MUTATED AMP PEAK 15(4Q31.21) WILD-TYPE
  NO                             9                            408
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 15(4Q31.21) MUTATED              4                       0    6
  AMP PEAK 15(4Q31.21) WILD-TYPE          126                      16  322
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 15(4Q31.21) MUTATED                     0
  AMP PEAK 15(4Q31.21) WILD-TYPE                   1
D13V11, multiclass
                         clus
vv                        AMP PEAK 15(4Q31.21) MUTATED
  MINIMAL (T3)                                       4
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               6
  VERY ADVANCED (T4B)                                0
                         clus
vv                        AMP PEAK 15(4Q31.21) WILD-TYPE
  MINIMAL (T3)                                       126
  MODERATE/ADVANCED (T4A)                             16
  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
  AMP PEAK 15(4Q31.21) MUTATED     8   1   0   1
  AMP PEAK 15(4Q31.21) WILD-TYPE 370  50   4  29
D13V12, multiclass
    clus
vv   AMP PEAK 15(4Q31.21) MUTATED AMP PEAK 15(4Q31.21) WILD-TYPE
  R0                            8                            370
  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"
D13V13, continuous
D13V14, binary
                                cls
clus                               0   1
  AMP PEAK 15(4Q31.21) MUTATED     7   3
  AMP PEAK 15(4Q31.21) WILD-TYPE 217 258
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(4Q31.21) MUTATED      7    3
  AMP PEAK 15(4Q31.21) WILD-TYPE  217  258
            clus
vv           AMP PEAK 15(4Q31.21) MUTATED AMP PEAK 15(4Q31.21) WILD-TYPE
  MULTIFOCAL                            7                            217
  UNIFOCAL                              3                            258
[1] 2 2
[1] FALSE
D13V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 15(4Q31.21) MUTATED                                  0     0
  AMP PEAK 15(4Q31.21) WILD-TYPE                                1    49
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(4Q31.21) MUTATED                           3     5
  AMP PEAK 15(4Q31.21) WILD-TYPE                        23   316
D13V16, multiclass
                                  clus
vv                                 AMP PEAK 15(4Q31.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                       5
                                  clus
vv                                 AMP PEAK 15(4Q31.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        49
  BLACK OR AFRICAN AMERICAN                                    23
  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"
D13V17, binary
                                cls
clus                               0   1
  AMP PEAK 15(4Q31.21) MUTATED     0   8
  AMP PEAK 15(4Q31.21) WILD-TYPE  38 342
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(4Q31.21) MUTATED      0    8
  AMP PEAK 15(4Q31.21) WILD-TYPE   38  342
                        clus
vv                       AMP PEAK 15(4Q31.21) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            8
                        clus
vv                       AMP PEAK 15(4Q31.21) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            342
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 16(4Q32.3) MUTATION ANALYSIS
D14V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 16(4Q32.3) MUTATED     6   1
  AMP PEAK 16(4Q32.3) WILD-TYPE 471  13
  AMP PEAK 16(4Q32.3) MUTATED AMP PEAK 16(4Q32.3) WILD-TYPE 
                            7                           484 
  AMP PEAK 16(4Q32.3) MUTATED AMP PEAK 16(4Q32.3) WILD-TYPE 
                            1                            13 
$`AMP PEAK 16(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         1.64 
TCGA-FY-A3NM 
        0.99 

$`AMP PEAK 16(4Q32.3) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        5.52         8.78         8.42         8.12         9.34         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
        9.21         9.44         9.90         8.61        10.09         7.07 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       10.36        12.43        10.85        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        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 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.07        14.27         3.02        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
        1.45        74.30        45.40        33.47       108.36        39.32 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        30.18       102.84        65.39       124.04        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       37.25       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        38.66        52.73       139.00       131.15       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        12.16       147.42       130.72 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       116.91        98.24        41.29        95.38 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       50.33        53.06        47.38        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       37.78        29.95        13.32        11.87         8.71        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        12.36        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       54.21        54.08        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       14.53        11.74        11.15        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT 
       23.51         6.05         2.99        12.30        15.19        10.49 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        13.84        19.73        17.59        12.07 
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        17.46        18.97 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        19.63        13.38         8.35        16.44 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       16.77        27.95        23.77        16.80        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        11.15 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33        12.53         9.24        13.91         7.82        11.51 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       16.41        15.62        13.51        12.79        70.65        16.90 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        9.01         4.83         8.61         8.38         9.80         5.03 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       37.87        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       29.49        54.05        22.09        12.26        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       65.36        84.89        98.56        61.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        59.15        28.24         5.85         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        24.69        68.22       102.90        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       81.34        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        46.06         4.08         0.89        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON 
       48.10        91.17         1.25         1.15        17.82         1.51 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        0.76         0.03         4.67        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         6.87         4.14         6.58         4.54 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
        0.89         1.35         1.15         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        10.26        16.90         9.80         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        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        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       12.43         6.74        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         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

  AMP PEAK 16(4Q32.3) MUTATED AMP PEAK 16(4Q32.3) WILD-TYPE 
                         0.99                          0.03 
  AMP PEAK 16(4Q32.3) MUTATED AMP PEAK 16(4Q32.3) WILD-TYPE 
                       155.54                        158.83 
  AMP PEAK 16(4Q32.3) MUTATED AMP PEAK 16(4Q32.3) WILD-TYPE 
                       14.240                        16.605 
[1] "1.0 - 155.5 (14.2)" "0.0 - 158.8 (16.6)"
[1] "hr=" "3.4"
D14V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 16(4Q32.3) MUTATED         2        2         3        0         0
  AMP PEAK 16(4Q32.3) WILD-TYPE     278       49       106        2        45
                               vv
clus                            STAGE IVC
  AMP PEAK 16(4Q32.3) MUTATED           0
  AMP PEAK 16(4Q32.3) WILD-TYPE         6
D14V3, multiclass
           clus
vv          AMP PEAK 16(4Q32.3) MUTATED AMP PEAK 16(4Q32.3) WILD-TYPE
  STAGE I                             2                           278
  STAGE II                            2                            49
  STAGE III                           3                           106
  STAGE IV                            0                             2
  STAGE IVA                           0                            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 16(4Q32.3) MUTATED     1   1   5   0
  AMP PEAK 16(4Q32.3) WILD-TYPE 139 165 160  21
D14V4, multiclass
    clus
vv   AMP PEAK 16(4Q32.3) MUTATED AMP PEAK 16(4Q32.3) WILD-TYPE
  T1                           1                           139
  T2                           1                           165
  T3                           5                           160
  T4                           0                            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 16(4Q32.3) MUTATED     7   0
  AMP PEAK 16(4Q32.3) WILD-TYPE 216 222
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(4Q32.3) MUTATED      7    0
  AMP PEAK 16(4Q32.3) WILD-TYPE  216  222
   clus
vv  AMP PEAK 16(4Q32.3) MUTATED AMP PEAK 16(4Q32.3) WILD-TYPE
  0                           7                           216
  1                           0                           222
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK 16(4Q32.3) MUTATED     1   0   6
  AMP PEAK 16(4Q32.3) WILD-TYPE 272   9 206
D14V6, multiclass
    clus
vv   AMP PEAK 16(4Q32.3) MUTATED AMP PEAK 16(4Q32.3) WILD-TYPE
  M0                           1                           272
  M1                           0                             9
  MX                           6                           206
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                               cls
clus                              0   1
  AMP PEAK 16(4Q32.3) MUTATED     5   2
  AMP PEAK 16(4Q32.3) WILD-TYPE 359 129
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(4Q32.3) MUTATED      5    2
  AMP PEAK 16(4Q32.3) WILD-TYPE  359  129
        clus
vv       AMP PEAK 16(4Q32.3) MUTATED AMP PEAK 16(4Q32.3) WILD-TYPE
  FEMALE                           5                           359
  MALE                             2                           129
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 16(4Q32.3) MUTATED                0
  AMP PEAK 16(4Q32.3) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 16(4Q32.3) MUTATED                                               3
  AMP PEAK 16(4Q32.3) WILD-TYPE                                           350
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 16(4Q32.3) MUTATED                                                                        4
  AMP PEAK 16(4Q32.3) WILD-TYPE                                                                     94
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 16(4Q32.3) MUTATED                                                                     0
  AMP PEAK 16(4Q32.3) WILD-TYPE                                                                  35
D14V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 16(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 16(4Q32.3) WILD-TYPE
  OTHER  SPECIFY                                                                                     9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            94
  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"
D14V9, binary
                               cls
clus                              0   1
  AMP PEAK 16(4Q32.3) MUTATED     1   6
  AMP PEAK 16(4Q32.3) WILD-TYPE  13 475
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(4Q32.3) MUTATED      1    6
  AMP PEAK 16(4Q32.3) WILD-TYPE   13  475
     clus
vv    AMP PEAK 16(4Q32.3) MUTATED AMP PEAK 16(4Q32.3) WILD-TYPE
  NO                            1                            13
  YES                           6                           475
[1] 2 2
[1] FALSE
D14V10, binary
                               cls
clus                              0   1
  AMP PEAK 16(4Q32.3) MUTATED     6   0
  AMP PEAK 16(4Q32.3) WILD-TYPE 411  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(4Q32.3) MUTATED      6    0
  AMP PEAK 16(4Q32.3) WILD-TYPE  411   17
     clus
vv    AMP PEAK 16(4Q32.3) MUTATED AMP PEAK 16(4Q32.3) WILD-TYPE
  NO                            6                           411
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 16(4Q32.3) MUTATED              2                       0    5
  AMP PEAK 16(4Q32.3) WILD-TYPE          128                      16  323
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 16(4Q32.3) MUTATED                     0
  AMP PEAK 16(4Q32.3) WILD-TYPE                   1
D14V11, multiclass
                         clus
vv                        AMP PEAK 16(4Q32.3) MUTATED
  MINIMAL (T3)                                      2
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              5
  VERY ADVANCED (T4B)                               0
                         clus
vv                        AMP PEAK 16(4Q32.3) WILD-TYPE
  MINIMAL (T3)                                      128
  MODERATE/ADVANCED (T4A)                            16
  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 16(4Q32.3) MUTATED     5   0   1   1
  AMP PEAK 16(4Q32.3) WILD-TYPE 373  51   3  29
D14V12, multiclass
    clus
vv   AMP PEAK 16(4Q32.3) MUTATED AMP PEAK 16(4Q32.3) WILD-TYPE
  R0                           5                           373
  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"
D14V13, continuous
D14V14, binary
                               cls
clus                              0   1
  AMP PEAK 16(4Q32.3) MUTATED     4   3
  AMP PEAK 16(4Q32.3) WILD-TYPE 220 258
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(4Q32.3) MUTATED      4    3
  AMP PEAK 16(4Q32.3) WILD-TYPE  220  258
            clus
vv           AMP PEAK 16(4Q32.3) MUTATED AMP PEAK 16(4Q32.3) WILD-TYPE
  MULTIFOCAL                           4                           220
  UNIFOCAL                             3                           258
[1] 2 2
[1] FALSE
D14V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 16(4Q32.3) MUTATED                                  0     0
  AMP PEAK 16(4Q32.3) WILD-TYPE                                1    49
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(4Q32.3) MUTATED                           0     4
  AMP PEAK 16(4Q32.3) WILD-TYPE                        26   317
D14V16, multiclass
                                  clus
vv                                 AMP PEAK 16(4Q32.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      4
                                  clus
vv                                 AMP PEAK 16(4Q32.3) 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"
D14V17, binary
                               cls
clus                              0   1
  AMP PEAK 16(4Q32.3) MUTATED     0   4
  AMP PEAK 16(4Q32.3) WILD-TYPE  38 346
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(4Q32.3) MUTATED      0    4
  AMP PEAK 16(4Q32.3) WILD-TYPE   38  346
                        clus
vv                       AMP PEAK 16(4Q32.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           4
                        clus
vv                       AMP PEAK 16(4Q32.3) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           346
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 17(5P14.3) MUTATION ANALYSIS
D15V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 17(5P14.3) MUTATED    20   2
  AMP PEAK 17(5P14.3) WILD-TYPE 457  12
  AMP PEAK 17(5P14.3) MUTATED AMP PEAK 17(5P14.3) WILD-TYPE 
                           22                           469 
  AMP PEAK 17(5P14.3) MUTATED AMP PEAK 17(5P14.3) WILD-TYPE 
                            2                            12 
$`AMP PEAK 17(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       124.04         5.72 
TCGA-EL-A3ZO TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO 
       47.38         8.71        54.21        57.01        10.65         6.05 
TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3O3 TCGA-EM-A3SY TCGA-ET-A25L TCGA-ET-A2MZ 
       17.59        17.46        14.50        13.51        14.79        12.26 
TCGA-ET-A39N TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3NM 
       98.56        33.63         1.64         0.99 

$`AMP PEAK 17(5P14.3) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ 
       18.87        11.57        16.73         7.56        15.12        17.69 
TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S 
       23.34        20.71         4.83         8.09         4.87        21.04 
TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 
        2.79         5.10        11.31        17.52         1.22        30.21 
TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ 
       22.88        18.38        16.57        18.97         7.04        16.01 
TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D 
       13.94        15.48        23.31        18.64         5.75         6.48 
TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J 
        0.03         3.45         6.35         7.82         6.18         5.06 
TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD 
        8.98         4.93         5.98         0.53         0.10         0.20 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 
        0.23        11.38        10.68         0.10         0.39         0.10 
TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       20.22        15.42        36.46         5.98        15.85        18.54 
TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K 
       18.84        30.12        30.02        25.12         4.27         3.22 
TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        2.76        17.26        14.07       137.88         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       25.35        13.41        11.90        14.60         7.99        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      100.01        18.51        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45         8.88         1.02         5.95        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33         8.48        10.45         1.51         9.60        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
        8.28         7.69         5.52         8.78         8.42         8.12 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
        9.34         6.77         9.21         9.44         9.90         8.61 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.07        10.36        12.43        10.85        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        12.49        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        24.23        17.69        43.00        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       21.37        12.76        25.02        20.22        30.61        14.56 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20         9.83        21.27        20.48        11.93        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL 
       21.01        18.97         7.76         8.32        17.36        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       27.62        18.21        10.78        10.98        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       17.82         3.12        15.81        24.33        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 
       30.31        14.04         1.15        22.29        19.59        13.61 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 
       14.27        13.81        14.07        14.27         3.02        14.43 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
       14.70        14.10        14.96         7.69        20.68        13.78 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
       13.58        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 
       80.91         4.18        58.82         1.45        74.30        45.40 
TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR 
       33.47       108.36        39.32         1.41        30.18       102.84 
TCGA-EL-A3GS TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
       65.39        50.37        37.25       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        38.66        52.73       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 
      131.15       108.66        57.63        17.52        52.50        12.16 
TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
      147.42       130.72       129.57        32.48       116.91        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
       41.29        95.38        66.90        82.82        77.36        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       31.50        50.33        53.06        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT 
       37.78        29.95        13.32        11.87        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE 
       20.91        12.36        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        11.74 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.15        14.24        16.44        17.88        13.18        23.51 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        2.99        12.30        15.19        10.49        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       13.84        19.73        12.07        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        18.97        15.68        14.14        19.63        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        16.44        16.77        27.95        23.77        16.80 
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-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       11.15         7.33        12.53         9.24        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       11.51        16.41        15.62        12.79        70.65        16.90 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        9.01         4.83         8.61         8.38         9.80         5.03 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       37.87        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       32.35        12.33        14.79        27.09        18.38        29.49 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       54.05        22.09        16.08        29.19        19.76         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       58.22        13.74        71.01        80.02        65.36        84.89 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
       61.02        58.72        57.11        55.10        59.15        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
        5.85         4.18         2.43         5.56        24.72        38.30 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       42.25         2.37         4.50        80.81        69.24        59.87 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       43.50         0.30        17.98        25.32       132.36        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
        3.22         7.17         4.80         5.03         2.14         4.01 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
        1.94        73.74        59.70        31.59        44.25        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A 
       68.22       102.90        66.77        81.34        39.95        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        46.06         4.08 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        0.89        22.03         0.92        48.10        91.17         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        1.15        17.82         1.51         0.76         0.03         4.67 
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         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74        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         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  AMP PEAK 17(5P14.3) MUTATED AMP PEAK 17(5P14.3) WILD-TYPE 
                         0.99                          0.03 
  AMP PEAK 17(5P14.3) MUTATED AMP PEAK 17(5P14.3) WILD-TYPE 
                       124.04                        158.83 
  AMP PEAK 17(5P14.3) MUTATED AMP PEAK 17(5P14.3) WILD-TYPE 
                       14.645                        16.640 
[1] "1.0 - 124.0 (14.6)" "0.0 - 158.8 (16.6)"
[1] "hr=" "3.3"
D15V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 17(5P14.3) MUTATED         5        5         8        1         3
  AMP PEAK 17(5P14.3) WILD-TYPE     275       46       101        1        42
                               vv
clus                            STAGE IVC
  AMP PEAK 17(5P14.3) MUTATED           0
  AMP PEAK 17(5P14.3) WILD-TYPE         6
D15V3, multiclass
           clus
vv          AMP PEAK 17(5P14.3) MUTATED AMP PEAK 17(5P14.3) WILD-TYPE
  STAGE I                             5                           275
  STAGE II                            5                            46
  STAGE III                           8                           101
  STAGE IV                            1                             1
  STAGE IVA                           3                            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 17(5P14.3) MUTATED     3   7  11   1
  AMP PEAK 17(5P14.3) WILD-TYPE 137 159 154  20
D15V4, multiclass
    clus
vv   AMP PEAK 17(5P14.3) MUTATED AMP PEAK 17(5P14.3) WILD-TYPE
  T1                           3                           137
  T2                           7                           159
  T3                          11                           154
  T4                           1                            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"
D15V5, binary
                               cls
clus                              0   1
  AMP PEAK 17(5P14.3) MUTATED    11   7
  AMP PEAK 17(5P14.3) WILD-TYPE 212 215
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(5P14.3) MUTATED     11    7
  AMP PEAK 17(5P14.3) WILD-TYPE  212  215
   clus
vv  AMP PEAK 17(5P14.3) MUTATED AMP PEAK 17(5P14.3) WILD-TYPE
  0                          11                           212
  1                           7                           215
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK 17(5P14.3) MUTATED     5   0  17
  AMP PEAK 17(5P14.3) WILD-TYPE 268   9 195
D15V6, multiclass
    clus
vv   AMP PEAK 17(5P14.3) MUTATED AMP PEAK 17(5P14.3) WILD-TYPE
  M0                           5                           268
  M1                           0                             9
  MX                          17                           195
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                               cls
clus                              0   1
  AMP PEAK 17(5P14.3) MUTATED    16   6
  AMP PEAK 17(5P14.3) WILD-TYPE 348 125
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(5P14.3) MUTATED     16    6
  AMP PEAK 17(5P14.3) WILD-TYPE  348  125
        clus
vv       AMP PEAK 17(5P14.3) MUTATED AMP PEAK 17(5P14.3) WILD-TYPE
  FEMALE                          16                           348
  MALE                             6                           125
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 17(5P14.3) MUTATED                0
  AMP PEAK 17(5P14.3) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 17(5P14.3) MUTATED                                              13
  AMP PEAK 17(5P14.3) WILD-TYPE                                           340
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 17(5P14.3) MUTATED                                                                        8
  AMP PEAK 17(5P14.3) WILD-TYPE                                                                     90
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 17(5P14.3) MUTATED                                                                     1
  AMP PEAK 17(5P14.3) WILD-TYPE                                                                  34
D15V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 17(5P14.3) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   13
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           8
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              1
                                                                        clus
vv                                                                       AMP PEAK 17(5P14.3) WILD-TYPE
  OTHER  SPECIFY                                                                                     9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    340
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            90
  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"
D15V9, binary
                               cls
clus                              0   1
  AMP PEAK 17(5P14.3) MUTATED     1  21
  AMP PEAK 17(5P14.3) WILD-TYPE  13 460
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(5P14.3) MUTATED      1   21
  AMP PEAK 17(5P14.3) WILD-TYPE   13  460
     clus
vv    AMP PEAK 17(5P14.3) MUTATED AMP PEAK 17(5P14.3) WILD-TYPE
  NO                            1                            13
  YES                          21                           460
[1] 2 2
[1] FALSE
D15V10, binary
                               cls
clus                              0   1
  AMP PEAK 17(5P14.3) MUTATED    21   0
  AMP PEAK 17(5P14.3) WILD-TYPE 396  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(5P14.3) MUTATED     21    0
  AMP PEAK 17(5P14.3) WILD-TYPE  396   17
     clus
vv    AMP PEAK 17(5P14.3) MUTATED AMP PEAK 17(5P14.3) WILD-TYPE
  NO                           21                           396
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 17(5P14.3) MUTATED              6                       1   14
  AMP PEAK 17(5P14.3) WILD-TYPE          124                      15  314
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 17(5P14.3) MUTATED                     1
  AMP PEAK 17(5P14.3) WILD-TYPE                   0
D15V11, multiclass
                         clus
vv                        AMP PEAK 17(5P14.3) MUTATED
  MINIMAL (T3)                                      6
  MODERATE/ADVANCED (T4A)                           1
  NONE                                             14
  VERY ADVANCED (T4B)                               1
                         clus
vv                        AMP PEAK 17(5P14.3) WILD-TYPE
  MINIMAL (T3)                                      124
  MODERATE/ADVANCED (T4A)                            15
  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 17(5P14.3) MUTATED    15   5   0   2
  AMP PEAK 17(5P14.3) WILD-TYPE 363  46   4  28
D15V12, multiclass
    clus
vv   AMP PEAK 17(5P14.3) MUTATED AMP PEAK 17(5P14.3) WILD-TYPE
  R0                          15                           363
  R1                           5                            46
  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"
D15V13, continuous
D15V14, binary
                               cls
clus                              0   1
  AMP PEAK 17(5P14.3) MUTATED     9  13
  AMP PEAK 17(5P14.3) WILD-TYPE 215 248
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(5P14.3) MUTATED      9   13
  AMP PEAK 17(5P14.3) WILD-TYPE  215  248
            clus
vv           AMP PEAK 17(5P14.3) MUTATED AMP PEAK 17(5P14.3) WILD-TYPE
  MULTIFOCAL                           9                           215
  UNIFOCAL                            13                           248
[1] 2 2
[1] FALSE
D15V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 17(5P14.3) MUTATED                                  0     0
  AMP PEAK 17(5P14.3) WILD-TYPE                                1    49
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(5P14.3) MUTATED                           0    14
  AMP PEAK 17(5P14.3) WILD-TYPE                        26   307
D15V16, multiclass
                                  clus
vv                                 AMP PEAK 17(5P14.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                     14
                                  clus
vv                                 AMP PEAK 17(5P14.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       49
  BLACK OR AFRICAN AMERICAN                                   26
  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"
D15V17, binary
                               cls
clus                              0   1
  AMP PEAK 17(5P14.3) MUTATED     2  12
  AMP PEAK 17(5P14.3) WILD-TYPE  36 338
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(5P14.3) MUTATED      2   12
  AMP PEAK 17(5P14.3) WILD-TYPE   36  338
                        clus
vv                       AMP PEAK 17(5P14.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          12
                        clus
vv                       AMP PEAK 17(5P14.3) WILD-TYPE
  HISPANIC OR LATINO                                36
  NOT HISPANIC OR LATINO                           338
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 18(5Q21.1) MUTATION ANALYSIS
D16V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 18(5Q21.1) MUTATED    20   2
  AMP PEAK 18(5Q21.1) WILD-TYPE 457  12
  AMP PEAK 18(5Q21.1) MUTATED AMP PEAK 18(5Q21.1) WILD-TYPE 
                           22                           469 
  AMP PEAK 18(5Q21.1) MUTATED AMP PEAK 18(5Q21.1) WILD-TYPE 
                            2                            12 
$`AMP PEAK 18(5Q21.1) MUTATED`
TCGA-BJ-A190 TCGA-BJ-A28X TCGA-BJ-A2N9 TCGA-DJ-A3UK TCGA-DJ-A3US TCGA-DO-A2HM 
       20.58        17.52        20.48        15.09        32.81         2.33 
TCGA-EL-A3T3 TCGA-EL-A3T9 TCGA-EL-A4K9 TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A1YD 
      116.91         5.72        37.78         8.71        54.21        57.01 
TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3SY TCGA-ET-A2MZ 
       10.65         6.05        17.59        17.46        13.51        12.26 
TCGA-ET-A39N TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3NM 
       98.56        33.63         1.64         0.99 

$`AMP PEAK 18(5Q21.1) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28Z TCGA-BJ-A290 
       21.04         2.79         5.10        11.31         1.22        30.21 
TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ 
       22.88        18.38        16.57        18.97         7.04        16.01 
TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D 
       13.94        15.48        23.31        18.64         5.75         6.48 
TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J 
        0.03         3.45         6.35         7.82         6.18         5.06 
TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD 
        8.98         4.93         5.98         0.53         0.10         0.20 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 
        0.23        11.38        10.68         0.10         0.39         0.10 
TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       20.22        15.42        36.46         5.98        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         4.27 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
        3.22         2.76        17.26        14.07       137.88         3.39 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        25.35        13.41        11.90        14.60         7.99 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       11.01       100.01        18.51        13.12         7.99        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
        7.20         1.45         8.88         1.02         5.95        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT 
        7.99         5.33         8.48        10.45         1.51         9.60 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       12.56         8.28         7.69         5.52         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
        8.12         9.34         6.77         9.21         9.44         9.90 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
        8.61        10.09         7.07        10.36        12.43        10.85 
TCGA-DJ-A2QC TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.88        31.04        12.49        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY 
       36.33        24.23        17.69        43.00        11.34        21.37 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       12.76        25.02        20.22        30.61        14.56        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
        9.83        21.27        20.48        11.93        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76         8.32        17.36        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       18.21        10.78        10.98        14.14        14.70        17.82 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY 
        3.12        15.81        24.33        54.90        21.53        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.07        14.27         3.02        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        13.78        13.58        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        80.91         4.18 
TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 
       58.82         1.45        74.30        45.40        33.47       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
       39.32         1.41        30.18       102.84        65.39       124.04 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        37.25       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        38.66        52.73       139.00       131.15 
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        12.16       147.42 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      130.72       129.57        32.48        98.24        41.29        95.38 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4KD 
       19.59        30.51        33.60        28.73        41.13        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       13.32        11.87        26.86        18.18        20.91        12.36 
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        11.74        11.15        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ 
       16.44        17.88        13.18        23.51         2.99        12.30 
TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        10.49        13.15        22.16        13.84        19.73 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ 
       12.07        17.59        17.46        17.29        14.60        18.97 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        19.63        13.38         8.35        16.44 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       16.77        27.95        23.77        16.80        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        11.15 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33        12.53         9.24        13.91         7.82        11.51 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       16.41        15.62        12.79        70.65        16.90         9.01 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        4.83         8.61         8.38         9.80         5.03        37.87 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       12.72         0.95        47.47        48.20        29.69        32.35 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       14.79        12.33        14.79        27.09        18.38        29.49 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       54.05        22.09        16.08        29.19        19.76         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       58.22        13.74        71.01        80.02        65.36        84.89 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
       61.02        58.72        57.11        55.10        59.15        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
        5.85         4.18         2.43         5.56        24.72        38.30 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       42.25         2.37         4.50        80.81        69.24        59.87 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       43.50         0.30        17.98        25.32       132.36        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
        3.22         7.17         4.80         5.03         2.14         4.01 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
        1.94        73.74        59.70        31.59        44.25        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A 
       68.22       102.90        66.77        81.34        39.95        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        46.06         4.08 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        0.89        22.03         0.92        48.10        91.17         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        1.15        17.82         1.51         0.76         0.03         4.67 
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         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74        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         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  AMP PEAK 18(5Q21.1) MUTATED AMP PEAK 18(5Q21.1) WILD-TYPE 
                         0.99                          0.03 
  AMP PEAK 18(5Q21.1) MUTATED AMP PEAK 18(5Q21.1) WILD-TYPE 
                       116.91                        158.83 
  AMP PEAK 18(5Q21.1) MUTATED AMP PEAK 18(5Q21.1) WILD-TYPE 
                        17.49                         16.57 
[1] "1.0 - 116.9 (17.5)" "0.0 - 158.8 (16.6)"
[1] "hr=" "3.3"
D16V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 18(5Q21.1) MUTATED         8        7         5        1         1
  AMP PEAK 18(5Q21.1) WILD-TYPE     272       44       104        1        44
                               vv
clus                            STAGE IVC
  AMP PEAK 18(5Q21.1) MUTATED           0
  AMP PEAK 18(5Q21.1) WILD-TYPE         6
D16V3, multiclass
           clus
vv          AMP PEAK 18(5Q21.1) MUTATED AMP PEAK 18(5Q21.1) WILD-TYPE
  STAGE I                             8                           272
  STAGE II                            7                            44
  STAGE III                           5                           104
  STAGE IV                            1                             1
  STAGE IVA                           1                            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 18(5Q21.1) MUTATED     6   8   7   1
  AMP PEAK 18(5Q21.1) WILD-TYPE 134 158 158  20
D16V4, multiclass
    clus
vv   AMP PEAK 18(5Q21.1) MUTATED AMP PEAK 18(5Q21.1) WILD-TYPE
  T1                           6                           134
  T2                           8                           158
  T3                           7                           158
  T4                           1                            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"
D16V5, binary
                               cls
clus                              0   1
  AMP PEAK 18(5Q21.1) MUTATED    15   3
  AMP PEAK 18(5Q21.1) WILD-TYPE 208 219
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(5Q21.1) MUTATED     15    3
  AMP PEAK 18(5Q21.1) WILD-TYPE  208  219
   clus
vv  AMP PEAK 18(5Q21.1) MUTATED AMP PEAK 18(5Q21.1) WILD-TYPE
  0                          15                           208
  1                           3                           219
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK 18(5Q21.1) MUTATED     6   0  16
  AMP PEAK 18(5Q21.1) WILD-TYPE 267   9 196
D16V6, multiclass
    clus
vv   AMP PEAK 18(5Q21.1) MUTATED AMP PEAK 18(5Q21.1) WILD-TYPE
  M0                           6                           267
  M1                           0                             9
  MX                          16                           196
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                               cls
clus                              0   1
  AMP PEAK 18(5Q21.1) MUTATED    14   8
  AMP PEAK 18(5Q21.1) WILD-TYPE 350 123
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(5Q21.1) MUTATED     14    8
  AMP PEAK 18(5Q21.1) WILD-TYPE  350  123
        clus
vv       AMP PEAK 18(5Q21.1) MUTATED AMP PEAK 18(5Q21.1) WILD-TYPE
  FEMALE                          14                           350
  MALE                             8                           123
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 18(5Q21.1) MUTATED                0
  AMP PEAK 18(5Q21.1) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 18(5Q21.1) MUTATED                                              13
  AMP PEAK 18(5Q21.1) WILD-TYPE                                           340
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 18(5Q21.1) MUTATED                                                                        8
  AMP PEAK 18(5Q21.1) WILD-TYPE                                                                     90
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 18(5Q21.1) MUTATED                                                                     1
  AMP PEAK 18(5Q21.1) WILD-TYPE                                                                  34
D16V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 18(5Q21.1) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   13
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           8
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              1
                                                                        clus
vv                                                                       AMP PEAK 18(5Q21.1) WILD-TYPE
  OTHER  SPECIFY                                                                                     9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    340
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            90
  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"
D16V9, binary
                               cls
clus                              0   1
  AMP PEAK 18(5Q21.1) MUTATED     1  21
  AMP PEAK 18(5Q21.1) WILD-TYPE  13 460
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(5Q21.1) MUTATED      1   21
  AMP PEAK 18(5Q21.1) WILD-TYPE   13  460
     clus
vv    AMP PEAK 18(5Q21.1) MUTATED AMP PEAK 18(5Q21.1) WILD-TYPE
  NO                            1                            13
  YES                          21                           460
[1] 2 2
[1] FALSE
D16V10, binary
                               cls
clus                              0   1
  AMP PEAK 18(5Q21.1) MUTATED    20   0
  AMP PEAK 18(5Q21.1) WILD-TYPE 397  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(5Q21.1) MUTATED     20    0
  AMP PEAK 18(5Q21.1) WILD-TYPE  397   17
     clus
vv    AMP PEAK 18(5Q21.1) MUTATED AMP PEAK 18(5Q21.1) WILD-TYPE
  NO                           20                           397
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 18(5Q21.1) MUTATED              4                       0   17
  AMP PEAK 18(5Q21.1) WILD-TYPE          126                      16  311
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 18(5Q21.1) MUTATED                     1
  AMP PEAK 18(5Q21.1) WILD-TYPE                   0
D16V11, multiclass
                         clus
vv                        AMP PEAK 18(5Q21.1) MUTATED
  MINIMAL (T3)                                      4
  MODERATE/ADVANCED (T4A)                           0
  NONE                                             17
  VERY ADVANCED (T4B)                               1
                         clus
vv                        AMP PEAK 18(5Q21.1) WILD-TYPE
  MINIMAL (T3)                                      126
  MODERATE/ADVANCED (T4A)                            16
  NONE                                              311
  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(5Q21.1) MUTATED    17   2   0   3
  AMP PEAK 18(5Q21.1) WILD-TYPE 361  49   4  27
D16V12, multiclass
    clus
vv   AMP PEAK 18(5Q21.1) MUTATED AMP PEAK 18(5Q21.1) WILD-TYPE
  R0                          17                           361
  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"
D16V13, continuous
D16V14, binary
                               cls
clus                              0   1
  AMP PEAK 18(5Q21.1) MUTATED    10  12
  AMP PEAK 18(5Q21.1) WILD-TYPE 214 249
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(5Q21.1) MUTATED     10   12
  AMP PEAK 18(5Q21.1) WILD-TYPE  214  249
            clus
vv           AMP PEAK 18(5Q21.1) MUTATED AMP PEAK 18(5Q21.1) WILD-TYPE
  MULTIFOCAL                          10                           214
  UNIFOCAL                            12                           249
[1] 2 2
[1] FALSE
D16V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 18(5Q21.1) MUTATED                                  0     0
  AMP PEAK 18(5Q21.1) WILD-TYPE                                1    49
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(5Q21.1) MUTATED                           0    15
  AMP PEAK 18(5Q21.1) WILD-TYPE                        26   306
D16V16, multiclass
                                  clus
vv                                 AMP PEAK 18(5Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                     15
                                  clus
vv                                 AMP PEAK 18(5Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       49
  BLACK OR AFRICAN AMERICAN                                   26
  WHITE                                                      306
[1] 4 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 18(5Q21.1) MUTATED     1  14
  AMP PEAK 18(5Q21.1) WILD-TYPE  37 336
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(5Q21.1) MUTATED      1   14
  AMP PEAK 18(5Q21.1) WILD-TYPE   37  336
                        clus
vv                       AMP PEAK 18(5Q21.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          14
                        clus
vv                       AMP PEAK 18(5Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                37
  NOT HISPANIC OR LATINO                           336
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 19(5Q21.1) MUTATION ANALYSIS
D17V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 19(5Q21.1) MUTATED    17   2
  AMP PEAK 19(5Q21.1) WILD-TYPE 460  12
  AMP PEAK 19(5Q21.1) MUTATED AMP PEAK 19(5Q21.1) WILD-TYPE 
                           19                           472 
  AMP PEAK 19(5Q21.1) MUTATED AMP PEAK 19(5Q21.1) WILD-TYPE 
                            2                            12 
$`AMP PEAK 19(5Q21.1) MUTATED`
TCGA-BJ-A190 TCGA-BJ-A2N9 TCGA-DJ-A13X TCGA-EL-A3T3 TCGA-EL-A3T9 TCGA-EL-A4K9 
       20.58        20.48         7.99       116.91         5.72        37.78 
TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY 
        8.71        54.21        57.01        10.65         6.05        17.59 
TCGA-EM-A3AI TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FE-A239 TCGA-FY-A3I5 
       17.46        13.51        12.26        98.56        33.63         1.64 
TCGA-FY-A3NM 
        0.99 

$`AMP PEAK 19(5Q21.1) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
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        15.48        23.31        18.64         5.75 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
        6.48         0.03         3.45         6.35         7.82         6.18 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
        5.06         8.98         4.93         5.98         0.53         0.10 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
        0.20         0.23        11.38        10.68         0.10         0.39 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.10        20.22        15.42        36.46         5.98        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-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
        4.27         3.22         2.76        17.26        14.07       137.88 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
        3.39         8.71        25.35        13.41        11.90        14.60 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       11.01       100.01        18.51        13.12         7.99        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
        7.20         1.45         8.88         1.02         5.95        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT 
        7.99         5.33         8.48        10.45         1.51         9.60 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       12.56         8.28         7.69         5.52         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
        8.12         9.34         6.77         9.21         9.44         9.90 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
        8.61        10.09         7.07        10.36        12.43        10.85 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       15.88        15.09        31.04        12.49        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        24.23        17.69        43.00 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       11.34        21.37        12.76        25.02        20.22        30.61 
TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       14.56        19.20         9.83        21.27        20.48        11.93 
TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ 
       22.92        21.01        18.97         7.76         8.32        17.36 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       17.23        27.62        18.21        10.78        10.98        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        30.31        14.04         1.15        22.29        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       14.43        14.70        14.10        14.96         7.69        20.68 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       13.78        13.58        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        80.91         4.18        58.82         1.45        74.30 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       45.40        33.47       108.36        39.32         1.41        30.18 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
      102.84        65.39       124.04        50.37        37.25       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        38.66 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       52.73       139.00       131.15       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        12.16       147.42       130.72       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        95.38        66.90        82.82        77.36 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       78.97        31.50        50.33        53.06        47.38        52.50 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       45.53        48.16         7.07        44.65        45.80        19.30 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        37.94        31.04        19.59        30.51        33.60 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS 
       28.73        41.13        29.95        13.32        11.87        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        12.36        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 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         2.99        12.30        15.19        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        13.84        19.73        12.07        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        18.97        15.68        14.14        19.63 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        16.44        16.77        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        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        11.15         7.33        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ 
       13.91         7.82        11.51        16.41        15.62        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        9.80         5.03        37.87        12.72         0.95        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 
       27.09        18.38        29.49        54.05        22.09        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       80.02        65.36        84.89        61.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        59.15        28.24         5.85         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        24.69        68.22       102.90        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       81.34        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        46.06         4.08         0.89        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON 
       48.10        91.17         1.25         1.15        17.82         1.51 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        0.76         0.03         4.67        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         6.87         4.14         6.58         4.54 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
        0.89         1.35         1.15         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        10.26        16.90         9.80         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        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        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       12.43         6.74        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         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

  AMP PEAK 19(5Q21.1) MUTATED AMP PEAK 19(5Q21.1) WILD-TYPE 
                         0.99                          0.03 
  AMP PEAK 19(5Q21.1) MUTATED AMP PEAK 19(5Q21.1) WILD-TYPE 
                       116.91                        158.83 
  AMP PEAK 19(5Q21.1) MUTATED AMP PEAK 19(5Q21.1) WILD-TYPE 
                        17.46                         16.57 
[1] "1.0 - 116.9 (17.5)" "0.0 - 158.8 (16.6)"
[1] "hr=" "3.4"
D17V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 19(5Q21.1) MUTATED         5        7         6        1         0
  AMP PEAK 19(5Q21.1) WILD-TYPE     275       44       103        1        45
                               vv
clus                            STAGE IVC
  AMP PEAK 19(5Q21.1) MUTATED           0
  AMP PEAK 19(5Q21.1) WILD-TYPE         6
D17V3, multiclass
           clus
vv          AMP PEAK 19(5Q21.1) MUTATED AMP PEAK 19(5Q21.1) WILD-TYPE
  STAGE I                             5                           275
  STAGE II                            7                            44
  STAGE III                           6                           103
  STAGE IV                            1                             1
  STAGE IVA                           0                            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 19(5Q21.1) MUTATED     3   8   7   1
  AMP PEAK 19(5Q21.1) WILD-TYPE 137 158 158  20
D17V4, multiclass
    clus
vv   AMP PEAK 19(5Q21.1) MUTATED AMP PEAK 19(5Q21.1) WILD-TYPE
  T1                           3                           137
  T2                           8                           158
  T3                           7                           158
  T4                           1                            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"
D17V5, binary
                               cls
clus                              0   1
  AMP PEAK 19(5Q21.1) MUTATED    14   1
  AMP PEAK 19(5Q21.1) WILD-TYPE 209 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 19(5Q21.1) MUTATED     14    1
  AMP PEAK 19(5Q21.1) WILD-TYPE  209  221
   clus
vv  AMP PEAK 19(5Q21.1) MUTATED AMP PEAK 19(5Q21.1) WILD-TYPE
  0                          14                           209
  1                           1                           221
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK 19(5Q21.1) MUTATED     4   0  15
  AMP PEAK 19(5Q21.1) WILD-TYPE 269   9 197
D17V6, multiclass
    clus
vv   AMP PEAK 19(5Q21.1) MUTATED AMP PEAK 19(5Q21.1) WILD-TYPE
  M0                           4                           269
  M1                           0                             9
  MX                          15                           197
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                               cls
clus                              0   1
  AMP PEAK 19(5Q21.1) MUTATED    12   7
  AMP PEAK 19(5Q21.1) WILD-TYPE 352 124
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 19(5Q21.1) MUTATED     12    7
  AMP PEAK 19(5Q21.1) WILD-TYPE  352  124
        clus
vv       AMP PEAK 19(5Q21.1) MUTATED AMP PEAK 19(5Q21.1) WILD-TYPE
  FEMALE                          12                           352
  MALE                             7                           124
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 19(5Q21.1) MUTATED                0
  AMP PEAK 19(5Q21.1) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 19(5Q21.1) MUTATED                                              10
  AMP PEAK 19(5Q21.1) WILD-TYPE                                           343
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 19(5Q21.1) MUTATED                                                                        9
  AMP PEAK 19(5Q21.1) WILD-TYPE                                                                     89
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 19(5Q21.1) MUTATED                                                                     0
  AMP PEAK 19(5Q21.1) WILD-TYPE                                                                  35
D17V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 19(5Q21.1) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   10
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           9
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       AMP PEAK 19(5Q21.1) WILD-TYPE
  OTHER  SPECIFY                                                                                     9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    343
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            89
  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"
D17V9, binary
                               cls
clus                              0   1
  AMP PEAK 19(5Q21.1) MUTATED     1  18
  AMP PEAK 19(5Q21.1) WILD-TYPE  13 463
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 19(5Q21.1) MUTATED      1   18
  AMP PEAK 19(5Q21.1) WILD-TYPE   13  463
     clus
vv    AMP PEAK 19(5Q21.1) MUTATED AMP PEAK 19(5Q21.1) WILD-TYPE
  NO                            1                            13
  YES                          18                           463
[1] 2 2
[1] FALSE
D17V10, binary
                               cls
clus                              0   1
  AMP PEAK 19(5Q21.1) MUTATED    18   0
  AMP PEAK 19(5Q21.1) WILD-TYPE 399  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 19(5Q21.1) MUTATED     18    0
  AMP PEAK 19(5Q21.1) WILD-TYPE  399   17
     clus
vv    AMP PEAK 19(5Q21.1) MUTATED AMP PEAK 19(5Q21.1) WILD-TYPE
  NO                           18                           399
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 19(5Q21.1) MUTATED              3                       0   15
  AMP PEAK 19(5Q21.1) WILD-TYPE          127                      16  313
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 19(5Q21.1) MUTATED                     1
  AMP PEAK 19(5Q21.1) WILD-TYPE                   0
D17V11, multiclass
                         clus
vv                        AMP PEAK 19(5Q21.1) MUTATED
  MINIMAL (T3)                                      3
  MODERATE/ADVANCED (T4A)                           0
  NONE                                             15
  VERY ADVANCED (T4B)                               1
                         clus
vv                        AMP PEAK 19(5Q21.1) WILD-TYPE
  MINIMAL (T3)                                      127
  MODERATE/ADVANCED (T4A)                            16
  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 19(5Q21.1) MUTATED    15   2   0   2
  AMP PEAK 19(5Q21.1) WILD-TYPE 363  49   4  28
D17V12, multiclass
    clus
vv   AMP PEAK 19(5Q21.1) MUTATED AMP PEAK 19(5Q21.1) WILD-TYPE
  R0                          15                           363
  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"
D17V13, continuous
D17V14, binary
                               cls
clus                              0   1
  AMP PEAK 19(5Q21.1) MUTATED     8  11
  AMP PEAK 19(5Q21.1) WILD-TYPE 216 250
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 19(5Q21.1) MUTATED      8   11
  AMP PEAK 19(5Q21.1) WILD-TYPE  216  250
            clus
vv           AMP PEAK 19(5Q21.1) MUTATED AMP PEAK 19(5Q21.1) WILD-TYPE
  MULTIFOCAL                           8                           216
  UNIFOCAL                            11                           250
[1] 2 2
[1] FALSE
D17V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 19(5Q21.1) MUTATED                                  0     0
  AMP PEAK 19(5Q21.1) WILD-TYPE                                1    49
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(5Q21.1) MUTATED                           0    11
  AMP PEAK 19(5Q21.1) WILD-TYPE                        26   310
D17V16, multiclass
                                  clus
vv                                 AMP PEAK 19(5Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                     11
                                  clus
vv                                 AMP PEAK 19(5Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       49
  BLACK OR AFRICAN AMERICAN                                   26
  WHITE                                                      310
[1] 4 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 19(5Q21.1) MUTATED     1  11
  AMP PEAK 19(5Q21.1) WILD-TYPE  37 339
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 19(5Q21.1) MUTATED      1   11
  AMP PEAK 19(5Q21.1) WILD-TYPE   37  339
                        clus
vv                       AMP PEAK 19(5Q21.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          11
                        clus
vv                       AMP PEAK 19(5Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                37
  NOT HISPANIC OR LATINO                           339
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 20(5Q33.1) MUTATION ANALYSIS
D18V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 20(5Q33.1) MUTATED    18   2
  AMP PEAK 20(5Q33.1) WILD-TYPE 459  12
  AMP PEAK 20(5Q33.1) MUTATED AMP PEAK 20(5Q33.1) WILD-TYPE 
                           20                           471 
  AMP PEAK 20(5Q33.1) MUTATED AMP PEAK 20(5Q33.1) WILD-TYPE 
                            2                            12 
$`AMP PEAK 20(5Q33.1) MUTATED`
TCGA-BJ-A0Z0 TCGA-BJ-A190 TCGA-BJ-A2N9 TCGA-DJ-A4UW TCGA-EL-A3T9 TCGA-EL-A4K9 
       13.78        20.58        20.48        14.70         5.72        37.78 
TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OW 
        8.71        54.21        57.01        10.65         6.05        13.84 
TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FE-A239 
       17.59        17.46        13.51        12.26        98.56        33.63 
TCGA-FY-A3I5 TCGA-FY-A3NM 
        1.64         0.99 

$`AMP PEAK 20(5Q33.1) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       24.79        18.21        16.34        14.73         8.25        18.87 
TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ 
        4.01        11.57        16.73         7.56        15.12        17.69 
TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S 
       23.34        20.71         4.83         8.09         4.87        21.04 
TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 
        2.79         5.10        11.31        17.52         1.22        30.21 
TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ 
       22.88        18.38        16.57        18.97         7.04        16.01 
TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D 
       13.94        15.48        23.31        18.64         5.75         6.48 
TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J 
        0.03         3.45         6.35         7.82         6.18         5.06 
TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD 
        8.98         4.93         5.98         0.53         0.10         0.20 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 
        0.23        11.38        10.68         0.10         0.39         0.10 
TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       20.22        15.42        36.46         5.98        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         4.27 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
        3.22         2.76        17.26        14.07       137.88         3.39 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        25.35        13.41        11.90        14.60         7.99 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       11.01       100.01        18.51        13.12         7.99        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
        7.20         1.45         8.88         1.02         5.95        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT 
        7.99         5.33         8.48        10.45         1.51         9.60 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       12.56         8.28         7.69         5.52         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
        8.12         9.34         6.77         9.21         9.44         9.90 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
        8.61        10.09         7.07        10.36        12.43        10.85 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       15.88        15.09        31.04        12.49        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        24.23        17.69        43.00 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       11.34        21.37        12.76        25.02        20.22        30.61 
TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       14.56        19.20         9.83        21.27        20.48        11.93 
TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ 
       22.92        21.01        18.97         7.76         8.32        17.36 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       17.23        27.62        18.21        10.78        10.98        14.14 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       17.82         3.12        15.81        24.33        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 
       30.31        14.04         1.15        22.29        19.59        13.61 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 
       14.27        13.81        14.07        14.27         3.02        14.43 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
       14.70        14.10        14.96         7.69        20.68        13.78 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
       13.58        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 
       80.91         4.18        58.82         1.45        74.30        45.40 
TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR 
       33.47       108.36        39.32         1.41        30.18       102.84 
TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY 
       65.39       124.04        50.37        37.25       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        38.66        52.73 
TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ 
      139.00       131.15       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 
       12.16       147.42       130.72       129.57        32.48       116.91 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       98.24        41.29        95.38        66.90        82.82        77.36 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       78.97        31.50        50.33        53.06        47.38        52.50 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       45.53        48.16         7.07        44.65        45.80        19.30 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        37.94        31.04        19.59        30.51        33.60 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS 
       28.73        41.13        29.95        13.32        11.87        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        12.36        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 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         2.99        12.30        15.19        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       22.16        19.73        12.07        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        18.97        15.68        14.14        19.63        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        16.44        16.77        27.95        23.77        16.80 
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        11.15         7.33        12.53         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
        7.82        11.51        16.41        15.62        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        29.49        54.05        22.09        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        61.02        58.72        57.11        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       59.15        28.24         5.85         4.18         2.43         5.56 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       24.72        38.30        42.25         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       69.24        59.87        43.50         0.30        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       102.90        66.77        81.34 
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 
       46.06         4.08         0.89        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 
       91.17         1.25         1.15        17.82         1.51         0.76 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
        0.03         4.67        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         6.87         4.14         6.58         4.54         0.89 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35         1.15         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 
       10.26        16.90         9.80         9.63         2.96         8.65 
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        86.70         6.02        12.43 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
        6.74        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         0.72        16.64        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        8.71        10.98         5.19 

  AMP PEAK 20(5Q33.1) MUTATED AMP PEAK 20(5Q33.1) WILD-TYPE 
                         0.99                          0.03 
  AMP PEAK 20(5Q33.1) MUTATED AMP PEAK 20(5Q33.1) WILD-TYPE 
                        98.56                        158.83 
  AMP PEAK 20(5Q33.1) MUTATED AMP PEAK 20(5Q33.1) WILD-TYPE 
                        14.27                         16.64 
[1] "1.0 - 98.6 (14.3)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "4.6"
D18V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 20(5Q33.1) MUTATED         7        7         5        1         0
  AMP PEAK 20(5Q33.1) WILD-TYPE     273       44       104        1        45
                               vv
clus                            STAGE IVC
  AMP PEAK 20(5Q33.1) MUTATED           0
  AMP PEAK 20(5Q33.1) WILD-TYPE         6
D18V3, multiclass
           clus
vv          AMP PEAK 20(5Q33.1) MUTATED AMP PEAK 20(5Q33.1) WILD-TYPE
  STAGE I                             7                           273
  STAGE II                            7                            44
  STAGE III                           5                           104
  STAGE IV                            1                             1
  STAGE IVA                           0                            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 20(5Q33.1) MUTATED     5   8   6   1
  AMP PEAK 20(5Q33.1) WILD-TYPE 135 158 159  20
D18V4, multiclass
    clus
vv   AMP PEAK 20(5Q33.1) MUTATED AMP PEAK 20(5Q33.1) WILD-TYPE
  T1                           5                           135
  T2                           8                           158
  T3                           6                           159
  T4                           1                            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 20(5Q33.1) MUTATED    13   2
  AMP PEAK 20(5Q33.1) WILD-TYPE 210 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 20(5Q33.1) MUTATED     13    2
  AMP PEAK 20(5Q33.1) WILD-TYPE  210  220
   clus
vv  AMP PEAK 20(5Q33.1) MUTATED AMP PEAK 20(5Q33.1) WILD-TYPE
  0                          13                           210
  1                           2                           220
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK 20(5Q33.1) MUTATED     3   0  17
  AMP PEAK 20(5Q33.1) WILD-TYPE 270   9 195
D18V6, multiclass
    clus
vv   AMP PEAK 20(5Q33.1) MUTATED AMP PEAK 20(5Q33.1) WILD-TYPE
  M0                           3                           270
  M1                           0                             9
  MX                          17                           195
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                               cls
clus                              0   1
  AMP PEAK 20(5Q33.1) MUTATED    13   7
  AMP PEAK 20(5Q33.1) WILD-TYPE 351 124
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 20(5Q33.1) MUTATED     13    7
  AMP PEAK 20(5Q33.1) WILD-TYPE  351  124
        clus
vv       AMP PEAK 20(5Q33.1) MUTATED AMP PEAK 20(5Q33.1) WILD-TYPE
  FEMALE                          13                           351
  MALE                             7                           124
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 20(5Q33.1) MUTATED                0
  AMP PEAK 20(5Q33.1) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 20(5Q33.1) MUTATED                                              10
  AMP PEAK 20(5Q33.1) WILD-TYPE                                           343
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 20(5Q33.1) MUTATED                                                                        9
  AMP PEAK 20(5Q33.1) WILD-TYPE                                                                     89
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 20(5Q33.1) MUTATED                                                                     1
  AMP PEAK 20(5Q33.1) WILD-TYPE                                                                  34
D18V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 20(5Q33.1) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   10
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           9
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              1
                                                                        clus
vv                                                                       AMP PEAK 20(5Q33.1) WILD-TYPE
  OTHER  SPECIFY                                                                                     9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    343
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            89
  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"
D18V9, binary
                               cls
clus                              0   1
  AMP PEAK 20(5Q33.1) MUTATED     1  19
  AMP PEAK 20(5Q33.1) WILD-TYPE  13 462
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 20(5Q33.1) MUTATED      1   19
  AMP PEAK 20(5Q33.1) WILD-TYPE   13  462
     clus
vv    AMP PEAK 20(5Q33.1) MUTATED AMP PEAK 20(5Q33.1) WILD-TYPE
  NO                            1                            13
  YES                          19                           462
[1] 2 2
[1] FALSE
D18V10, binary
                               cls
clus                              0   1
  AMP PEAK 20(5Q33.1) MUTATED    18   0
  AMP PEAK 20(5Q33.1) WILD-TYPE 399  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 20(5Q33.1) MUTATED     18    0
  AMP PEAK 20(5Q33.1) WILD-TYPE  399   17
     clus
vv    AMP PEAK 20(5Q33.1) MUTATED AMP PEAK 20(5Q33.1) WILD-TYPE
  NO                           18                           399
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 20(5Q33.1) MUTATED              3                       0   16
  AMP PEAK 20(5Q33.1) WILD-TYPE          127                      16  312
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 20(5Q33.1) MUTATED                     1
  AMP PEAK 20(5Q33.1) WILD-TYPE                   0
D18V11, multiclass
                         clus
vv                        AMP PEAK 20(5Q33.1) MUTATED
  MINIMAL (T3)                                      3
  MODERATE/ADVANCED (T4A)                           0
  NONE                                             16
  VERY ADVANCED (T4B)                               1
                         clus
vv                        AMP PEAK 20(5Q33.1) WILD-TYPE
  MINIMAL (T3)                                      127
  MODERATE/ADVANCED (T4A)                            16
  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
  AMP PEAK 20(5Q33.1) MUTATED    15   3   0   2
  AMP PEAK 20(5Q33.1) WILD-TYPE 363  48   4  28
D18V12, multiclass
    clus
vv   AMP PEAK 20(5Q33.1) MUTATED AMP PEAK 20(5Q33.1) WILD-TYPE
  R0                          15                           363
  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 20(5Q33.1) MUTATED    10  10
  AMP PEAK 20(5Q33.1) WILD-TYPE 214 251
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 20(5Q33.1) MUTATED     10   10
  AMP PEAK 20(5Q33.1) WILD-TYPE  214  251
            clus
vv           AMP PEAK 20(5Q33.1) MUTATED AMP PEAK 20(5Q33.1) WILD-TYPE
  MULTIFOCAL                          10                           214
  UNIFOCAL                            10                           251
[1] 2 2
[1] FALSE
D18V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 20(5Q33.1) MUTATED                                  0     1
  AMP PEAK 20(5Q33.1) WILD-TYPE                                1    48
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(5Q33.1) MUTATED                           0    10
  AMP PEAK 20(5Q33.1) WILD-TYPE                        26   311
D18V16, multiclass
                                  clus
vv                                 AMP PEAK 20(5Q33.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                     10
                                  clus
vv                                 AMP PEAK 20(5Q33.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       48
  BLACK OR AFRICAN AMERICAN                                   26
  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"
D18V17, binary
                               cls
clus                              0   1
  AMP PEAK 20(5Q33.1) MUTATED     0  12
  AMP PEAK 20(5Q33.1) WILD-TYPE  38 338
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 20(5Q33.1) MUTATED      0   12
  AMP PEAK 20(5Q33.1) WILD-TYPE   38  338
                        clus
vv                       AMP PEAK 20(5Q33.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          12
                        clus
vv                       AMP PEAK 20(5Q33.1) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           338
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 21(5Q35.2) MUTATION ANALYSIS
D19V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 21(5Q35.2) MUTATED    17   2
  AMP PEAK 21(5Q35.2) WILD-TYPE 460  12
  AMP PEAK 21(5Q35.2) MUTATED AMP PEAK 21(5Q35.2) WILD-TYPE 
                           19                           472 
  AMP PEAK 21(5Q35.2) MUTATED AMP PEAK 21(5Q35.2) WILD-TYPE 
                            2                            12 
$`AMP PEAK 21(5Q35.2) MUTATED`
TCGA-BJ-A190 TCGA-BJ-A2N9 TCGA-EL-A3T9 TCGA-EL-A4K9 TCGA-EL-A4KI TCGA-EM-A1YC 
       20.58        20.48         5.72        37.78         8.71        54.21 
TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A2P2 TCGA-EM-A3AI 
       57.01        10.65         6.05        17.59        17.29        17.46 
TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FE-A22Z TCGA-FE-A239 TCGA-FY-A3I5 
       13.51        12.26        98.56        73.74        33.63         1.64 
TCGA-FY-A3NM 
        0.99 

$`AMP PEAK 21(5Q35.2) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
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        15.48        23.31        18.64         5.75 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
        6.48         0.03         3.45         6.35         7.82         6.18 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
        5.06         8.98         4.93         5.98         0.53         0.10 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
        0.20         0.23        11.38        10.68         0.10         0.39 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.10        20.22        15.42        36.46         5.98        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-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
        4.27         3.22         2.76        17.26        14.07       137.88 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
        3.39         8.71        25.35        13.41        11.90        14.60 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        7.99        11.01       100.01        18.51        13.12         7.99 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96         7.20         1.45         8.88         1.02         5.95 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS 
       10.09         7.99         5.33         8.48        10.45         1.51 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY 
        9.60        12.56         8.28         7.69         5.52         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.42         8.12         9.34         6.77         9.21         9.44 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
        9.90         8.61        10.09         7.07        10.36        12.43 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        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        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04         1.15        22.29 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA 
       32.48       116.91        98.24        41.29        95.38        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN 
       82.82        77.36        78.97        31.50        50.33        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        52.50        45.53        48.16         7.07        44.65 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       45.80        19.30        45.96        37.94        31.04        19.59 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4KD TCGA-EL-A4KG 
       30.51        33.60        28.73        41.13        29.95        13.32 
TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       11.87        26.86        18.18        20.91        12.36        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        11.74        11.15        14.24        16.44 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       17.88        13.18        23.51         2.99        12.30        15.19 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ 
       10.49        13.15        22.16        13.84        19.73        12.07 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.59        17.46        14.60        18.97        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       19.63        13.38         8.35        16.44        16.77        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        16.80        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        11.15         7.33        12.53 
TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
        9.24        13.91         7.82        11.51        16.41        15.62 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        70.65        16.90         9.01         4.83         8.61 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
        8.38         9.80         5.03        37.87        12.72         0.95 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       47.47        48.20        29.69        32.35        14.79        12.33 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       14.79        27.09        18.38        29.49        54.05        22.09 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
       71.01        80.02        65.36        84.89        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        2.43         5.56        24.72        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A230 
        4.80         5.03         2.14         4.01         1.94        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        24.69        68.22       102.90        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       81.34        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        46.06         4.08         0.89        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON 
       48.10        91.17         1.25         1.15        17.82         1.51 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        0.76         0.03         4.67        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         6.87         4.14         6.58         4.54 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
        0.89         1.35         1.15         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        10.26        16.90         9.80         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        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        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       12.43         6.74        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         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

  AMP PEAK 21(5Q35.2) MUTATED AMP PEAK 21(5Q35.2) WILD-TYPE 
                         0.99                          0.03 
  AMP PEAK 21(5Q35.2) MUTATED AMP PEAK 21(5Q35.2) WILD-TYPE 
                        98.56                        158.83 
  AMP PEAK 21(5Q35.2) MUTATED AMP PEAK 21(5Q35.2) WILD-TYPE 
                       17.460                        16.505 
[1] "1.0 - 98.6 (17.5)"  "0.0 - 158.8 (16.5)"
[1] "hr=" "3.7"
D19V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 21(5Q35.2) MUTATED         5        6         6        1         1
  AMP PEAK 21(5Q35.2) WILD-TYPE     275       45       103        1        44
                               vv
clus                            STAGE IVC
  AMP PEAK 21(5Q35.2) MUTATED           0
  AMP PEAK 21(5Q35.2) WILD-TYPE         6
D19V3, multiclass
           clus
vv          AMP PEAK 21(5Q35.2) MUTATED AMP PEAK 21(5Q35.2) WILD-TYPE
  STAGE I                             5                           275
  STAGE II                            6                            45
  STAGE III                           6                           103
  STAGE IV                            1                             1
  STAGE IVA                           1                            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 21(5Q35.2) MUTATED     3   7   7   2
  AMP PEAK 21(5Q35.2) WILD-TYPE 137 159 158  19
D19V4, multiclass
    clus
vv   AMP PEAK 21(5Q35.2) MUTATED AMP PEAK 21(5Q35.2) WILD-TYPE
  T1                           3                           137
  T2                           7                           159
  T3                           7                           158
  T4                           2                            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"
D19V5, binary
                               cls
clus                              0   1
  AMP PEAK 21(5Q35.2) MUTATED    13   2
  AMP PEAK 21(5Q35.2) WILD-TYPE 210 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 21(5Q35.2) MUTATED     13    2
  AMP PEAK 21(5Q35.2) WILD-TYPE  210  220
   clus
vv  AMP PEAK 21(5Q35.2) MUTATED AMP PEAK 21(5Q35.2) WILD-TYPE
  0                          13                           210
  1                           2                           220
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK 21(5Q35.2) MUTATED     2   0  17
  AMP PEAK 21(5Q35.2) WILD-TYPE 271   9 195
D19V6, multiclass
    clus
vv   AMP PEAK 21(5Q35.2) MUTATED AMP PEAK 21(5Q35.2) WILD-TYPE
  M0                           2                           271
  M1                           0                             9
  MX                          17                           195
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                               cls
clus                              0   1
  AMP PEAK 21(5Q35.2) MUTATED    12   7
  AMP PEAK 21(5Q35.2) WILD-TYPE 352 124
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 21(5Q35.2) MUTATED     12    7
  AMP PEAK 21(5Q35.2) WILD-TYPE  352  124
        clus
vv       AMP PEAK 21(5Q35.2) MUTATED AMP PEAK 21(5Q35.2) WILD-TYPE
  FEMALE                          12                           352
  MALE                             7                           124
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 21(5Q35.2) MUTATED                0
  AMP PEAK 21(5Q35.2) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 21(5Q35.2) MUTATED                                               9
  AMP PEAK 21(5Q35.2) WILD-TYPE                                           344
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 21(5Q35.2) MUTATED                                                                       10
  AMP PEAK 21(5Q35.2) WILD-TYPE                                                                     88
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 21(5Q35.2) MUTATED                                                                     0
  AMP PEAK 21(5Q35.2) WILD-TYPE                                                                  35
D19V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 21(5Q35.2) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    9
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          10
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       AMP PEAK 21(5Q35.2) WILD-TYPE
  OTHER  SPECIFY                                                                                     9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    344
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            88
  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"
D19V9, binary
                               cls
clus                              0   1
  AMP PEAK 21(5Q35.2) MUTATED     2  17
  AMP PEAK 21(5Q35.2) WILD-TYPE  12 464
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 21(5Q35.2) MUTATED      2   17
  AMP PEAK 21(5Q35.2) WILD-TYPE   12  464
     clus
vv    AMP PEAK 21(5Q35.2) MUTATED AMP PEAK 21(5Q35.2) WILD-TYPE
  NO                            2                            12
  YES                          17                           464
[1] 2 2
[1] FALSE
D19V10, binary
                               cls
clus                              0   1
  AMP PEAK 21(5Q35.2) MUTATED    18   0
  AMP PEAK 21(5Q35.2) WILD-TYPE 399  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 21(5Q35.2) MUTATED     18    0
  AMP PEAK 21(5Q35.2) WILD-TYPE  399   17
     clus
vv    AMP PEAK 21(5Q35.2) MUTATED AMP PEAK 21(5Q35.2) WILD-TYPE
  NO                           18                           399
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 21(5Q35.2) MUTATED              3                       1   14
  AMP PEAK 21(5Q35.2) WILD-TYPE          127                      15  314
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 21(5Q35.2) MUTATED                     1
  AMP PEAK 21(5Q35.2) WILD-TYPE                   0
D19V11, multiclass
                         clus
vv                        AMP PEAK 21(5Q35.2) MUTATED
  MINIMAL (T3)                                      3
  MODERATE/ADVANCED (T4A)                           1
  NONE                                             14
  VERY ADVANCED (T4B)                               1
                         clus
vv                        AMP PEAK 21(5Q35.2) WILD-TYPE
  MINIMAL (T3)                                      127
  MODERATE/ADVANCED (T4A)                            15
  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 21(5Q35.2) MUTATED    15   2   0   2
  AMP PEAK 21(5Q35.2) WILD-TYPE 363  49   4  28
D19V12, multiclass
    clus
vv   AMP PEAK 21(5Q35.2) MUTATED AMP PEAK 21(5Q35.2) WILD-TYPE
  R0                          15                           363
  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"
D19V13, continuous
D19V14, binary
                               cls
clus                              0   1
  AMP PEAK 21(5Q35.2) MUTATED     9  10
  AMP PEAK 21(5Q35.2) WILD-TYPE 215 251
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 21(5Q35.2) MUTATED      9   10
  AMP PEAK 21(5Q35.2) WILD-TYPE  215  251
            clus
vv           AMP PEAK 21(5Q35.2) MUTATED AMP PEAK 21(5Q35.2) WILD-TYPE
  MULTIFOCAL                           9                           215
  UNIFOCAL                            10                           251
[1] 2 2
[1] FALSE
D19V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 21(5Q35.2) MUTATED                                  0     0
  AMP PEAK 21(5Q35.2) WILD-TYPE                                1    49
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(5Q35.2) MUTATED                           0    11
  AMP PEAK 21(5Q35.2) WILD-TYPE                        26   310
D19V16, multiclass
                                  clus
vv                                 AMP PEAK 21(5Q35.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                     11
                                  clus
vv                                 AMP PEAK 21(5Q35.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       49
  BLACK OR AFRICAN AMERICAN                                   26
  WHITE                                                      310
[1] 4 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 21(5Q35.2) MUTATED     0  11
  AMP PEAK 21(5Q35.2) WILD-TYPE  38 339
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 21(5Q35.2) MUTATED      0   11
  AMP PEAK 21(5Q35.2) WILD-TYPE   38  339
                        clus
vv                       AMP PEAK 21(5Q35.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          11
                        clus
vv                       AMP PEAK 21(5Q35.2) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           339
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 22(6P22.3) MUTATION ANALYSIS
D20V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 22(6P22.3) MUTATED     2   1
  AMP PEAK 22(6P22.3) WILD-TYPE 475  13
  AMP PEAK 22(6P22.3) MUTATED AMP PEAK 22(6P22.3) WILD-TYPE 
                            3                           488 
  AMP PEAK 22(6P22.3) MUTATED AMP PEAK 22(6P22.3) WILD-TYPE 
                            1                            13 
$`AMP PEAK 22(6P22.3) MUTATED`
TCGA-DJ-A2Q0 TCGA-E8-A413 TCGA-FE-A239 
        8.12        13.61        33.63 

$`AMP PEAK 22(6P22.3) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        5.52         8.78         8.42         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       22.29        19.59        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        12.36        18.05        19.79        19.46        54.21 
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        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        10.49        13.15        22.16        13.84        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       17.59        12.07        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 
       17.46        18.97        15.68        14.14        19.63        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        16.44        16.77        27.95        23.77        16.80 
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        11.15         7.33        12.53         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        16.41        15.62        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        9.80         5.03        37.87        12.72         0.95        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
       71.01        80.02        65.36        84.89        98.56        61.02 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       58.72        57.11        55.10        59.15        28.24         5.85 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
        4.18         2.43         5.56        24.72        38.30        42.25 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
        2.37         4.50        80.81        69.24        59.87        43.50 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
        0.30        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        59.70        31.59        44.25        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA 
      102.90        66.77        81.34        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        46.06         4.08         0.89 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10        91.17         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       17.82         1.64         0.99         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
        4.67        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 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
        1.15         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        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90         9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74 
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         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  AMP PEAK 22(6P22.3) MUTATED AMP PEAK 22(6P22.3) WILD-TYPE 
                         8.12                          0.03 
  AMP PEAK 22(6P22.3) MUTATED AMP PEAK 22(6P22.3) WILD-TYPE 
                        33.63                        158.83 
  AMP PEAK 22(6P22.3) MUTATED AMP PEAK 22(6P22.3) WILD-TYPE 
                       13.610                        16.605 
[1] "8.1 - 33.6 (13.6)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "23" 
D20V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 22(6P22.3) MUTATED         1        1         1        0         0
  AMP PEAK 22(6P22.3) WILD-TYPE     279       50       108        2        45
                               vv
clus                            STAGE IVC
  AMP PEAK 22(6P22.3) MUTATED           0
  AMP PEAK 22(6P22.3) WILD-TYPE         6
D20V3, multiclass
           clus
vv          AMP PEAK 22(6P22.3) MUTATED AMP PEAK 22(6P22.3) WILD-TYPE
  STAGE I                             1                           279
  STAGE II                            1                            50
  STAGE III                           1                           108
  STAGE IV                            0                             2
  STAGE IVA                           0                            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 22(6P22.3) MUTATED     1   1   1   0
  AMP PEAK 22(6P22.3) WILD-TYPE 139 165 164  21
D20V4, multiclass
    clus
vv   AMP PEAK 22(6P22.3) MUTATED AMP PEAK 22(6P22.3) WILD-TYPE
  T1                           1                           139
  T2                           1                           165
  T3                           1                           164
  T4                           0                            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"
D20V5, binary
                               cls
clus                              0   1
  AMP PEAK 22(6P22.3) MUTATED     3   0
  AMP PEAK 22(6P22.3) WILD-TYPE 220 222
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 22(6P22.3) MUTATED      3    0
  AMP PEAK 22(6P22.3) WILD-TYPE  220  222
   clus
vv  AMP PEAK 22(6P22.3) MUTATED AMP PEAK 22(6P22.3) WILD-TYPE
  0                           3                           220
  1                           0                           222
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK 22(6P22.3) MUTATED     2   0   1
  AMP PEAK 22(6P22.3) WILD-TYPE 271   9 211
D20V6, multiclass
    clus
vv   AMP PEAK 22(6P22.3) MUTATED AMP PEAK 22(6P22.3) WILD-TYPE
  M0                           2                           271
  M1                           0                             9
  MX                           1                           211
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                               cls
clus                              0   1
  AMP PEAK 22(6P22.3) MUTATED     2   1
  AMP PEAK 22(6P22.3) WILD-TYPE 362 130
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 22(6P22.3) MUTATED      2    1
  AMP PEAK 22(6P22.3) WILD-TYPE  362  130
        clus
vv       AMP PEAK 22(6P22.3) MUTATED AMP PEAK 22(6P22.3) WILD-TYPE
  FEMALE                           2                           362
  MALE                             1                           130
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 22(6P22.3) MUTATED                0
  AMP PEAK 22(6P22.3) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 22(6P22.3) MUTATED                                               3
  AMP PEAK 22(6P22.3) WILD-TYPE                                           350
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 22(6P22.3) MUTATED                                                                        0
  AMP PEAK 22(6P22.3) WILD-TYPE                                                                     98
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 22(6P22.3) MUTATED                                                                     0
  AMP PEAK 22(6P22.3) WILD-TYPE                                                                  35
D20V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 22(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 22(6P22.3) WILD-TYPE
  OTHER  SPECIFY                                                                                     9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    350
  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"
D20V9, binary
                               cls
clus                              0   1
  AMP PEAK 22(6P22.3) MUTATED     1   2
  AMP PEAK 22(6P22.3) WILD-TYPE  13 479
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 22(6P22.3) MUTATED      1    2
  AMP PEAK 22(6P22.3) WILD-TYPE   13  479
     clus
vv    AMP PEAK 22(6P22.3) MUTATED AMP PEAK 22(6P22.3) WILD-TYPE
  NO                            1                            13
  YES                           2                           479
[1] 2 2
[1] FALSE
D20V10, binary
                               cls
clus                              0   1
  AMP PEAK 22(6P22.3) MUTATED     3   0
  AMP PEAK 22(6P22.3) WILD-TYPE 414  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 22(6P22.3) MUTATED      3    0
  AMP PEAK 22(6P22.3) WILD-TYPE  414   17
     clus
vv    AMP PEAK 22(6P22.3) MUTATED AMP PEAK 22(6P22.3) WILD-TYPE
  NO                            3                           414
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 22(6P22.3) MUTATED              0                       0    3
  AMP PEAK 22(6P22.3) WILD-TYPE          130                      16  325
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 22(6P22.3) MUTATED                     0
  AMP PEAK 22(6P22.3) WILD-TYPE                   1
D20V11, multiclass
                         clus
vv                        AMP PEAK 22(6P22.3) MUTATED
  MINIMAL (T3)                                      0
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              3
  VERY ADVANCED (T4B)                               0
                         clus
vv                        AMP PEAK 22(6P22.3) WILD-TYPE
  MINIMAL (T3)                                      130
  MODERATE/ADVANCED (T4A)                            16
  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 22(6P22.3) MUTATED     3   0   0   0
  AMP PEAK 22(6P22.3) WILD-TYPE 375  51   4  30
D20V12, multiclass
    clus
vv   AMP PEAK 22(6P22.3) MUTATED AMP PEAK 22(6P22.3) WILD-TYPE
  R0                           3                           375
  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
[1] "Remove cluster labels:"      "AMP PEAK 22(6P22.3) MUTATED"
clus
  AMP PEAK 22(6P22.3) MUTATED AMP PEAK 22(6P22.3) WILD-TYPE 
                            2                           389 
                   TCGA-BJ-A0Z0                    TCGA-BJ-A0Z3 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A0Z9                    TCGA-BJ-A0ZA 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A0ZB                    TCGA-BJ-A0ZH 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A0ZJ                    TCGA-BJ-A18Y 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A18Z                    TCGA-BJ-A190 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A191                    TCGA-BJ-A28R 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A28T                    TCGA-BJ-A28W 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A28X                    TCGA-BJ-A28Z 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A290                    TCGA-BJ-A291 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A2N8                    TCGA-BJ-A2N9 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A2NA                    TCGA-BJ-A3EZ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A3PR                    TCGA-BJ-A3PU 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A45C                    TCGA-BJ-A45D 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A45E                    TCGA-BJ-A45G 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A45I                    TCGA-BJ-A45J 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A45K                    TCGA-BJ-A4O8 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A4O9                    TCGA-CE-A13K 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-CE-A3MD                    TCGA-DE-A0XZ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DE-A0Y2                    TCGA-DE-A0Y3 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DE-A3KN                    TCGA-DE-A4M8 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DE-A4MA                    TCGA-DE-A4MB 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DE-A4MC                    TCGA-DE-A4MD 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DE-A69K                    TCGA-DE-A7U5 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A13M                    TCGA-DJ-A13O 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A13P                    TCGA-DJ-A13R 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A13T                    TCGA-DJ-A13U 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A13V                    TCGA-DJ-A13W 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A13X                    TCGA-DJ-A1QG 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A1QH                    TCGA-DJ-A1QM 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PO                    TCGA-DJ-A2PP 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PQ                    TCGA-DJ-A2PR 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PS                    TCGA-DJ-A2PT 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PU                    TCGA-DJ-A2PV 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PW                    TCGA-DJ-A2PX 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PY                    TCGA-DJ-A2PZ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q1                    TCGA-DJ-A2Q2 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q3                    TCGA-DJ-A2Q4 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q5                    TCGA-DJ-A2Q6 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q7                    TCGA-DJ-A2Q8 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q9                    TCGA-DJ-A2QA 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2QB                    TCGA-DJ-A3UK 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UM                    TCGA-DJ-A3UN 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UO                    TCGA-DJ-A3UP 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UQ                    TCGA-DJ-A3UR 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UU                    TCGA-DJ-A3UW 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UX                    TCGA-DJ-A3UZ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3V0                    TCGA-DJ-A3V2 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3V3                    TCGA-DJ-A3V4 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3V5                    TCGA-DJ-A3V7 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3V8                    TCGA-DJ-A3V9 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3VA                    TCGA-DJ-A3VB 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3VD                    TCGA-DJ-A3VF 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3VG                    TCGA-DJ-A3VJ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3VL                    TCGA-DJ-A4UL 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A4UQ                    TCGA-DJ-A4UR 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A4UW                    TCGA-DJ-A4V2 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A4V5                    TCGA-DO-A1K0 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DO-A2HM                    TCGA-E3-A3DY 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-E3-A3DZ                    TCGA-E3-A3E0 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-E3-A3E1                    TCGA-E3-A3E2 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-E3-A3E3                    TCGA-E3-A3E5 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-E8-A242                    TCGA-E8-A2EA 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-E8-A2JQ                    TCGA-E8-A414 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-E8-A415                    TCGA-E8-A417 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-E8-A419                    TCGA-E8-A433 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-E8-A436                    TCGA-E8-A438 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-E8-A44K                    TCGA-EL-A3CM 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3CN                    TCGA-EL-A3CO 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3CR                    TCGA-EL-A3CS 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3CT                    TCGA-EL-A3CU 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3CV                    TCGA-EL-A3CW 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3CX                    TCGA-EL-A3CY 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3CZ                    TCGA-EL-A3D0 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3D1                    TCGA-EL-A3D4 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3D5                    TCGA-EL-A3D6 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3GO                    TCGA-EL-A3GP 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3GQ                    TCGA-EL-A3GS 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3GU                    TCGA-EL-A3GV 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3GX                    TCGA-EL-A3H3 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3H4                    TCGA-EL-A3H5 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3H7                    TCGA-EL-A3H8 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3MW                    TCGA-EL-A3MX 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3MZ                    TCGA-EL-A3N2 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3T0                    TCGA-EL-A3T1 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3T2                    TCGA-EL-A3TB 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZH                    TCGA-EL-A3ZK 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZL                    TCGA-EL-A3ZN 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZO                    TCGA-EL-A3ZP 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZS                    TCGA-EL-A4JV 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A4JW                    TCGA-EL-A4JX 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A4JZ                    TCGA-EL-A4K0 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A4K1                    TCGA-EL-A4K2 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A4K4                    TCGA-EL-A4K6 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A4K7                    TCGA-EL-A4KD 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A4KG                    TCGA-EL-A4KI 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A1CS                    TCGA-EM-A1CT 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A1CU                    TCGA-EM-A1CV 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A1CW                    TCGA-EM-A1YA 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A1YB                    TCGA-EM-A1YC 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A1YD                    TCGA-EM-A1YE 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A22I                    TCGA-EM-A22J 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A22K                    TCGA-EM-A22L 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A22M                    TCGA-EM-A22N 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A22O                    TCGA-EM-A22P 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A22Q                    TCGA-EM-A2CK 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2CN                    TCGA-EM-A2CP 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2CQ                    TCGA-EM-A2CS 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2CT                    TCGA-EM-A2CU 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2OV                    TCGA-EM-A2OW 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2OX                    TCGA-EM-A2OY 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2OZ                    TCGA-EM-A2P0 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2P1                    TCGA-EM-A2P2 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2P3                    TCGA-EM-A3AJ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3AK                    TCGA-EM-A3AL 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3AN                    TCGA-EM-A3AO 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3AQ                    TCGA-EM-A3AR 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3FJ                    TCGA-EM-A3FK 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3FL                    TCGA-EM-A3FM 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3FN                    TCGA-EM-A3FO 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3FP                    TCGA-EM-A3FQ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3FR                    TCGA-EM-A3O3 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3O7                    TCGA-EM-A3O8 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3O9                    TCGA-EM-A3OA 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3OB                    TCGA-EM-A3ST 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3SU                    TCGA-EM-A3SX 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3SY                    TCGA-EM-A3SZ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A4FF                    TCGA-EM-A4FH 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A4FK                    TCGA-EM-A4FM 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A4FN                    TCGA-EM-A4FO 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A4FQ                    TCGA-EM-A4FR 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A4FU                    TCGA-EM-A4FV 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A4G1                    TCGA-ET-A25G 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A25I                    TCGA-ET-A25J 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A25K                    TCGA-ET-A25L 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A25M                    TCGA-ET-A25N 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A25O                    TCGA-ET-A25P 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A2MX                    TCGA-ET-A2MZ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A2N0                    TCGA-ET-A2N1 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A2N4                    TCGA-ET-A39K 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A39L                    TCGA-ET-A39O 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A39P                    TCGA-ET-A39R 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A39S                    TCGA-ET-A39T 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A3BO                    TCGA-ET-A3BP 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A3BQ                    TCGA-ET-A3BS 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A3BT                    TCGA-ET-A3BU 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A3BV                    TCGA-ET-A3BX 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A3DQ                    TCGA-ET-A3DR 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A3DS                    TCGA-ET-A3DT 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A3DU                    TCGA-ET-A3DV 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A3DW                    TCGA-ET-A40P 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A40Q                    TCGA-ET-A40R 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A40S                    TCGA-ET-A40T 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A4KN                    TCGA-FE-A22Z 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FE-A230                    TCGA-FE-A231 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FE-A232                    TCGA-FE-A233 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FE-A234                    TCGA-FE-A235 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FE-A236                    TCGA-FE-A237 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FE-A238                    TCGA-FE-A23A 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FE-A3PB                    TCGA-FE-A3PC 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FE-A3PD                    TCGA-FK-A3S3 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FK-A3SB                    TCGA-FK-A3SE 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FK-A3SG                    TCGA-FK-A3SH 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FK-A4UB                    TCGA-FY-A2QD 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FY-A3I4                    TCGA-FY-A3I5 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FY-A3NM                    TCGA-FY-A3NN 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FY-A3ON                    TCGA-FY-A3R6 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FY-A3R7                    TCGA-FY-A3R9 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FY-A3TY                    TCGA-FY-A3W9 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FY-A3YR                    TCGA-FY-A40K 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FY-A40L                    TCGA-FY-A40M 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FY-A40N                    TCGA-FY-A4B3 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FY-A4B4                    TCGA-GE-A2C6 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-H2-A26U                    TCGA-H2-A2K9 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-H2-A3RH                    TCGA-H2-A3RI 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-H2-A421                    TCGA-H2-A422 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-IM-A3EB                    TCGA-IM-A3ED 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-IM-A3U2                    TCGA-IM-A3U3 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-IM-A41Y                    TCGA-IM-A41Z 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-IM-A420                    TCGA-IM-A4EB 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-J8-A3NZ                    TCGA-J8-A3O0 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-J8-A3O1                    TCGA-J8-A3O2 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-J8-A3YD                    TCGA-J8-A3YE 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-J8-A3YF                    TCGA-J8-A3YG 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-J8-A3YH                    TCGA-J8-A42S 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-J8-A4HW                    TCGA-J8-A4HY 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-KS-A41F                    TCGA-KS-A41I 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-KS-A41J                    TCGA-KS-A41L 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-KS-A4I1                    TCGA-KS-A4I3 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-KS-A4I5                    TCGA-KS-A4I7 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-KS-A4I9                    TCGA-KS-A4IB 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-KS-A4IC                    TCGA-KS-A4ID 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-L6-A4EP                    TCGA-L6-A4EQ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-L6-A4EU                    TCGA-MK-A4N6 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-MK-A4N7                    TCGA-MK-A4N9 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-QD-A8IV 
"AMP PEAK 22(6P22.3) WILD-TYPE" 
D20V14, binary
                               cls
clus                              0   1
  AMP PEAK 22(6P22.3) MUTATED     0   3
  AMP PEAK 22(6P22.3) WILD-TYPE 224 258
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 22(6P22.3) MUTATED      0    3
  AMP PEAK 22(6P22.3) WILD-TYPE  224  258
            clus
vv           AMP PEAK 22(6P22.3) MUTATED AMP PEAK 22(6P22.3) WILD-TYPE
  MULTIFOCAL                           0                           224
  UNIFOCAL                             3                           258
[1] 2 2
[1] FALSE
D20V15, continuous
[1] "Remove cluster labels:"      "AMP PEAK 22(6P22.3) MUTATED"
clus
  AMP PEAK 22(6P22.3) MUTATED AMP PEAK 22(6P22.3) WILD-TYPE 
                            2                           395 
                   TCGA-BJ-A0Z2                    TCGA-BJ-A0Z3 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A0Z9                    TCGA-BJ-A0ZA 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A0ZB                    TCGA-BJ-A0ZC 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A0ZE                    TCGA-BJ-A0ZG 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A0ZH                    TCGA-BJ-A0ZJ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A18Y                    TCGA-BJ-A18Z 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A190                    TCGA-BJ-A191 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A192                    TCGA-BJ-A28R 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A28S                    TCGA-BJ-A28T 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A28V                    TCGA-BJ-A28W 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A28Z                    TCGA-BJ-A290 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A291                    TCGA-BJ-A2N8 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A2N9                    TCGA-BJ-A2P4 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A3PU                    TCGA-BJ-A45C 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A45D                    TCGA-BJ-A45E 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A45F                    TCGA-BJ-A45G 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A45H                    TCGA-BJ-A45I 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A45J                    TCGA-BJ-A45K 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-BJ-A4O8                    TCGA-BJ-A4O9 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-CE-A13K                    TCGA-CE-A27D 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-CE-A3MD                    TCGA-CE-A3ME 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-CE-A481                    TCGA-CE-A482 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-CE-A483                    TCGA-CE-A484 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-CE-A485                    TCGA-DE-A0XZ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DE-A0Y2                    TCGA-DE-A0Y3 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DE-A2OL                    TCGA-DE-A3KN 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DE-A4M8                    TCGA-DE-A4M9 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DE-A4MA                    TCGA-DE-A4MB 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DE-A4MC                    TCGA-DE-A4MD 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DE-A69J                    TCGA-DE-A69K 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DE-A7U5                    TCGA-DJ-A13M 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A13O                    TCGA-DJ-A13R 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A13S                    TCGA-DJ-A13U 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A13V                    TCGA-DJ-A13W 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A13X                    TCGA-DJ-A1QD 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A1QE                    TCGA-DJ-A1QF 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A1QG                    TCGA-DJ-A1QH 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A1QI                    TCGA-DJ-A1QL 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A1QM                    TCGA-DJ-A1QN 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A1QO                    TCGA-DJ-A1QQ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PN                    TCGA-DJ-A2PO 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PP                    TCGA-DJ-A2PQ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PR                    TCGA-DJ-A2PS 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PT                    TCGA-DJ-A2PU 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PV                    TCGA-DJ-A2PW 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2PY                    TCGA-DJ-A2PZ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q1                    TCGA-DJ-A2Q2 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q3                    TCGA-DJ-A2Q4 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q5                    TCGA-DJ-A2Q6 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q7                    TCGA-DJ-A2Q8 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q9                    TCGA-DJ-A2QA 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A2QC                    TCGA-DJ-A3UK 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UM                    TCGA-DJ-A3UN 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UO                    TCGA-DJ-A3UP 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UQ                    TCGA-DJ-A3UR 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3US                    TCGA-DJ-A3UT 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UU                    TCGA-DJ-A3UW 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3UX                    TCGA-DJ-A3UY 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3V0                    TCGA-DJ-A3V2 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3V3                    TCGA-DJ-A3V4 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3V5                    TCGA-DJ-A3V7 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3V8                    TCGA-DJ-A3VA 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3VB                    TCGA-DJ-A3VD 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3VE                    TCGA-DJ-A3VF 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3VG                    TCGA-DJ-A3VJ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A3VL                    TCGA-DJ-A3VM 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A4UL                    TCGA-DJ-A4UQ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A4UT                    TCGA-DJ-A4V0 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A4V2                    TCGA-DJ-A4V4 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DJ-A4V5                    TCGA-DO-A1JZ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-DO-A1K0                    TCGA-DO-A2HM 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-E3-A3DY                    TCGA-E3-A3DZ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-E3-A3E0                    TCGA-E3-A3E1 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-E3-A3E2                    TCGA-E3-A3E3 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-E8-A419                    TCGA-EL-A3CN 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3CO                    TCGA-EL-A3CR 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3CS                    TCGA-EL-A3CT 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3CU                    TCGA-EL-A3CV 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3CW                    TCGA-EL-A3CX 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3CY                    TCGA-EL-A3CZ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3D0                    TCGA-EL-A3D1 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3D4                    TCGA-EL-A3D5 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3D6                    TCGA-EL-A3GO 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3GP                    TCGA-EL-A3GQ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3GR                    TCGA-EL-A3GS 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3GU                    TCGA-EL-A3GV 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3GW                    TCGA-EL-A3GX 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3GY                    TCGA-EL-A3GZ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3H2                    TCGA-EL-A3H3 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3H4                    TCGA-EL-A3H5 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3H7                    TCGA-EL-A3H8 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3MW                    TCGA-EL-A3MX 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3MY                    TCGA-EL-A3MZ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3N2                    TCGA-EL-A3N3 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3T1                    TCGA-EL-A3T2 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3T3                    TCGA-EL-A3T6 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3T7                    TCGA-EL-A3T8 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3T9                    TCGA-EL-A3TA 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3TB                    TCGA-EL-A3ZG 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZH                    TCGA-EL-A3ZK 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZL                    TCGA-EL-A3ZN 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZO                    TCGA-EL-A3ZP 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZQ                    TCGA-EL-A3ZR 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A3ZS                    TCGA-EL-A3ZT 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A4JV                    TCGA-EL-A4JW 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A4JX                    TCGA-EL-A4JZ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A4K0                    TCGA-EL-A4K1 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A4K2                    TCGA-EL-A4K4 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A4K6                    TCGA-EL-A4K7 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A4K9                    TCGA-EL-A4KD 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A4KG                    TCGA-EL-A4KH 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EL-A4KI                    TCGA-EM-A1CS 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A1CT                    TCGA-EM-A1CU 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A1CV                    TCGA-EM-A1CW 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A1YA                    TCGA-EM-A1YB 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A1YC                    TCGA-EM-A1YD 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A1YE                    TCGA-EM-A22I 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A22J                    TCGA-EM-A22K 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A22L                    TCGA-EM-A22N 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A22O                    TCGA-EM-A22P 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A22Q                    TCGA-EM-A2CJ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2CK                    TCGA-EM-A2CL 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2CN                    TCGA-EM-A2CO 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2CP                    TCGA-EM-A2CQ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2CS                    TCGA-EM-A2CT 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2CU                    TCGA-EM-A2OW 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2OX                    TCGA-EM-A2OY 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2P0                    TCGA-EM-A2P1 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A2P2                    TCGA-EM-A2P3 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3AI                    TCGA-EM-A3AJ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3AK                    TCGA-EM-A3AL 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3AN                    TCGA-EM-A3AO 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3AP                    TCGA-EM-A3AQ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3AR                    TCGA-EM-A3FJ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3FM                    TCGA-EM-A3FN 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3FO                    TCGA-EM-A3FP 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3FR                    TCGA-EM-A3O3 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3O6                    TCGA-EM-A3O7 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3O8                    TCGA-EM-A3O9 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3OA                    TCGA-EM-A3OB 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3ST                    TCGA-EM-A3SU 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3SX                    TCGA-EM-A3SY 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A3SZ                    TCGA-EM-A4FF 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A4FH                    TCGA-EM-A4FK 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A4FM                    TCGA-EM-A4FN 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A4FQ                    TCGA-EM-A4FR 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A4FU                    TCGA-EM-A4FV 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-EM-A4G1                    TCGA-ET-A25G 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A25I                    TCGA-ET-A25J 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A25K                    TCGA-ET-A25L 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A25M                    TCGA-ET-A25N 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A25O                    TCGA-ET-A25P 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A25R                    TCGA-ET-A2MY 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A2MZ                    TCGA-ET-A2N0 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A2N5                    TCGA-ET-A39J 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A39M                    TCGA-ET-A39N 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A39O                    TCGA-ET-A39P 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A39T                    TCGA-ET-A3BN 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A3BO                    TCGA-ET-A3BP 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A3BQ                    TCGA-ET-A3BS 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A3BT                    TCGA-ET-A3BU 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A3BV                    TCGA-ET-A3BW 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A3BX                    TCGA-ET-A3DO 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A3DS                    TCGA-ET-A3DT 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A40P                    TCGA-ET-A40Q 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A40R                    TCGA-ET-A40S 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-ET-A4KN                    TCGA-ET-A4KQ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FE-A22Z                    TCGA-FE-A230 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FE-A232                    TCGA-FE-A233 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FE-A234                    TCGA-FE-A235 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FE-A236                    TCGA-FE-A237 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FE-A238                    TCGA-FE-A23A 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FE-A3PA                    TCGA-FE-A3PB 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FE-A3PC                    TCGA-FE-A3PD 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FY-A2QD                    TCGA-FY-A3I4 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FY-A3I5                    TCGA-FY-A3ON 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FY-A3R8                    TCGA-FY-A3TY 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FY-A3W9                    TCGA-FY-A3YR 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FY-A40K                    TCGA-FY-A40L 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FY-A40M                    TCGA-FY-A40N 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-FY-A4B3                    TCGA-FY-A76V 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-GE-A2C6                    TCGA-H2-A421 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-IM-A3EB                    TCGA-IM-A3ED 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-IM-A3U2                    TCGA-IM-A3U3 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-IM-A41Y                    TCGA-IM-A41Z 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-IM-A420                    TCGA-IM-A4EB 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-J8-A3O0                    TCGA-J8-A3YD 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-J8-A3YG                    TCGA-KS-A41F 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-KS-A41I                    TCGA-KS-A41J 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-KS-A41L                    TCGA-KS-A4I3 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-KS-A4I5                    TCGA-KS-A4I7 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-KS-A4I9                    TCGA-KS-A4IB 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-KS-A4IC                    TCGA-KS-A4ID 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-L6-A4EP                    TCGA-L6-A4EQ 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-L6-A4ET                    TCGA-L6-A4EU 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-MK-A4N6                    TCGA-MK-A4N7 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-MK-A4N9                    TCGA-MK-A84Z 
"AMP PEAK 22(6P22.3) WILD-TYPE" "AMP PEAK 22(6P22.3) WILD-TYPE" 
                   TCGA-QD-A8IV 
"AMP PEAK 22(6P22.3) WILD-TYPE" 
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 22(6P22.3) MUTATED                                  0     1
  AMP PEAK 22(6P22.3) WILD-TYPE                                1    48
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(6P22.3) MUTATED                           0     2
  AMP PEAK 22(6P22.3) WILD-TYPE                        26   319
D20V16, multiclass
                                  clus
vv                                 AMP PEAK 22(6P22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      2
                                  clus
vv                                 AMP PEAK 22(6P22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       48
  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"
D20V17, binary
                               cls
clus                              0   1
  AMP PEAK 22(6P22.3) MUTATED     0   3
  AMP PEAK 22(6P22.3) WILD-TYPE  38 347
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 22(6P22.3) MUTATED      0    3
  AMP PEAK 22(6P22.3) WILD-TYPE   38  347
                        clus
vv                       AMP PEAK 22(6P22.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           3
                        clus
vv                       AMP PEAK 22(6P22.3) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           347
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 23(6P22.2) MUTATION ANALYSIS
D21V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 23(6P22.2) MUTATED     2   2
  AMP PEAK 23(6P22.2) WILD-TYPE 475  12
  AMP PEAK 23(6P22.2) MUTATED AMP PEAK 23(6P22.2) WILD-TYPE 
                            4                           487 
  AMP PEAK 23(6P22.2) MUTATED AMP PEAK 23(6P22.2) WILD-TYPE 
                            2                            12 
$`AMP PEAK 23(6P22.2) MUTATED`
TCGA-DJ-A2Q0 TCGA-EL-A3CW TCGA-EM-A3FP TCGA-FE-A239 
        8.12        57.01        17.39        33.63 

$`AMP PEAK 23(6P22.2) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        5.52         8.78         8.42         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        12.36        18.05        19.79        19.46        54.21 
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        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        10.49        13.15        22.16        13.84        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       17.59        12.07        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 
       17.46        18.97        15.68        14.14        19.63        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        16.44        16.77        27.95        23.77        16.80 
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 
       11.15         7.33        12.53         9.24        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        16.41        15.62        13.51        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
       80.02        65.36        84.89        98.56        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        2.43         5.56        24.72        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       59.70        31.59        44.25        24.69        68.22       102.90 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       66.77        81.34        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        46.06         4.08         0.89        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10        91.17         1.25         1.15        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        1.64         0.99         1.51         0.76         0.03         4.67 
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         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74        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         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  AMP PEAK 23(6P22.2) MUTATED AMP PEAK 23(6P22.2) WILD-TYPE 
                         8.12                          0.03 
  AMP PEAK 23(6P22.2) MUTATED AMP PEAK 23(6P22.2) WILD-TYPE 
                        57.01                        158.83 
  AMP PEAK 23(6P22.2) MUTATED AMP PEAK 23(6P22.2) WILD-TYPE 
                        25.51                         16.57 
[1] "8.1 - 57.0 (25.5)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "17" 
D21V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 23(6P22.2) MUTATED         0        2         2        0         0
  AMP PEAK 23(6P22.2) WILD-TYPE     280       49       107        2        45
                               vv
clus                            STAGE IVC
  AMP PEAK 23(6P22.2) MUTATED           0
  AMP PEAK 23(6P22.2) WILD-TYPE         6
D21V3, multiclass
           clus
vv          AMP PEAK 23(6P22.2) MUTATED AMP PEAK 23(6P22.2) WILD-TYPE
  STAGE I                             0                           280
  STAGE II                            2                            49
  STAGE III                           2                           107
  STAGE IV                            0                             2
  STAGE IVA                           0                            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 23(6P22.2) MUTATED     0   3   1   0
  AMP PEAK 23(6P22.2) WILD-TYPE 140 163 164  21
D21V4, multiclass
    clus
vv   AMP PEAK 23(6P22.2) MUTATED AMP PEAK 23(6P22.2) WILD-TYPE
  T1                           0                           140
  T2                           3                           163
  T3                           1                           164
  T4                           0                            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"
D21V5, binary
                               cls
clus                              0   1
  AMP PEAK 23(6P22.2) MUTATED     3   1
  AMP PEAK 23(6P22.2) WILD-TYPE 220 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 23(6P22.2) MUTATED      3    1
  AMP PEAK 23(6P22.2) WILD-TYPE  220  221
   clus
vv  AMP PEAK 23(6P22.2) MUTATED AMP PEAK 23(6P22.2) WILD-TYPE
  0                           3                           220
  1                           1                           221
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK 23(6P22.2) MUTATED     2   0   2
  AMP PEAK 23(6P22.2) WILD-TYPE 271   9 210
D21V6, multiclass
    clus
vv   AMP PEAK 23(6P22.2) MUTATED AMP PEAK 23(6P22.2) WILD-TYPE
  M0                           2                           271
  M1                           0                             9
  MX                           2                           210
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                               cls
clus                              0   1
  AMP PEAK 23(6P22.2) MUTATED     3   1
  AMP PEAK 23(6P22.2) WILD-TYPE 361 130
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 23(6P22.2) MUTATED      3    1
  AMP PEAK 23(6P22.2) WILD-TYPE  361  130
        clus
vv       AMP PEAK 23(6P22.2) MUTATED AMP PEAK 23(6P22.2) WILD-TYPE
  FEMALE                           3                           361
  MALE                             1                           130
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 23(6P22.2) MUTATED                0
  AMP PEAK 23(6P22.2) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 23(6P22.2) MUTATED                                               3
  AMP PEAK 23(6P22.2) WILD-TYPE                                           350
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 23(6P22.2) MUTATED                                                                        1
  AMP PEAK 23(6P22.2) WILD-TYPE                                                                     97
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 23(6P22.2) MUTATED                                                                     0
  AMP PEAK 23(6P22.2) WILD-TYPE                                                                  35
D21V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 23(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 23(6P22.2) WILD-TYPE
  OTHER  SPECIFY                                                                                     9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    350
  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"
D21V9, binary
                               cls
clus                              0   1
  AMP PEAK 23(6P22.2) MUTATED     1   3
  AMP PEAK 23(6P22.2) WILD-TYPE  13 478
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 23(6P22.2) MUTATED      1    3
  AMP PEAK 23(6P22.2) WILD-TYPE   13  478
     clus
vv    AMP PEAK 23(6P22.2) MUTATED AMP PEAK 23(6P22.2) WILD-TYPE
  NO                            1                            13
  YES                           3                           478
[1] 2 2
[1] FALSE
D21V10, binary
                               cls
clus                              0   1
  AMP PEAK 23(6P22.2) MUTATED     4   0
  AMP PEAK 23(6P22.2) WILD-TYPE 413  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 23(6P22.2) MUTATED      4    0
  AMP PEAK 23(6P22.2) WILD-TYPE  413   17
     clus
vv    AMP PEAK 23(6P22.2) MUTATED AMP PEAK 23(6P22.2) WILD-TYPE
  NO                            4                           413
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 23(6P22.2) MUTATED              0                       0    4
  AMP PEAK 23(6P22.2) WILD-TYPE          130                      16  324
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 23(6P22.2) MUTATED                     0
  AMP PEAK 23(6P22.2) WILD-TYPE                   1
D21V11, multiclass
                         clus
vv                        AMP PEAK 23(6P22.2) MUTATED
  MINIMAL (T3)                                      0
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              4
  VERY ADVANCED (T4B)                               0
                         clus
vv                        AMP PEAK 23(6P22.2) WILD-TYPE
  MINIMAL (T3)                                      130
  MODERATE/ADVANCED (T4A)                            16
  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 23(6P22.2) MUTATED     4   0   0   0
  AMP PEAK 23(6P22.2) WILD-TYPE 374  51   4  30
D21V12, multiclass
    clus
vv   AMP PEAK 23(6P22.2) MUTATED AMP PEAK 23(6P22.2) WILD-TYPE
  R0                           4                           374
  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"
D21V13, continuous
D21V14, binary
                               cls
clus                              0   1
  AMP PEAK 23(6P22.2) MUTATED     1   3
  AMP PEAK 23(6P22.2) WILD-TYPE 223 258
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 23(6P22.2) MUTATED      1    3
  AMP PEAK 23(6P22.2) WILD-TYPE  223  258
            clus
vv           AMP PEAK 23(6P22.2) MUTATED AMP PEAK 23(6P22.2) WILD-TYPE
  MULTIFOCAL                           1                           223
  UNIFOCAL                             3                           258
[1] 2 2
[1] FALSE
D21V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 23(6P22.2) MUTATED                                  0     0
  AMP PEAK 23(6P22.2) WILD-TYPE                                1    49
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(6P22.2) MUTATED                           0     3
  AMP PEAK 23(6P22.2) WILD-TYPE                        26   318
D21V16, multiclass
                                  clus
vv                                 AMP PEAK 23(6P22.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      3
                                  clus
vv                                 AMP PEAK 23(6P22.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       49
  BLACK OR AFRICAN AMERICAN                                   26
  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"
D21V17, binary
                               cls
clus                              0   1
  AMP PEAK 23(6P22.2) MUTATED     0   3
  AMP PEAK 23(6P22.2) WILD-TYPE  38 347
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 23(6P22.2) MUTATED      0    3
  AMP PEAK 23(6P22.2) WILD-TYPE   38  347
                        clus
vv                       AMP PEAK 23(6P22.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           3
                        clus
vv                       AMP PEAK 23(6P22.2) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           347
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 24(6P21.31) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 24(6P21.31) MUTATED     2   1
  AMP PEAK 24(6P21.31) WILD-TYPE 475  13
  AMP PEAK 24(6P21.31) MUTATED AMP PEAK 24(6P21.31) WILD-TYPE 
                             3                            488 
  AMP PEAK 24(6P21.31) MUTATED AMP PEAK 24(6P21.31) WILD-TYPE 
                             1                             13 
$`AMP PEAK 24(6P21.31) MUTATED`
TCGA-DE-A0Y3 TCGA-DJ-A2Q0 TCGA-FE-A239 
       36.46         8.12        33.63 

$`AMP PEAK 24(6P21.31) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A2OL 
        0.10         0.39         0.10        20.22        15.42         5.98 
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-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.78         8.42         9.34         6.77         9.21         9.44 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
        9.90         8.61        10.09         7.07        10.36        12.43 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        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        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04         1.15        22.29 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        12.36        18.05        19.79        19.46        54.21 
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        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        10.49        13.15        22.16        13.84        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       17.59        12.07        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 
       17.46        18.97        15.68        14.14        19.63        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        16.44        16.77        27.95        23.77        16.80 
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        11.15         7.33        12.53         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        16.41        15.62        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        9.80         5.03        37.87        12.72         0.95        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
       71.01        80.02        65.36        84.89        98.56        61.02 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       58.72        57.11        55.10        59.15        28.24         5.85 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
        4.18         2.43         5.56        24.72        38.30        42.25 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
        2.37         4.50        80.81        69.24        59.87        43.50 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
        0.30        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        59.70        31.59        44.25        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA 
      102.90        66.77        81.34        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        46.06         4.08         0.89 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10        91.17         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       17.82         1.64         0.99         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
        4.67        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 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
        1.15         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        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90         9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74 
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         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  AMP PEAK 24(6P21.31) MUTATED AMP PEAK 24(6P21.31) WILD-TYPE 
                          8.12                           0.03 
  AMP PEAK 24(6P21.31) MUTATED AMP PEAK 24(6P21.31) WILD-TYPE 
                         36.46                         158.83 
  AMP PEAK 24(6P21.31) MUTATED AMP PEAK 24(6P21.31) WILD-TYPE 
                         33.63                          16.57 
[1] "8.1 - 36.5 (33.6)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "13" 
D22V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 24(6P21.31) MUTATED         0        1         1        0         0
  AMP PEAK 24(6P21.31) WILD-TYPE     280       50       108        2        45
                                vv
clus                             STAGE IVC
  AMP PEAK 24(6P21.31) MUTATED           1
  AMP PEAK 24(6P21.31) WILD-TYPE         5
D22V3, multiclass
           clus
vv          AMP PEAK 24(6P21.31) MUTATED AMP PEAK 24(6P21.31) WILD-TYPE
  STAGE I                              0                            280
  STAGE II                             1                             50
  STAGE III                            1                            108
  STAGE IV                             0                              2
  STAGE IVA                            0                             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
  AMP PEAK 24(6P21.31) MUTATED     0   1   1   1
  AMP PEAK 24(6P21.31) WILD-TYPE 140 165 164  20
D22V4, multiclass
    clus
vv   AMP PEAK 24(6P21.31) MUTATED AMP PEAK 24(6P21.31) WILD-TYPE
  T1                            0                            140
  T2                            1                            165
  T3                            1                            164
  T4                            1                             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"
D22V5, binary
                                cls
clus                               0   1
  AMP PEAK 24(6P21.31) MUTATED     2   1
  AMP PEAK 24(6P21.31) WILD-TYPE 221 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(6P21.31) MUTATED      2    1
  AMP PEAK 24(6P21.31) WILD-TYPE  221  221
   clus
vv  AMP PEAK 24(6P21.31) MUTATED AMP PEAK 24(6P21.31) WILD-TYPE
  0                            2                            221
  1                            1                            221
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 24(6P21.31) MUTATED     1   1   1
  AMP PEAK 24(6P21.31) WILD-TYPE 272   8 211
D22V6, multiclass
    clus
vv   AMP PEAK 24(6P21.31) MUTATED AMP PEAK 24(6P21.31) WILD-TYPE
  M0                            1                            272
  M1                            1                              8
  MX                            1                            211
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                                cls
clus                               0   1
  AMP PEAK 24(6P21.31) MUTATED     2   1
  AMP PEAK 24(6P21.31) WILD-TYPE 362 130
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(6P21.31) MUTATED      2    1
  AMP PEAK 24(6P21.31) WILD-TYPE  362  130
        clus
vv       AMP PEAK 24(6P21.31) MUTATED AMP PEAK 24(6P21.31) WILD-TYPE
  FEMALE                            2                            362
  MALE                              1                            130
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 24(6P21.31) MUTATED                0
  AMP PEAK 24(6P21.31) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 24(6P21.31) MUTATED                                               3
  AMP PEAK 24(6P21.31) WILD-TYPE                                           350
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 24(6P21.31) MUTATED                                                                        0
  AMP PEAK 24(6P21.31) WILD-TYPE                                                                     98
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 24(6P21.31) MUTATED                                                                     0
  AMP PEAK 24(6P21.31) WILD-TYPE                                                                  35
D22V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 24(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 24(6P21.31) WILD-TYPE
  OTHER  SPECIFY                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     350
  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"
D22V9, binary
                                cls
clus                               0   1
  AMP PEAK 24(6P21.31) MUTATED     1   2
  AMP PEAK 24(6P21.31) WILD-TYPE  13 479
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(6P21.31) MUTATED      1    2
  AMP PEAK 24(6P21.31) WILD-TYPE   13  479
     clus
vv    AMP PEAK 24(6P21.31) MUTATED AMP PEAK 24(6P21.31) WILD-TYPE
  NO                             1                             13
  YES                            2                            479
[1] 2 2
[1] FALSE
D22V10, binary
                                cls
clus                               0   1
  AMP PEAK 24(6P21.31) MUTATED     3   0
  AMP PEAK 24(6P21.31) WILD-TYPE 414  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(6P21.31) MUTATED      3    0
  AMP PEAK 24(6P21.31) WILD-TYPE  414   17
     clus
vv    AMP PEAK 24(6P21.31) MUTATED AMP PEAK 24(6P21.31) WILD-TYPE
  NO                             3                            414
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 24(6P21.31) MUTATED              0                       0    2
  AMP PEAK 24(6P21.31) WILD-TYPE          130                      16  326
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 24(6P21.31) MUTATED                     0
  AMP PEAK 24(6P21.31) WILD-TYPE                   1
D22V11, multiclass
[1] "Remove cluster labels:"       "AMP PEAK 24(6P21.31) MUTATED"
clus
  AMP PEAK 24(6P21.31) MUTATED AMP PEAK 24(6P21.31) WILD-TYPE 
                             2                            473 
                    TCGA-BJ-A0YZ                     TCGA-BJ-A0Z0 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A0Z2                     TCGA-BJ-A0Z3 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A0Z9                     TCGA-BJ-A0ZA 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A0ZB                     TCGA-BJ-A0ZC 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A0ZE                     TCGA-BJ-A0ZG 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A0ZH                     TCGA-BJ-A0ZJ 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A18Y                     TCGA-BJ-A18Z 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A190                     TCGA-BJ-A191 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A192                     TCGA-BJ-A28X 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A28Z                     TCGA-BJ-A290 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A2N7                     TCGA-BJ-A2N9 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A2NA                     TCGA-BJ-A3EZ 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A3F0                     TCGA-BJ-A3PR 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A3PU                     TCGA-BJ-A45C 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A45D                     TCGA-BJ-A45G 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A45H                     TCGA-BJ-A45I 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A45K                     TCGA-BJ-A4O8 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-BJ-A4O9                     TCGA-CE-A13K 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-CE-A27D                     TCGA-CE-A3MD 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-CE-A3ME                     TCGA-CE-A481 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-CE-A482                     TCGA-CE-A483 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-CE-A484                     TCGA-CE-A485 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DE-A0XZ                     TCGA-DE-A0Y2 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DE-A2OL                     TCGA-DE-A3KN 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DE-A4M8                     TCGA-DE-A4M9 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DE-A4MA                     TCGA-DE-A4MB 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DE-A4MC                     TCGA-DE-A4MD 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DE-A69J                     TCGA-DE-A69K 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A13M                     TCGA-DJ-A13O 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A13P                     TCGA-DJ-A13R 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A13S                     TCGA-DJ-A13T 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A13U                     TCGA-DJ-A13V 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A13W                     TCGA-DJ-A13X 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A1QD                     TCGA-DJ-A1QE 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A1QF                     TCGA-DJ-A1QG 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A1QH                     TCGA-DJ-A1QI 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A1QL                     TCGA-DJ-A1QM 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A1QN                     TCGA-DJ-A1QO 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A1QQ                     TCGA-DJ-A2PN 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A2PO                     TCGA-DJ-A2PP 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A2PQ                     TCGA-DJ-A2PR 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A2PS                     TCGA-DJ-A2PT 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A2PU                     TCGA-DJ-A2PV 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A2PW                     TCGA-DJ-A2PX 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A2PY                     TCGA-DJ-A2PZ 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A2Q1                     TCGA-DJ-A2Q2 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A2Q3                     TCGA-DJ-A2Q4 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A2Q5                     TCGA-DJ-A2Q6 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A2Q7                     TCGA-DJ-A2Q8 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A2Q9                     TCGA-DJ-A2QA 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A2QB                     TCGA-DJ-A2QC 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3UK                     TCGA-DJ-A3UM 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3UN                     TCGA-DJ-A3UO 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3UP                     TCGA-DJ-A3UQ 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3UR                     TCGA-DJ-A3US 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3UT                     TCGA-DJ-A3UU 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3UW                     TCGA-DJ-A3UX 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3UY                     TCGA-DJ-A3UZ 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3V0                     TCGA-DJ-A3V2 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3V3                     TCGA-DJ-A3V4 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3V5                     TCGA-DJ-A3V7 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3V8                     TCGA-DJ-A3V9 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3VA                     TCGA-DJ-A3VB 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3VD                     TCGA-DJ-A3VE 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3VF                     TCGA-DJ-A3VG 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3VJ                     TCGA-DJ-A3VL 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A3VM                     TCGA-DJ-A4UL 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A4UQ                     TCGA-DJ-A4UR 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A4UT                     TCGA-DJ-A4UW 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A4V0                     TCGA-DJ-A4V2 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DJ-A4V4                     TCGA-DJ-A4V5 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DO-A1JZ                     TCGA-DO-A1K0 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-DO-A2HM                     TCGA-E3-A3DY 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-E3-A3DZ                     TCGA-E3-A3E0 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-E3-A3E1                     TCGA-E3-A3E2 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-E3-A3E3                     TCGA-E3-A3E5 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-E8-A242                     TCGA-E8-A2EA 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-E8-A2JQ                     TCGA-E8-A3X7 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-E8-A413                     TCGA-E8-A414 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-E8-A415                     TCGA-E8-A416 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-E8-A417                     TCGA-E8-A418 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-E8-A419                     TCGA-E8-A432 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-E8-A433                     TCGA-E8-A434 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-E8-A436                     TCGA-E8-A437 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-E8-A438                     TCGA-E8-A44K 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-E8-A44M                     TCGA-EL-A3CL 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3CM                     TCGA-EL-A3CN 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3CO                     TCGA-EL-A3CP 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3CR                     TCGA-EL-A3CS 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3CT                     TCGA-EL-A3CU 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3CV                     TCGA-EL-A3CW 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3CX                     TCGA-EL-A3CY 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3CZ                     TCGA-EL-A3D0 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3D1                     TCGA-EL-A3D4 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3D5                     TCGA-EL-A3D6 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3GO                     TCGA-EL-A3GP 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3GQ                     TCGA-EL-A3GR 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3GS                     TCGA-EL-A3GU 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3GV                     TCGA-EL-A3GW 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3GX                     TCGA-EL-A3GY 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3GZ                     TCGA-EL-A3H1 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3H2                     TCGA-EL-A3H3 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3H4                     TCGA-EL-A3H5 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3H7                     TCGA-EL-A3H8 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3MW                     TCGA-EL-A3MX 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3MY                     TCGA-EL-A3MZ 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3N2                     TCGA-EL-A3N3 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3T0                     TCGA-EL-A3T1 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3T2                     TCGA-EL-A3T3 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3T6                     TCGA-EL-A3T7 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3T8                     TCGA-EL-A3T9 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3TA                     TCGA-EL-A3TB 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3ZG                     TCGA-EL-A3ZH 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3ZK                     TCGA-EL-A3ZL 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3ZN                     TCGA-EL-A3ZO 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3ZP                     TCGA-EL-A3ZQ 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3ZR                     TCGA-EL-A3ZS 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A3ZT                     TCGA-EL-A4JV 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A4JW                     TCGA-EL-A4JX 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A4JZ                     TCGA-EL-A4K0 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A4K1                     TCGA-EL-A4K2 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A4K4                     TCGA-EL-A4K6 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A4K7                     TCGA-EL-A4K9 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A4KD                     TCGA-EL-A4KG 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EL-A4KH                     TCGA-EL-A4KI 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A1CS                     TCGA-EM-A1CT 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A1CU                     TCGA-EM-A1CV 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A1CW                     TCGA-EM-A1YA 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A1YB                     TCGA-EM-A1YC 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A1YD                     TCGA-EM-A1YE 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A22I                     TCGA-EM-A22J 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A22K                     TCGA-EM-A22L 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A22M                     TCGA-EM-A22N 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A22O                     TCGA-EM-A22P 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A22Q                     TCGA-EM-A2CJ 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A2CK                     TCGA-EM-A2CL 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A2CN                     TCGA-EM-A2CO 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A2CP                     TCGA-EM-A2CQ 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A2CS                     TCGA-EM-A2CT 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A2CU                     TCGA-EM-A2OV 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A2OW                     TCGA-EM-A2OX 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A2OY                     TCGA-EM-A2OZ 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A2P0                     TCGA-EM-A2P1 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A2P2                     TCGA-EM-A2P3 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3AI                     TCGA-EM-A3AJ 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3AK                     TCGA-EM-A3AL 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3AN                     TCGA-EM-A3AO 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3AP                     TCGA-EM-A3AQ 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3AR                     TCGA-EM-A3FJ 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3FK                     TCGA-EM-A3FL 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3FM                     TCGA-EM-A3FN 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3FO                     TCGA-EM-A3FP 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3FQ                     TCGA-EM-A3FR 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3O3                     TCGA-EM-A3O6 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3O7                     TCGA-EM-A3O8 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3O9                     TCGA-EM-A3OA 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3OB                     TCGA-EM-A3ST 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3SU                     TCGA-EM-A3SX 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A3SY                     TCGA-EM-A3SZ 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A4FF                     TCGA-EM-A4FH 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A4FK                     TCGA-EM-A4FM 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A4FN                     TCGA-EM-A4FO 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A4FQ                     TCGA-EM-A4FR 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A4FU                     TCGA-EM-A4FV 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-EM-A4G1                     TCGA-ET-A25G 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-ET-A25I                     TCGA-ET-A25J 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-ET-A25K                     TCGA-ET-A25L 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-ET-A25M                     TCGA-ET-A25N 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-ET-A25O                     TCGA-ET-A25P 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-ET-A25R                     TCGA-ET-A2MX 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-ET-A2MY                     TCGA-ET-A2MZ 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-ET-A2N0                     TCGA-ET-A2N1 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-ET-A2N3                     TCGA-ET-A2N4 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-ET-A2N5                     TCGA-ET-A39I 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-ET-A39J                     TCGA-ET-A39K 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-ET-A39L                     TCGA-ET-A39M 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-ET-A39N                     TCGA-ET-A39O 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-ET-A39P                     TCGA-ET-A39R 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-ET-A39S                     TCGA-ET-A39T 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-ET-A3BN                     TCGA-ET-A3BO 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-ET-A3BP                     TCGA-ET-A3BQ 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-ET-A3BS                     TCGA-ET-A3BT 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-ET-A3BU                     TCGA-ET-A3BV 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-ET-A3BW                     TCGA-ET-A3BX 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-ET-A3DO                     TCGA-ET-A3DP 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-ET-A3DQ                     TCGA-ET-A3DR 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-ET-A3DS                     TCGA-ET-A3DT 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-ET-A3DU                     TCGA-ET-A3DV 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-ET-A3DW                     TCGA-ET-A40P 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-ET-A40Q                     TCGA-ET-A40R 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-ET-A40S                     TCGA-ET-A40T 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-ET-A4KN                     TCGA-ET-A4KQ 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-FE-A22Z                     TCGA-FE-A230 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-FE-A231                     TCGA-FE-A232 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-FE-A233                     TCGA-FE-A234 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-FE-A235                     TCGA-FE-A236 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-FE-A237                     TCGA-FE-A238 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-FE-A23A                     TCGA-FE-A3PA 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-FE-A3PB                     TCGA-FE-A3PC 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-FE-A3PD                     TCGA-FK-A3S3 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-FK-A3SB                     TCGA-FK-A3SE 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-FK-A3SG                     TCGA-FK-A3SH 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-FK-A4UB                     TCGA-FY-A2QD 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-FY-A3BL                     TCGA-FY-A3I4 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-FY-A3I5                     TCGA-FY-A3NM 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-FY-A3NN                     TCGA-FY-A3ON 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-FY-A3R6                     TCGA-FY-A3R7 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-FY-A3R8                     TCGA-FY-A3R9 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-FY-A3RA                     TCGA-FY-A3TY 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-FY-A3W9                     TCGA-FY-A3WA 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-FY-A3YR                     TCGA-FY-A40K 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-FY-A40L                     TCGA-FY-A40M 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-FY-A40N                     TCGA-FY-A4B0 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-FY-A4B3                     TCGA-FY-A4B4 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-FY-A76V                     TCGA-GE-A2C6 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-H2-A26U                     TCGA-H2-A2K9 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-H2-A3RH                     TCGA-H2-A3RI 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-H2-A421                     TCGA-H2-A422 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-IM-A3EB                     TCGA-IM-A3ED 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-IM-A3U2                     TCGA-IM-A3U3 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-IM-A41Y                     TCGA-IM-A41Z 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-IM-A420                     TCGA-IM-A4EB 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-J8-A3NZ                     TCGA-J8-A3O0 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-J8-A3O1                     TCGA-J8-A3O2 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-J8-A3YD                     TCGA-J8-A3YE 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-J8-A3YF                     TCGA-J8-A3YG 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-J8-A3YH                     TCGA-J8-A42S 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-J8-A4HW                     TCGA-J8-A4HY 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-KS-A41F                     TCGA-KS-A41I 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-KS-A41J                     TCGA-KS-A41L 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-KS-A4I1                     TCGA-KS-A4I5 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-KS-A4I7                     TCGA-KS-A4I9 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-KS-A4IB                     TCGA-KS-A4IC 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-KS-A4ID                     TCGA-L6-A4EP 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-L6-A4EQ                     TCGA-L6-A4ET 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-L6-A4EU                     TCGA-MK-A4N7 
"AMP PEAK 24(6P21.31) WILD-TYPE" "AMP PEAK 24(6P21.31) WILD-TYPE" 
                    TCGA-QD-A8IV 
"AMP PEAK 24(6P21.31) WILD-TYPE" 
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 24(6P21.31) MUTATED     2   1   0   0
  AMP PEAK 24(6P21.31) WILD-TYPE 376  50   4  30
D22V12, multiclass
    clus
vv   AMP PEAK 24(6P21.31) MUTATED AMP PEAK 24(6P21.31) WILD-TYPE
  R0                            2                            376
  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"
D22V13, continuous
D22V14, binary
                                cls
clus                               0   1
  AMP PEAK 24(6P21.31) MUTATED     1   2
  AMP PEAK 24(6P21.31) WILD-TYPE 223 259
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(6P21.31) MUTATED      1    2
  AMP PEAK 24(6P21.31) WILD-TYPE  223  259
            clus
vv           AMP PEAK 24(6P21.31) MUTATED AMP PEAK 24(6P21.31) WILD-TYPE
  MULTIFOCAL                            1                            223
  UNIFOCAL                              2                            259
[1] 2 2
[1] FALSE
D22V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 24(6P21.31) MUTATED                                  0     1
  AMP PEAK 24(6P21.31) WILD-TYPE                                1    48
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(6P21.31) MUTATED                           0     2
  AMP PEAK 24(6P21.31) WILD-TYPE                        26   319
D22V16, multiclass
                                  clus
vv                                 AMP PEAK 24(6P21.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       2
                                  clus
vv                                 AMP PEAK 24(6P21.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        48
  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"
D22V17, binary
                                cls
clus                               0   1
  AMP PEAK 24(6P21.31) MUTATED     0   3
  AMP PEAK 24(6P21.31) WILD-TYPE  38 347
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(6P21.31) MUTATED      0    3
  AMP PEAK 24(6P21.31) WILD-TYPE   38  347
                        clus
vv                       AMP PEAK 24(6P21.31) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            3
                        clus
vv                       AMP PEAK 24(6P21.31) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            347
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 25(6P21.2) MUTATION ANALYSIS
D23V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 25(6P21.2) MUTATED     3   1
  AMP PEAK 25(6P21.2) WILD-TYPE 474  13
  AMP PEAK 25(6P21.2) MUTATED AMP PEAK 25(6P21.2) WILD-TYPE 
                            4                           487 
  AMP PEAK 25(6P21.2) MUTATED AMP PEAK 25(6P21.2) WILD-TYPE 
                            1                            13 
$`AMP PEAK 25(6P21.2) MUTATED`
TCGA-DJ-A2Q0 TCGA-E8-A433 TCGA-EL-A3GS TCGA-FE-A239 
        8.12        14.70        65.39        33.63 

$`AMP PEAK 25(6P21.2) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        5.52         8.78         8.42         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       14.27         3.02        14.43        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
       30.18       102.84       124.04        50.37        37.25       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        38.66 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       52.73       139.00       131.15       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        12.16       147.42       130.72       129.57        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      116.91        98.24        41.29        95.38         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN 
       82.82        77.36        78.97        31.50        50.33        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        52.50        45.53        48.16         7.07        44.65 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       45.80        19.30        45.96        37.94        31.04        19.59 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        33.60        28.73        41.13        37.78        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       13.32        11.87         8.71        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
       12.36        18.05        19.79        19.46        54.21        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        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       10.49        13.15        22.16        13.84        19.73        17.59 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       12.07        17.59        17.46        17.29        14.60        17.46 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       18.97        15.68        14.14        19.63        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       16.44        16.77        27.95        23.77        16.80        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 
       11.15         7.33        12.53         9.24        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        16.41        15.62        13.51        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
       80.02        65.36        84.89        98.56        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        2.43         5.56        24.72        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       59.70        31.59        44.25        24.69        68.22       102.90 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       66.77        81.34        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        46.06         4.08         0.89        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10        91.17         1.25         1.15        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        1.64         0.99         1.51         0.76         0.03         4.67 
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         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74        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         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  AMP PEAK 25(6P21.2) MUTATED AMP PEAK 25(6P21.2) WILD-TYPE 
                         8.12                          0.03 
  AMP PEAK 25(6P21.2) MUTATED AMP PEAK 25(6P21.2) WILD-TYPE 
                        65.39                        158.83 
  AMP PEAK 25(6P21.2) MUTATED AMP PEAK 25(6P21.2) WILD-TYPE 
                       24.165                        16.570 
[1] "8.1 - 65.4 (24.2)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "6"  
D23V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 25(6P21.2) MUTATED         2        1         1        0         0
  AMP PEAK 25(6P21.2) WILD-TYPE     278       50       108        2        45
                               vv
clus                            STAGE IVC
  AMP PEAK 25(6P21.2) MUTATED           0
  AMP PEAK 25(6P21.2) WILD-TYPE         6
D23V3, multiclass
           clus
vv          AMP PEAK 25(6P21.2) MUTATED AMP PEAK 25(6P21.2) WILD-TYPE
  STAGE I                             2                           278
  STAGE II                            1                            50
  STAGE III                           1                           108
  STAGE IV                            0                             2
  STAGE IVA                           0                            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 25(6P21.2) MUTATED     0   2   2   0
  AMP PEAK 25(6P21.2) WILD-TYPE 140 164 163  21
D23V4, multiclass
    clus
vv   AMP PEAK 25(6P21.2) MUTATED AMP PEAK 25(6P21.2) WILD-TYPE
  T1                           0                           140
  T2                           2                           164
  T3                           2                           163
  T4                           0                            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"
D23V5, binary
                               cls
clus                              0   1
  AMP PEAK 25(6P21.2) MUTATED     3   1
  AMP PEAK 25(6P21.2) WILD-TYPE 220 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 25(6P21.2) MUTATED      3    1
  AMP PEAK 25(6P21.2) WILD-TYPE  220  221
   clus
vv  AMP PEAK 25(6P21.2) MUTATED AMP PEAK 25(6P21.2) WILD-TYPE
  0                           3                           220
  1                           1                           221
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK 25(6P21.2) MUTATED     3   0   1
  AMP PEAK 25(6P21.2) WILD-TYPE 270   9 211
D23V6, multiclass
    clus
vv   AMP PEAK 25(6P21.2) MUTATED AMP PEAK 25(6P21.2) WILD-TYPE
  M0                           3                           270
  M1                           0                             9
  MX                           1                           211
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                               cls
clus                              0   1
  AMP PEAK 25(6P21.2) MUTATED     3   1
  AMP PEAK 25(6P21.2) WILD-TYPE 361 130
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 25(6P21.2) MUTATED      3    1
  AMP PEAK 25(6P21.2) WILD-TYPE  361  130
        clus
vv       AMP PEAK 25(6P21.2) MUTATED AMP PEAK 25(6P21.2) WILD-TYPE
  FEMALE                           3                           361
  MALE                             1                           130
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 25(6P21.2) MUTATED                0
  AMP PEAK 25(6P21.2) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 25(6P21.2) MUTATED                                               4
  AMP PEAK 25(6P21.2) WILD-TYPE                                           349
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 25(6P21.2) MUTATED                                                                        0
  AMP PEAK 25(6P21.2) WILD-TYPE                                                                     98
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 25(6P21.2) MUTATED                                                                     0
  AMP PEAK 25(6P21.2) WILD-TYPE                                                                  35
D23V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 25(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 25(6P21.2) WILD-TYPE
  OTHER  SPECIFY                                                                                     9
  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"
D23V9, binary
                               cls
clus                              0   1
  AMP PEAK 25(6P21.2) MUTATED     1   3
  AMP PEAK 25(6P21.2) WILD-TYPE  13 478
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 25(6P21.2) MUTATED      1    3
  AMP PEAK 25(6P21.2) WILD-TYPE   13  478
     clus
vv    AMP PEAK 25(6P21.2) MUTATED AMP PEAK 25(6P21.2) WILD-TYPE
  NO                            1                            13
  YES                           3                           478
[1] 2 2
[1] FALSE
D23V10, binary
                               cls
clus                              0   1
  AMP PEAK 25(6P21.2) MUTATED     4   0
  AMP PEAK 25(6P21.2) WILD-TYPE 413  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 25(6P21.2) MUTATED      4    0
  AMP PEAK 25(6P21.2) WILD-TYPE  413   17
     clus
vv    AMP PEAK 25(6P21.2) MUTATED AMP PEAK 25(6P21.2) WILD-TYPE
  NO                            4                           413
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 25(6P21.2) MUTATED              1                       0    3
  AMP PEAK 25(6P21.2) WILD-TYPE          129                      16  325
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 25(6P21.2) MUTATED                     0
  AMP PEAK 25(6P21.2) WILD-TYPE                   1
D23V11, multiclass
                         clus
vv                        AMP PEAK 25(6P21.2) MUTATED
  MINIMAL (T3)                                      1
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              3
  VERY ADVANCED (T4B)                               0
                         clus
vv                        AMP PEAK 25(6P21.2) WILD-TYPE
  MINIMAL (T3)                                      129
  MODERATE/ADVANCED (T4A)                            16
  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 25(6P21.2) MUTATED     4   0   0   0
  AMP PEAK 25(6P21.2) WILD-TYPE 374  51   4  30
D23V12, multiclass
    clus
vv   AMP PEAK 25(6P21.2) MUTATED AMP PEAK 25(6P21.2) WILD-TYPE
  R0                           4                           374
  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 25(6P21.2) MUTATED     1   3
  AMP PEAK 25(6P21.2) WILD-TYPE 223 258
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 25(6P21.2) MUTATED      1    3
  AMP PEAK 25(6P21.2) WILD-TYPE  223  258
            clus
vv           AMP PEAK 25(6P21.2) MUTATED AMP PEAK 25(6P21.2) WILD-TYPE
  MULTIFOCAL                           1                           223
  UNIFOCAL                             3                           258
[1] 2 2
[1] FALSE
D23V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 25(6P21.2) MUTATED                                  0     1
  AMP PEAK 25(6P21.2) WILD-TYPE                                1    48
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(6P21.2) MUTATED                           0     3
  AMP PEAK 25(6P21.2) WILD-TYPE                        26   318
D23V16, multiclass
                                  clus
vv                                 AMP PEAK 25(6P21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      3
                                  clus
vv                                 AMP PEAK 25(6P21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       48
  BLACK OR AFRICAN AMERICAN                                   26
  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"
D23V17, binary
                               cls
clus                              0   1
  AMP PEAK 25(6P21.2) MUTATED     1   3
  AMP PEAK 25(6P21.2) WILD-TYPE  37 347
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 25(6P21.2) MUTATED      1    3
  AMP PEAK 25(6P21.2) WILD-TYPE   37  347
                        clus
vv                       AMP PEAK 25(6P21.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                           3
                        clus
vv                       AMP PEAK 25(6P21.2) WILD-TYPE
  HISPANIC OR LATINO                                37
  NOT HISPANIC OR LATINO                           347
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 26(6P12.2) MUTATION ANALYSIS
D24V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 26(6P12.2) MUTATED     2   1
  AMP PEAK 26(6P12.2) WILD-TYPE 475  13
  AMP PEAK 26(6P12.2) MUTATED AMP PEAK 26(6P12.2) WILD-TYPE 
                            3                           488 
  AMP PEAK 26(6P12.2) MUTATED AMP PEAK 26(6P12.2) WILD-TYPE 
                            1                            13 
$`AMP PEAK 26(6P12.2) MUTATED`
TCGA-DJ-A2Q0 TCGA-ET-A25J TCGA-FE-A239 
        8.12        29.69        33.63 

$`AMP PEAK 26(6P12.2) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        5.52         8.78         8.42         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
        1.45        74.30        45.40        33.47       108.36        39.32 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        30.18       102.84        65.39       124.04        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       37.25       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        38.66        52.73       139.00       131.15       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        12.16       147.42       130.72 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       116.91        98.24        41.29        95.38 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       50.33        53.06        47.38        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       37.78        29.95        13.32        11.87         8.71        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        12.36        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       54.21        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        11.74        11.15        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       16.44        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
       12.30        15.19        10.49        13.15        22.16        13.84 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        17.59        12.07        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        17.46        18.97        15.68        14.14        19.63 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        16.44        16.77        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        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        11.15         7.33        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       13.91         7.82        11.51        16.41        15.62        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        70.65        16.90         9.01         4.83         8.61 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
        8.38         9.80         5.03        37.87        12.72         0.95 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       47.47        48.20        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
       71.01        80.02        65.36        84.89        98.56        61.02 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       58.72        57.11        55.10        59.15        28.24         5.85 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
        4.18         2.43         5.56        24.72        38.30        42.25 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
        2.37         4.50        80.81        69.24        59.87        43.50 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
        0.30        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        59.70        31.59        44.25        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA 
      102.90        66.77        81.34        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        46.06         4.08         0.89 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10        91.17         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       17.82         1.64         0.99         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
        4.67        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 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
        1.15         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        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90         9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74 
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         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  AMP PEAK 26(6P12.2) MUTATED AMP PEAK 26(6P12.2) WILD-TYPE 
                         8.12                          0.03 
  AMP PEAK 26(6P12.2) MUTATED AMP PEAK 26(6P12.2) WILD-TYPE 
                        33.63                        158.83 
  AMP PEAK 26(6P12.2) MUTATED AMP PEAK 26(6P12.2) WILD-TYPE 
                        29.69                         16.57 
[1] "8.1 - 33.6 (29.7)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "19" 
D24V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 26(6P12.2) MUTATED         1        1         1        0         0
  AMP PEAK 26(6P12.2) WILD-TYPE     279       50       108        2        45
                               vv
clus                            STAGE IVC
  AMP PEAK 26(6P12.2) MUTATED           0
  AMP PEAK 26(6P12.2) WILD-TYPE         6
D24V3, multiclass
           clus
vv          AMP PEAK 26(6P12.2) MUTATED AMP PEAK 26(6P12.2) WILD-TYPE
  STAGE I                             1                           279
  STAGE II                            1                            50
  STAGE III                           1                           108
  STAGE IV                            0                             2
  STAGE IVA                           0                            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(6P12.2) MUTATED     0   2   1   0
  AMP PEAK 26(6P12.2) WILD-TYPE 140 164 164  21
D24V4, multiclass
    clus
vv   AMP PEAK 26(6P12.2) MUTATED AMP PEAK 26(6P12.2) WILD-TYPE
  T1                           0                           140
  T2                           2                           164
  T3                           1                           164
  T4                           0                            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"
D24V5, binary
                               cls
clus                              0   1
  AMP PEAK 26(6P12.2) MUTATED     2   1
  AMP PEAK 26(6P12.2) WILD-TYPE 221 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 26(6P12.2) MUTATED      2    1
  AMP PEAK 26(6P12.2) WILD-TYPE  221  221
   clus
vv  AMP PEAK 26(6P12.2) MUTATED AMP PEAK 26(6P12.2) WILD-TYPE
  0                           2                           221
  1                           1                           221
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK 26(6P12.2) MUTATED     1   0   2
  AMP PEAK 26(6P12.2) WILD-TYPE 272   9 210
D24V6, multiclass
    clus
vv   AMP PEAK 26(6P12.2) MUTATED AMP PEAK 26(6P12.2) WILD-TYPE
  M0                           1                           272
  M1                           0                             9
  MX                           2                           210
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                               cls
clus                              0   1
  AMP PEAK 26(6P12.2) MUTATED     2   1
  AMP PEAK 26(6P12.2) WILD-TYPE 362 130
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 26(6P12.2) MUTATED      2    1
  AMP PEAK 26(6P12.2) WILD-TYPE  362  130
        clus
vv       AMP PEAK 26(6P12.2) MUTATED AMP PEAK 26(6P12.2) WILD-TYPE
  FEMALE                           2                           362
  MALE                             1                           130
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 26(6P12.2) MUTATED                0
  AMP PEAK 26(6P12.2) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 26(6P12.2) MUTATED                                               3
  AMP PEAK 26(6P12.2) WILD-TYPE                                           350
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 26(6P12.2) MUTATED                                                                        0
  AMP PEAK 26(6P12.2) WILD-TYPE                                                                     98
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 26(6P12.2) MUTATED                                                                     0
  AMP PEAK 26(6P12.2) WILD-TYPE                                                                  35
D24V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 26(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 26(6P12.2) WILD-TYPE
  OTHER  SPECIFY                                                                                     9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    350
  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"
D24V9, binary
                               cls
clus                              0   1
  AMP PEAK 26(6P12.2) MUTATED     1   2
  AMP PEAK 26(6P12.2) WILD-TYPE  13 479
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 26(6P12.2) MUTATED      1    2
  AMP PEAK 26(6P12.2) WILD-TYPE   13  479
     clus
vv    AMP PEAK 26(6P12.2) MUTATED AMP PEAK 26(6P12.2) WILD-TYPE
  NO                            1                            13
  YES                           2                           479
[1] 2 2
[1] FALSE
D24V10, binary
                               cls
clus                              0   1
  AMP PEAK 26(6P12.2) MUTATED     3   0
  AMP PEAK 26(6P12.2) WILD-TYPE 414  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 26(6P12.2) MUTATED      3    0
  AMP PEAK 26(6P12.2) WILD-TYPE  414   17
     clus
vv    AMP PEAK 26(6P12.2) MUTATED AMP PEAK 26(6P12.2) WILD-TYPE
  NO                            3                           414
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 26(6P12.2) MUTATED              0                       0    3
  AMP PEAK 26(6P12.2) WILD-TYPE          130                      16  325
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 26(6P12.2) MUTATED                     0
  AMP PEAK 26(6P12.2) WILD-TYPE                   1
D24V11, multiclass
                         clus
vv                        AMP PEAK 26(6P12.2) MUTATED
  MINIMAL (T3)                                      0
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              3
  VERY ADVANCED (T4B)                               0
                         clus
vv                        AMP PEAK 26(6P12.2) WILD-TYPE
  MINIMAL (T3)                                      130
  MODERATE/ADVANCED (T4A)                            16
  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 26(6P12.2) MUTATED     3   0   0   0
  AMP PEAK 26(6P12.2) WILD-TYPE 375  51   4  30
D24V12, multiclass
    clus
vv   AMP PEAK 26(6P12.2) MUTATED AMP PEAK 26(6P12.2) WILD-TYPE
  R0                           3                           375
  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 26(6P12.2) MUTATED     0   3
  AMP PEAK 26(6P12.2) WILD-TYPE 224 258
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 26(6P12.2) MUTATED      0    3
  AMP PEAK 26(6P12.2) WILD-TYPE  224  258
            clus
vv           AMP PEAK 26(6P12.2) MUTATED AMP PEAK 26(6P12.2) WILD-TYPE
  MULTIFOCAL                           0                           224
  UNIFOCAL                             3                           258
[1] 2 2
[1] FALSE
D24V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 26(6P12.2) MUTATED                                  0     0
  AMP PEAK 26(6P12.2) WILD-TYPE                                1    49
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 26(6P12.2) MUTATED                           0     3
  AMP PEAK 26(6P12.2) WILD-TYPE                        26   318
D24V16, multiclass
                                  clus
vv                                 AMP PEAK 26(6P12.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      3
                                  clus
vv                                 AMP PEAK 26(6P12.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       49
  BLACK OR AFRICAN AMERICAN                                   26
  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"
D24V17, binary
                               cls
clus                              0   1
  AMP PEAK 26(6P12.2) MUTATED     0   3
  AMP PEAK 26(6P12.2) WILD-TYPE  38 347
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 26(6P12.2) MUTATED      0    3
  AMP PEAK 26(6P12.2) WILD-TYPE   38  347
                        clus
vv                       AMP PEAK 26(6P12.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           3
                        clus
vv                       AMP PEAK 26(6P12.2) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           347
[1] 2 2
[1] FALSE

Clustering(25) Variable = AMP PEAK 27(6Q12) MUTATION ANALYSIS
D25V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 27(6Q12) MUTATED     3   0
  AMP PEAK 27(6Q12) WILD-TYPE 474  14
  AMP PEAK 27(6Q12) MUTATED AMP PEAK 27(6Q12) WILD-TYPE 
                          3                         488 
  AMP PEAK 27(6Q12) MUTATED AMP PEAK 27(6Q12) WILD-TYPE 
                          0                          14 
$`AMP PEAK 27(6Q12) MUTATED`
TCGA-DJ-A2Q0 TCGA-EL-A3ZS TCGA-J8-A3YE 
        8.12         7.07        27.85 

$`AMP PEAK 27(6Q12) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        5.52         8.78         8.42         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
        1.45        74.30        45.40        33.47       108.36        39.32 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        30.18       102.84        65.39       124.04        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       37.25       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        38.66        52.73       139.00       131.15       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        12.16       147.42       130.72 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       116.91        98.24        41.29        95.38 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       50.33        53.06        47.38        52.50        45.53        48.16 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        12.36        18.05        19.79        19.46        54.21 
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        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        10.49        13.15        22.16        13.84        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       17.59        12.07        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 
       17.46        18.97        15.68        14.14        19.63        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        16.44        16.77        27.95        23.77        16.80 
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        11.15         7.33        12.53         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        16.41        15.62        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        9.80         5.03        37.87        12.72         0.95        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
       71.01        80.02        65.36        84.89        98.56        61.02 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       58.72        57.11        55.10        59.15        28.24         5.85 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
        4.18         2.43         5.56        24.72        38.30        42.25 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
        2.37         4.50        80.81        69.24        59.87        43.50 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
        0.30        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        59.70        31.59        44.25        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      102.90        66.77        81.34        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        46.06         4.08 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        0.89        22.03         0.92        48.10        91.17         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
        1.15        17.82         1.64         0.99         1.51         0.76 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
        0.03         4.67        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         6.87         4.14         6.58         4.54         0.89 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35         1.15         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 
       10.26        16.90         9.80         9.63         2.96         8.65 
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        86.70         6.02        12.43         6.74 
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         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  AMP PEAK 27(6Q12) MUTATED AMP PEAK 27(6Q12) WILD-TYPE 
                       7.07                        0.03 
  AMP PEAK 27(6Q12) MUTATED AMP PEAK 27(6Q12) WILD-TYPE 
                      27.85                      158.83 
  AMP PEAK 27(6Q12) MUTATED AMP PEAK 27(6Q12) WILD-TYPE 
                      8.120                      16.605 
[1] "7.1 - 27.9 (8.1)"   "0.0 - 158.8 (16.6)"
[1] "hr="     "1200000"
D25V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 27(6Q12) MUTATED         2        1         0        0         0
  AMP PEAK 27(6Q12) WILD-TYPE     278       50       109        2        45
                             vv
clus                          STAGE IVC
  AMP PEAK 27(6Q12) MUTATED           0
  AMP PEAK 27(6Q12) WILD-TYPE         6
D25V3, multiclass
           clus
vv          AMP PEAK 27(6Q12) MUTATED AMP PEAK 27(6Q12) WILD-TYPE
  STAGE I                           2                         278
  STAGE II                          1                          50
  STAGE III                         0                         109
  STAGE IV                          0                           2
  STAGE IVA                         0                          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(6Q12) MUTATED     1   1   1   0
  AMP PEAK 27(6Q12) WILD-TYPE 139 165 164  21
D25V4, multiclass
    clus
vv   AMP PEAK 27(6Q12) MUTATED AMP PEAK 27(6Q12) WILD-TYPE
  T1                         1                         139
  T2                         1                         165
  T3                         1                         164
  T4                         0                          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"
D25V5, binary
                             cls
clus                            0   1
  AMP PEAK 27(6Q12) MUTATED     1   2
  AMP PEAK 27(6Q12) WILD-TYPE 222 220
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 27(6Q12) MUTATED      1    2
  AMP PEAK 27(6Q12) WILD-TYPE  222  220
   clus
vv  AMP PEAK 27(6Q12) MUTATED AMP PEAK 27(6Q12) WILD-TYPE
  0                         1                         222
  1                         2                         220
[1] 2 2
[1] FALSE
                             vv
clus                           M0  M1  MX
  AMP PEAK 27(6Q12) MUTATED     3   0   0
  AMP PEAK 27(6Q12) WILD-TYPE 270   9 212
D25V6, multiclass
    clus
vv   AMP PEAK 27(6Q12) MUTATED AMP PEAK 27(6Q12) WILD-TYPE
  M0                         3                         270
  M1                         0                           9
  MX                         0                         212
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                             cls
clus                            0   1
  AMP PEAK 27(6Q12) MUTATED     3   0
  AMP PEAK 27(6Q12) WILD-TYPE 361 131
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 27(6Q12) MUTATED      3    0
  AMP PEAK 27(6Q12) WILD-TYPE  361  131
        clus
vv       AMP PEAK 27(6Q12) MUTATED AMP PEAK 27(6Q12) WILD-TYPE
  FEMALE                         3                         361
  MALE                           0                         131
[1] 2 2
[1] FALSE
                             vv
clus                          OTHER  SPECIFY
  AMP PEAK 27(6Q12) MUTATED                0
  AMP PEAK 27(6Q12) WILD-TYPE              9
                             vv
clus                          THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 27(6Q12) MUTATED                                               3
  AMP PEAK 27(6Q12) WILD-TYPE                                           350
                             vv
clus                          THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 27(6Q12) MUTATED                                                                        0
  AMP PEAK 27(6Q12) WILD-TYPE                                                                     98
                             vv
clus                          THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 27(6Q12) MUTATED                                                                     0
  AMP PEAK 27(6Q12) WILD-TYPE                                                                  35
D25V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 27(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 27(6Q12) WILD-TYPE
  OTHER  SPECIFY                                                                                   9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  350
  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"
D25V9, binary
                             cls
clus                            0   1
  AMP PEAK 27(6Q12) MUTATED     0   3
  AMP PEAK 27(6Q12) WILD-TYPE  14 478
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 27(6Q12) MUTATED      0    3
  AMP PEAK 27(6Q12) WILD-TYPE   14  478
     clus
vv    AMP PEAK 27(6Q12) MUTATED AMP PEAK 27(6Q12) WILD-TYPE
  NO                          0                          14
  YES                         3                         478
[1] 2 2
[1] FALSE
D25V10, binary
                             cls
clus                            0   1
  AMP PEAK 27(6Q12) MUTATED     3   0
  AMP PEAK 27(6Q12) WILD-TYPE 414  17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 27(6Q12) MUTATED      3    0
  AMP PEAK 27(6Q12) WILD-TYPE  414   17
     clus
vv    AMP PEAK 27(6Q12) MUTATED AMP PEAK 27(6Q12) WILD-TYPE
  NO                          3                         414
  YES                         0                          17
[1] 2 2
[1] FALSE
                             vv
clus                          MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 27(6Q12) MUTATED              1                       0    2
  AMP PEAK 27(6Q12) WILD-TYPE          129                      16  326
                             vv
clus                          VERY ADVANCED (T4B)
  AMP PEAK 27(6Q12) MUTATED                     0
  AMP PEAK 27(6Q12) WILD-TYPE                   1
D25V11, multiclass
                         clus
vv                        AMP PEAK 27(6Q12) MUTATED AMP PEAK 27(6Q12) WILD-TYPE
  MINIMAL (T3)                                    1                         129
  MODERATE/ADVANCED (T4A)                         0                          16
  NONE                                            2                         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
  AMP PEAK 27(6Q12) MUTATED     3   0   0   0
  AMP PEAK 27(6Q12) WILD-TYPE 375  51   4  30
D25V12, multiclass
    clus
vv   AMP PEAK 27(6Q12) MUTATED AMP PEAK 27(6Q12) WILD-TYPE
  R0                         3                         375
  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"
D25V13, continuous
D25V14, binary
                             cls
clus                            0   1
  AMP PEAK 27(6Q12) MUTATED     0   3
  AMP PEAK 27(6Q12) WILD-TYPE 224 258
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 27(6Q12) MUTATED      0    3
  AMP PEAK 27(6Q12) WILD-TYPE  224  258
            clus
vv           AMP PEAK 27(6Q12) MUTATED AMP PEAK 27(6Q12) WILD-TYPE
  MULTIFOCAL                         0                         224
  UNIFOCAL                           3                         258
[1] 2 2
[1] FALSE
D25V15, continuous
[1] "Remove cluster labels:"    "AMP PEAK 27(6Q12) MUTATED"
clus
  AMP PEAK 27(6Q12) MUTATED AMP PEAK 27(6Q12) WILD-TYPE 
                          2                         395 
                 TCGA-BJ-A0Z2                  TCGA-BJ-A0Z3 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-BJ-A0Z9                  TCGA-BJ-A0ZA 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-BJ-A0ZB                  TCGA-BJ-A0ZC 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-BJ-A0ZE                  TCGA-BJ-A0ZG 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-BJ-A0ZH                  TCGA-BJ-A0ZJ 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-BJ-A18Y                  TCGA-BJ-A18Z 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-BJ-A190                  TCGA-BJ-A191 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-BJ-A192                  TCGA-BJ-A28R 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-BJ-A28S                  TCGA-BJ-A28T 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-BJ-A28V                  TCGA-BJ-A28W 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-BJ-A28Z                  TCGA-BJ-A290 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-BJ-A291                  TCGA-BJ-A2N8 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-BJ-A2N9                  TCGA-BJ-A2P4 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-BJ-A3PU                  TCGA-BJ-A45C 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-BJ-A45D                  TCGA-BJ-A45E 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-BJ-A45F                  TCGA-BJ-A45G 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-BJ-A45H                  TCGA-BJ-A45I 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-BJ-A45J                  TCGA-BJ-A45K 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-BJ-A4O8                  TCGA-BJ-A4O9 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-CE-A13K                  TCGA-CE-A27D 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-CE-A3MD                  TCGA-CE-A3ME 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-CE-A481                  TCGA-CE-A482 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-CE-A483                  TCGA-CE-A484 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-CE-A485                  TCGA-DE-A0XZ 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DE-A0Y2                  TCGA-DE-A0Y3 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DE-A2OL                  TCGA-DE-A3KN 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DE-A4M8                  TCGA-DE-A4M9 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DE-A4MA                  TCGA-DE-A4MB 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DE-A4MC                  TCGA-DE-A4MD 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DE-A69J                  TCGA-DE-A69K 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DE-A7U5                  TCGA-DJ-A13M 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A13O                  TCGA-DJ-A13R 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A13S                  TCGA-DJ-A13U 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A13V                  TCGA-DJ-A13W 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A13X                  TCGA-DJ-A1QD 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A1QE                  TCGA-DJ-A1QF 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A1QG                  TCGA-DJ-A1QH 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A1QI                  TCGA-DJ-A1QL 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A1QM                  TCGA-DJ-A1QN 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A1QO                  TCGA-DJ-A1QQ 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A2PN                  TCGA-DJ-A2PO 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A2PP                  TCGA-DJ-A2PQ 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A2PR                  TCGA-DJ-A2PS 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A2PT                  TCGA-DJ-A2PU 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A2PV                  TCGA-DJ-A2PW 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A2PY                  TCGA-DJ-A2PZ 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A2Q1                  TCGA-DJ-A2Q2 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A2Q3                  TCGA-DJ-A2Q4 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A2Q5                  TCGA-DJ-A2Q6 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A2Q7                  TCGA-DJ-A2Q8 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A2Q9                  TCGA-DJ-A2QA 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A2QC                  TCGA-DJ-A3UK 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A3UM                  TCGA-DJ-A3UN 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A3UO                  TCGA-DJ-A3UP 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A3UQ                  TCGA-DJ-A3UR 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A3US                  TCGA-DJ-A3UT 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A3UU                  TCGA-DJ-A3UW 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A3UX                  TCGA-DJ-A3UY 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A3V0                  TCGA-DJ-A3V2 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A3V3                  TCGA-DJ-A3V4 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A3V5                  TCGA-DJ-A3V7 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A3V8                  TCGA-DJ-A3VA 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A3VB                  TCGA-DJ-A3VD 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A3VE                  TCGA-DJ-A3VF 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A3VG                  TCGA-DJ-A3VJ 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A3VL                  TCGA-DJ-A3VM 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A4UL                  TCGA-DJ-A4UQ 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A4UT                  TCGA-DJ-A4V0 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A4V2                  TCGA-DJ-A4V4 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DJ-A4V5                  TCGA-DO-A1JZ 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-DO-A1K0                  TCGA-DO-A2HM 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-E3-A3DY                  TCGA-E3-A3DZ 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-E3-A3E0                  TCGA-E3-A3E1 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-E3-A3E2                  TCGA-E3-A3E3 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-E8-A419                  TCGA-EL-A3CN 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A3CO                  TCGA-EL-A3CR 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A3CS                  TCGA-EL-A3CT 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A3CU                  TCGA-EL-A3CV 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A3CW                  TCGA-EL-A3CX 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A3CY                  TCGA-EL-A3CZ 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A3D0                  TCGA-EL-A3D1 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A3D4                  TCGA-EL-A3D5 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A3D6                  TCGA-EL-A3GO 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A3GP                  TCGA-EL-A3GQ 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A3GR                  TCGA-EL-A3GS 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A3GU                  TCGA-EL-A3GV 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A3GW                  TCGA-EL-A3GX 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A3GY                  TCGA-EL-A3GZ 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A3H2                  TCGA-EL-A3H3 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A3H4                  TCGA-EL-A3H5 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A3H7                  TCGA-EL-A3H8 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A3MW                  TCGA-EL-A3MX 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A3MY                  TCGA-EL-A3MZ 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A3N2                  TCGA-EL-A3N3 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A3T1                  TCGA-EL-A3T2 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A3T3                  TCGA-EL-A3T6 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A3T7                  TCGA-EL-A3T8 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A3T9                  TCGA-EL-A3TA 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A3TB                  TCGA-EL-A3ZG 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A3ZH                  TCGA-EL-A3ZK 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A3ZL                  TCGA-EL-A3ZN 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A3ZO                  TCGA-EL-A3ZP 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A3ZQ                  TCGA-EL-A3ZR 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A3ZT                  TCGA-EL-A4JV 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A4JW                  TCGA-EL-A4JX 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A4JZ                  TCGA-EL-A4K0 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A4K1                  TCGA-EL-A4K2 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A4K4                  TCGA-EL-A4K6 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A4K7                  TCGA-EL-A4K9 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A4KD                  TCGA-EL-A4KG 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EL-A4KH                  TCGA-EL-A4KI 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A1CS                  TCGA-EM-A1CT 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A1CU                  TCGA-EM-A1CV 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A1CW                  TCGA-EM-A1YA 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A1YB                  TCGA-EM-A1YC 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A1YD                  TCGA-EM-A1YE 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A22I                  TCGA-EM-A22J 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A22K                  TCGA-EM-A22L 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A22N                  TCGA-EM-A22O 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A22P                  TCGA-EM-A22Q 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A2CJ                  TCGA-EM-A2CK 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A2CL                  TCGA-EM-A2CN 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A2CO                  TCGA-EM-A2CP 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A2CQ                  TCGA-EM-A2CS 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A2CT                  TCGA-EM-A2CU 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A2OW                  TCGA-EM-A2OX 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A2OY                  TCGA-EM-A2P0 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A2P1                  TCGA-EM-A2P2 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A2P3                  TCGA-EM-A3AI 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A3AJ                  TCGA-EM-A3AK 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A3AL                  TCGA-EM-A3AN 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A3AO                  TCGA-EM-A3AP 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A3AQ                  TCGA-EM-A3AR 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A3FJ                  TCGA-EM-A3FM 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A3FN                  TCGA-EM-A3FO 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A3FP                  TCGA-EM-A3FR 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A3O3                  TCGA-EM-A3O6 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A3O7                  TCGA-EM-A3O8 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A3O9                  TCGA-EM-A3OA 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A3OB                  TCGA-EM-A3ST 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A3SU                  TCGA-EM-A3SX 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A3SY                  TCGA-EM-A3SZ 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A4FF                  TCGA-EM-A4FH 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A4FK                  TCGA-EM-A4FM 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A4FN                  TCGA-EM-A4FQ 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A4FR                  TCGA-EM-A4FU 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-EM-A4FV                  TCGA-EM-A4G1 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-ET-A25G                  TCGA-ET-A25I 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-ET-A25J                  TCGA-ET-A25K 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-ET-A25L                  TCGA-ET-A25M 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-ET-A25N                  TCGA-ET-A25O 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-ET-A25P                  TCGA-ET-A25R 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-ET-A2MY                  TCGA-ET-A2MZ 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-ET-A2N0                  TCGA-ET-A2N5 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-ET-A39J                  TCGA-ET-A39M 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-ET-A39N                  TCGA-ET-A39O 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-ET-A39P                  TCGA-ET-A39T 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-ET-A3BN                  TCGA-ET-A3BO 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-ET-A3BP                  TCGA-ET-A3BQ 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-ET-A3BS                  TCGA-ET-A3BT 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-ET-A3BU                  TCGA-ET-A3BV 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-ET-A3BW                  TCGA-ET-A3BX 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-ET-A3DO                  TCGA-ET-A3DS 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-ET-A3DT                  TCGA-ET-A40P 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-ET-A40Q                  TCGA-ET-A40R 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-ET-A40S                  TCGA-ET-A4KN 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-ET-A4KQ                  TCGA-FE-A22Z 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-FE-A230                  TCGA-FE-A232 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-FE-A233                  TCGA-FE-A234 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-FE-A235                  TCGA-FE-A236 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-FE-A237                  TCGA-FE-A238 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-FE-A239                  TCGA-FE-A23A 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-FE-A3PA                  TCGA-FE-A3PB 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-FE-A3PC                  TCGA-FE-A3PD 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-FY-A2QD                  TCGA-FY-A3I4 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-FY-A3I5                  TCGA-FY-A3ON 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-FY-A3R8                  TCGA-FY-A3TY 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-FY-A3W9                  TCGA-FY-A3YR 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-FY-A40K                  TCGA-FY-A40L 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-FY-A40M                  TCGA-FY-A40N 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-FY-A4B3                  TCGA-FY-A76V 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-GE-A2C6                  TCGA-H2-A421 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-IM-A3EB                  TCGA-IM-A3ED 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-IM-A3U2                  TCGA-IM-A3U3 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-IM-A41Y                  TCGA-IM-A41Z 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-IM-A420                  TCGA-IM-A4EB 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-J8-A3O0                  TCGA-J8-A3YD 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-J8-A3YG                  TCGA-KS-A41F 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-KS-A41I                  TCGA-KS-A41J 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-KS-A41L                  TCGA-KS-A4I3 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-KS-A4I5                  TCGA-KS-A4I7 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-KS-A4I9                  TCGA-KS-A4IB 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-KS-A4IC                  TCGA-KS-A4ID 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-L6-A4EP                  TCGA-L6-A4EQ 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-L6-A4ET                  TCGA-L6-A4EU 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-MK-A4N6                  TCGA-MK-A4N7 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-MK-A4N9                  TCGA-MK-A84Z 
"AMP PEAK 27(6Q12) WILD-TYPE" "AMP PEAK 27(6Q12) WILD-TYPE" 
                 TCGA-QD-A8IV 
"AMP PEAK 27(6Q12) WILD-TYPE" 
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 27(6Q12) MUTATED                                  0     0
  AMP PEAK 27(6Q12) WILD-TYPE                                1    49
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 27(6Q12) MUTATED                           0     3
  AMP PEAK 27(6Q12) WILD-TYPE                        26   318
D25V16, multiclass
                                  clus
vv                                 AMP PEAK 27(6Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                0
  WHITE                                                    3
                                  clus
vv                                 AMP PEAK 27(6Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     49
  BLACK OR AFRICAN AMERICAN                                 26
  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"
D25V17, binary
                             cls
clus                            0   1
  AMP PEAK 27(6Q12) MUTATED     0   2
  AMP PEAK 27(6Q12) WILD-TYPE  38 348
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 27(6Q12) MUTATED      0    2
  AMP PEAK 27(6Q12) WILD-TYPE   38  348
                        clus
vv                       AMP PEAK 27(6Q12) MUTATED AMP PEAK 27(6Q12) WILD-TYPE
  HISPANIC OR LATINO                             0                          38
  NOT HISPANIC OR LATINO                         2                         348
[1] 2 2
[1] FALSE

Clustering(26) Variable = AMP PEAK 28(6Q27) MUTATION ANALYSIS
D26V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 28(6Q27) MUTATED     4   0
  AMP PEAK 28(6Q27) WILD-TYPE 473  14
  AMP PEAK 28(6Q27) MUTATED AMP PEAK 28(6Q27) WILD-TYPE 
                          4                         487 
  AMP PEAK 28(6Q27) MUTATED AMP PEAK 28(6Q27) WILD-TYPE 
                          0                          14 
$`AMP PEAK 28(6Q27) MUTATED`
TCGA-DJ-A2Q0 TCGA-EM-A22J TCGA-ET-A39N TCGA-FE-A22Z 
        8.12        14.50        98.56        73.74 

$`AMP PEAK 28(6Q27) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        5.52         8.78         8.42         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
        1.45        74.30        45.40        33.47       108.36        39.32 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        30.18       102.84        65.39       124.04        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       37.25       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        38.66        52.73       139.00       131.15       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        12.16       147.42       130.72 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       116.91        98.24        41.29        95.38 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       50.33        53.06        47.38        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       37.78        29.95        13.32        11.87         8.71        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        12.36        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22K TCGA-EM-A22L 
       54.21        57.01        54.08        14.73        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        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        10.49        13.15        22.16        13.84        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       17.59        12.07        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 
       17.46        18.97        15.68        14.14        19.63        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        16.44        16.77        27.95        23.77        16.80 
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        11.15         7.33        12.53         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        16.41        15.62        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        9.80         5.03        37.87        12.72         0.95        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
       71.01        80.02        65.36        84.89        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        2.43         5.56        24.72        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A230 
        4.80         5.03         2.14         4.01         1.94        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        24.69        68.22       102.90        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       81.34        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        46.06         4.08         0.89        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10        91.17         1.25         1.15        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        1.64         0.99         1.51         0.76         0.03         4.67 
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         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74        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         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  AMP PEAK 28(6Q27) MUTATED AMP PEAK 28(6Q27) WILD-TYPE 
                       8.12                        0.03 
  AMP PEAK 28(6Q27) MUTATED AMP PEAK 28(6Q27) WILD-TYPE 
                      98.56                      158.83 
  AMP PEAK 28(6Q27) MUTATED AMP PEAK 28(6Q27) WILD-TYPE 
                      44.12                       16.57 
[1] "8.1 - 98.6 (44.1)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "9300000"
D26V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 28(6Q27) MUTATED         1        2         0        0         1
  AMP PEAK 28(6Q27) WILD-TYPE     279       49       109        2        44
                             vv
clus                          STAGE IVC
  AMP PEAK 28(6Q27) MUTATED           0
  AMP PEAK 28(6Q27) WILD-TYPE         6
D26V3, multiclass
           clus
vv          AMP PEAK 28(6Q27) MUTATED AMP PEAK 28(6Q27) WILD-TYPE
  STAGE I                           1                         279
  STAGE II                          2                          49
  STAGE III                         0                         109
  STAGE IV                          0                           2
  STAGE IVA                         1                          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 28(6Q27) MUTATED     0   2   1   1
  AMP PEAK 28(6Q27) WILD-TYPE 140 164 164  20
D26V4, multiclass
    clus
vv   AMP PEAK 28(6Q27) MUTATED AMP PEAK 28(6Q27) WILD-TYPE
  T1                         0                         140
  T2                         2                         164
  T3                         1                         164
  T4                         1                          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"
D26V5, binary
                             cls
clus                            0   1
  AMP PEAK 28(6Q27) MUTATED     2   1
  AMP PEAK 28(6Q27) WILD-TYPE 221 221
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(6Q27) MUTATED      2    1
  AMP PEAK 28(6Q27) WILD-TYPE  221  221
   clus
vv  AMP PEAK 28(6Q27) MUTATED AMP PEAK 28(6Q27) WILD-TYPE
  0                         2                         221
  1                         1                         221
[1] 2 2
[1] FALSE
                             vv
clus                           M0  M1  MX
  AMP PEAK 28(6Q27) MUTATED     1   0   3
  AMP PEAK 28(6Q27) WILD-TYPE 272   9 209
D26V6, multiclass
    clus
vv   AMP PEAK 28(6Q27) MUTATED AMP PEAK 28(6Q27) WILD-TYPE
  M0                         1                         272
  M1                         0                           9
  MX                         3                         209
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                             cls
clus                            0   1
  AMP PEAK 28(6Q27) MUTATED     4   0
  AMP PEAK 28(6Q27) WILD-TYPE 360 131
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(6Q27) MUTATED      4    0
  AMP PEAK 28(6Q27) WILD-TYPE  360  131
        clus
vv       AMP PEAK 28(6Q27) MUTATED AMP PEAK 28(6Q27) WILD-TYPE
  FEMALE                         4                         360
  MALE                           0                         131
[1] 2 2
[1] FALSE
                             vv
clus                          OTHER  SPECIFY
  AMP PEAK 28(6Q27) MUTATED                0
  AMP PEAK 28(6Q27) WILD-TYPE              9
                             vv
clus                          THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 28(6Q27) MUTATED                                               2
  AMP PEAK 28(6Q27) WILD-TYPE                                           351
                             vv
clus                          THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 28(6Q27) MUTATED                                                                        2
  AMP PEAK 28(6Q27) WILD-TYPE                                                                     96
                             vv
clus                          THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 28(6Q27) MUTATED                                                                     0
  AMP PEAK 28(6Q27) WILD-TYPE                                                                  35
D26V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 28(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 28(6Q27) WILD-TYPE
  OTHER  SPECIFY                                                                                   9
  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"
D26V9, binary
                             cls
clus                            0   1
  AMP PEAK 28(6Q27) MUTATED     1   3
  AMP PEAK 28(6Q27) WILD-TYPE  13 478
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(6Q27) MUTATED      1    3
  AMP PEAK 28(6Q27) WILD-TYPE   13  478
     clus
vv    AMP PEAK 28(6Q27) MUTATED AMP PEAK 28(6Q27) WILD-TYPE
  NO                          1                          13
  YES                         3                         478
[1] 2 2
[1] FALSE
D26V10, binary
                             cls
clus                            0   1
  AMP PEAK 28(6Q27) MUTATED     3   1
  AMP PEAK 28(6Q27) WILD-TYPE 414  16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(6Q27) MUTATED      3    1
  AMP PEAK 28(6Q27) WILD-TYPE  414   16
     clus
vv    AMP PEAK 28(6Q27) MUTATED AMP PEAK 28(6Q27) WILD-TYPE
  NO                          3                         414
  YES                         1                          16
[1] 2 2
[1] FALSE
                             vv
clus                          MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 28(6Q27) MUTATED              0                       1    3
  AMP PEAK 28(6Q27) WILD-TYPE          130                      15  325
                             vv
clus                          VERY ADVANCED (T4B)
  AMP PEAK 28(6Q27) MUTATED                     0
  AMP PEAK 28(6Q27) WILD-TYPE                   1
D26V11, multiclass
                         clus
vv                        AMP PEAK 28(6Q27) MUTATED AMP PEAK 28(6Q27) WILD-TYPE
  MINIMAL (T3)                                    0                         130
  MODERATE/ADVANCED (T4A)                         1                          15
  NONE                                            3                         325
  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 28(6Q27) MUTATED     3   0   0   1
  AMP PEAK 28(6Q27) WILD-TYPE 375  51   4  29
D26V12, multiclass
    clus
vv   AMP PEAK 28(6Q27) MUTATED AMP PEAK 28(6Q27) WILD-TYPE
  R0                         3                         375
  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"
D26V13, continuous
D26V14, binary
                             cls
clus                            0   1
  AMP PEAK 28(6Q27) MUTATED     0   4
  AMP PEAK 28(6Q27) WILD-TYPE 224 257
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(6Q27) MUTATED      0    4
  AMP PEAK 28(6Q27) WILD-TYPE  224  257
            clus
vv           AMP PEAK 28(6Q27) MUTATED AMP PEAK 28(6Q27) WILD-TYPE
  MULTIFOCAL                         0                         224
  UNIFOCAL                           4                         257
[1] 2 2
[1] FALSE
D26V15, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 28(6Q27) MUTATED                                  0     0
  AMP PEAK 28(6Q27) WILD-TYPE                                1    49
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 28(6Q27) MUTATED                           0     3
  AMP PEAK 28(6Q27) WILD-TYPE                        26   318
D26V16, multiclass
                                  clus
vv                                 AMP PEAK 28(6Q27) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                0
  WHITE                                                    3
                                  clus
vv                                 AMP PEAK 28(6Q27) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     49
  BLACK OR AFRICAN AMERICAN                                 26
  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"
D26V17, binary
                             cls
clus                            0   1
  AMP PEAK 28(6Q27) MUTATED     0   3
  AMP PEAK 28(6Q27) WILD-TYPE  38 347
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(6Q27) MUTATED      0    3
  AMP PEAK 28(6Q27) WILD-TYPE   38  347
                        clus
vv                       AMP PEAK 28(6Q27) MUTATED AMP PEAK 28(6Q27) WILD-TYPE
  HISPANIC OR LATINO                             0                          38
  NOT HISPANIC OR LATINO                         3                         347
[1] 2 2
[1] FALSE

Clustering(27) Variable = AMP PEAK 29(7Q11.21) MUTATION ANALYSIS
D27V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 29(7Q11.21) MUTATED    18   1
  AMP PEAK 29(7Q11.21) WILD-TYPE 459  13
  AMP PEAK 29(7Q11.21) MUTATED AMP PEAK 29(7Q11.21) WILD-TYPE 
                            19                            472 
  AMP PEAK 29(7Q11.21) MUTATED AMP PEAK 29(7Q11.21) WILD-TYPE 
                             1                             13 
$`AMP PEAK 29(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         0.03         8.12        14.07         5.72 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A3AI 
       54.21        57.01        10.65         6.05        17.59        17.46 
TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FY-A3BL TCGA-FY-A3I5 
        9.24        13.51        12.26        98.56         1.15         1.64 
TCGA-FY-A3NM 
        0.99 

$`AMP PEAK 29(7Q11.21) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
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        15.48        23.31        18.64         5.75 
TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J 
        6.48         3.45         6.35         7.82         6.18         5.06 
TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD 
        8.98         4.93         5.98         0.53         0.10         0.20 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 
        0.23        11.38        10.68         0.10         0.39         0.10 
TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       20.22        15.42        36.46         5.98        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         4.27 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
        3.22         2.76        17.26        14.07       137.88         3.39 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        25.35        13.41        11.90        14.60         7.99 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       11.01       100.01        18.51        13.12         7.99        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
        7.20         1.45         8.88         1.02         5.95        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT 
        7.99         5.33         8.48        10.45         1.51         9.60 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       12.56         8.28         7.69         5.52         8.78         8.42 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
        9.34         6.77         9.21         9.44         9.90         8.61 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.07        10.36        12.43        10.85        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        12.49        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        24.23        17.69        43.00        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       21.37        12.76        25.02        20.22        30.61        14.56 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20         9.83        21.27        20.48        11.93        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL 
       21.01        18.97         7.76         8.32        17.36        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       27.62        18.21        10.78        10.98        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       17.82         3.12        15.81        24.33        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 
       30.31        14.04         1.15        22.29        19.59        13.61 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 
       14.27        13.81        14.27         3.02        14.43        14.70 
TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M 
       14.10        14.96         7.69        20.68        13.78        13.58 
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        80.91 
TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 
        4.18        58.82         1.45        74.30        45.40        33.47 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS 
      108.36        39.32         1.41        30.18       102.84        65.39 
TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
      124.04        50.37        37.25       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        38.66        52.73       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 
      131.15       108.66        57.63        17.52        52.50        12.16 
TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
      147.42       130.72       129.57        32.48       116.91        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
       41.29        95.38        66.90        82.82        77.36        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       31.50        50.33        53.06        47.38        52.50        45.53 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       48.16         7.07        44.65        45.80        19.30        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        19.59        30.51        33.60        28.73 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        37.78        29.95        13.32        11.87         8.71 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        12.36        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        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT 
       13.18        23.51         2.99        12.30        15.19        10.49 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 
       13.15        22.16        13.84        19.73        12.07        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        18.97        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       19.63        13.38         8.35        16.44        16.77        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        16.80        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        11.15         7.33        12.53 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ 
       13.91         7.82        11.51        16.41        15.62        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        9.80         5.03        37.87        12.72         0.95        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 
       27.09        18.38        29.49        54.05        22.09        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       80.02        65.36        84.89        61.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        59.15        28.24         5.85         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        24.69        68.22       102.90        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       81.34        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        46.06         4.08         0.89        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3I4 TCGA-FY-A3ON 
        0.92        48.10        91.17         1.25        17.82         1.51 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        0.76         0.03         4.67        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         6.87         4.14         6.58         4.54 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
        0.89         1.35         1.15         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        10.26        16.90         9.80         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        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        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       12.43         6.74        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         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

  AMP PEAK 29(7Q11.21) MUTATED AMP PEAK 29(7Q11.21) WILD-TYPE 
                          0.03                           0.03 
  AMP PEAK 29(7Q11.21) MUTATED AMP PEAK 29(7Q11.21) WILD-TYPE 
                         98.56                         158.83 
  AMP PEAK 29(7Q11.21) MUTATED AMP PEAK 29(7Q11.21) WILD-TYPE 
                         12.26                          16.75 
[1] "0.0 - 98.6 (12.3)"  "0.0 - 158.8 (16.8)"
[1] "hr=" "2.6"
D27V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 29(7Q11.21) MUTATED         9        6         3        1         0
  AMP PEAK 29(7Q11.21) WILD-TYPE     271       45       106        1        45
                                vv
clus                             STAGE IVC
  AMP PEAK 29(7Q11.21) MUTATED           0
  AMP PEAK 29(7Q11.21) WILD-TYPE         6
D27V3, multiclass
           clus
vv          AMP PEAK 29(7Q11.21) MUTATED AMP PEAK 29(7Q11.21) WILD-TYPE
  STAGE I                              9                            271
  STAGE II                             6                             45
  STAGE III                            3                            106
  STAGE IV                             1                              1
  STAGE IVA                            0                             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(7Q11.21) MUTATED     6   7   5   1
  AMP PEAK 29(7Q11.21) WILD-TYPE 134 159 160  20
D27V4, multiclass
    clus
vv   AMP PEAK 29(7Q11.21) MUTATED AMP PEAK 29(7Q11.21) WILD-TYPE
  T1                            6                            134
  T2                            7                            159
  T3                            5                            160
  T4                            1                             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"
D27V5, binary
                                cls
clus                               0   1
  AMP PEAK 29(7Q11.21) MUTATED    13   1
  AMP PEAK 29(7Q11.21) WILD-TYPE 210 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(7Q11.21) MUTATED     13    1
  AMP PEAK 29(7Q11.21) WILD-TYPE  210  221
   clus
vv  AMP PEAK 29(7Q11.21) MUTATED AMP PEAK 29(7Q11.21) WILD-TYPE
  0                           13                            210
  1                            1                            221
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 29(7Q11.21) MUTATED     5   0  14
  AMP PEAK 29(7Q11.21) WILD-TYPE 268   9 198
D27V6, multiclass
    clus
vv   AMP PEAK 29(7Q11.21) MUTATED AMP PEAK 29(7Q11.21) WILD-TYPE
  M0                            5                            268
  M1                            0                              9
  MX                           14                            198
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                                cls
clus                               0   1
  AMP PEAK 29(7Q11.21) MUTATED    14   5
  AMP PEAK 29(7Q11.21) WILD-TYPE 350 126
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(7Q11.21) MUTATED     14    5
  AMP PEAK 29(7Q11.21) WILD-TYPE  350  126
        clus
vv       AMP PEAK 29(7Q11.21) MUTATED AMP PEAK 29(7Q11.21) WILD-TYPE
  FEMALE                           14                            350
  MALE                              5                            126
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 29(7Q11.21) MUTATED                0
  AMP PEAK 29(7Q11.21) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 29(7Q11.21) MUTATED                                              10
  AMP PEAK 29(7Q11.21) WILD-TYPE                                           343
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 29(7Q11.21) MUTATED                                                                        9
  AMP PEAK 29(7Q11.21) WILD-TYPE                                                                     89
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 29(7Q11.21) MUTATED                                                                     0
  AMP PEAK 29(7Q11.21) WILD-TYPE                                                                  35
D27V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 29(7Q11.21) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    10
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            9
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               0
                                                                        clus
vv                                                                       AMP PEAK 29(7Q11.21) WILD-TYPE
  OTHER  SPECIFY                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     343
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             89
  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"
D27V9, binary
                                cls
clus                               0   1
  AMP PEAK 29(7Q11.21) MUTATED     0  19
  AMP PEAK 29(7Q11.21) WILD-TYPE  14 462
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(7Q11.21) MUTATED      0   19
  AMP PEAK 29(7Q11.21) WILD-TYPE   14  462
     clus
vv    AMP PEAK 29(7Q11.21) MUTATED AMP PEAK 29(7Q11.21) WILD-TYPE
  NO                             0                             14
  YES                           19                            462
[1] 2 2
[1] FALSE
D27V10, binary
                                cls
clus                               0   1
  AMP PEAK 29(7Q11.21) MUTATED    15   0
  AMP PEAK 29(7Q11.21) WILD-TYPE 402  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(7Q11.21) MUTATED     15    0
  AMP PEAK 29(7Q11.21) WILD-TYPE  402   17
     clus
vv    AMP PEAK 29(7Q11.21) MUTATED AMP PEAK 29(7Q11.21) WILD-TYPE
  NO                            15                            402
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 29(7Q11.21) MUTATED              1                       0   16
  AMP PEAK 29(7Q11.21) WILD-TYPE          129                      16  312
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 29(7Q11.21) MUTATED                     1
  AMP PEAK 29(7Q11.21) WILD-TYPE                   0
D27V11, multiclass
                         clus
vv                        AMP PEAK 29(7Q11.21) MUTATED
  MINIMAL (T3)                                       1
  MODERATE/ADVANCED (T4A)                            0
  NONE                                              16
  VERY ADVANCED (T4B)                                1
                         clus
vv                        AMP PEAK 29(7Q11.21) WILD-TYPE
  MINIMAL (T3)                                       129
  MODERATE/ADVANCED (T4A)                             16
  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
  AMP PEAK 29(7Q11.21) MUTATED    14   2   0   2
  AMP PEAK 29(7Q11.21) WILD-TYPE 364  49   4  28
D27V12, multiclass
    clus
vv   AMP PEAK 29(7Q11.21) MUTATED AMP PEAK 29(7Q11.21) WILD-TYPE
  R0                           14                            364
  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"
D27V13, continuous
D27V14, binary
                                cls
clus                               0   1
  AMP PEAK 29(7Q11.21) MUTATED     8  10
  AMP PEAK 29(7Q11.21) WILD-TYPE 216 251
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(7Q11.21) MUTATED      8   10
  AMP PEAK 29(7Q11.21) WILD-TYPE  216  251
            clus
vv           AMP PEAK 29(7Q11.21) MUTATED AMP PEAK 29(7Q11.21) WILD-TYPE
  MULTIFOCAL                            8                            216
  UNIFOCAL                             10                            251
[1] 2 2
[1] FALSE
D27V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 29(7Q11.21) MUTATED                                  0     1
  AMP PEAK 29(7Q11.21) WILD-TYPE                                1    48
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 29(7Q11.21) MUTATED                           0    10
  AMP PEAK 29(7Q11.21) WILD-TYPE                        26   311
D27V16, multiclass
                                  clus
vv                                 AMP PEAK 29(7Q11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                      10
                                  clus
vv                                 AMP PEAK 29(7Q11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        48
  BLACK OR AFRICAN AMERICAN                                    26
  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"
D27V17, binary
                                cls
clus                               0   1
  AMP PEAK 29(7Q11.21) MUTATED     0  11
  AMP PEAK 29(7Q11.21) WILD-TYPE  38 339
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(7Q11.21) MUTATED      0   11
  AMP PEAK 29(7Q11.21) WILD-TYPE   38  339
                        clus
vv                       AMP PEAK 29(7Q11.21) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           11
                        clus
vv                       AMP PEAK 29(7Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            339
[1] 2 2
[1] FALSE

Clustering(28) Variable = AMP PEAK 30(7Q21.11) MUTATION ANALYSIS
D28V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 30(7Q21.11) MUTATED    19   1
  AMP PEAK 30(7Q21.11) WILD-TYPE 458  13
  AMP PEAK 30(7Q21.11) MUTATED AMP PEAK 30(7Q21.11) WILD-TYPE 
                            20                            471 
  AMP PEAK 30(7Q21.11) MUTATED AMP PEAK 30(7Q21.11) WILD-TYPE 
                             1                             13 
$`AMP PEAK 30(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         0.03        10.09         8.12         5.72 
TCGA-EL-A4K7 TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY 
       41.13        54.21        57.01        10.65         6.05        17.59 
TCGA-EM-A3AI TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FY-A3I5 
       17.46         9.24        13.51        12.26        98.56         1.64 
TCGA-FY-A3NM TCGA-FY-A3WA 
        0.99        17.06 

$`AMP PEAK 30(7Q21.11) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
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        15.48        23.31        18.64         5.75 
TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J 
        6.48         3.45         6.35         7.82         6.18         5.06 
TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD 
        8.98         4.93         5.98         0.53         0.10         0.20 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 
        0.23        11.38        10.68         0.10         0.39         0.10 
TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       20.22        15.42        36.46         5.98        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         4.27 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
        3.22         2.76        17.26        14.07       137.88         3.39 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        25.35        13.41        11.90        14.60         7.99 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       11.01       100.01        18.51        13.12         7.99        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PO 
        7.20         1.45         8.88         1.02         5.95         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33         8.48        10.45         1.51         9.60        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
        8.28         7.69         5.52         8.78         8.42         9.34 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77         9.21         9.44         9.90         8.61        10.09 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
        7.07        10.36        12.43        10.85        15.88        15.09 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        12.49        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        24.23        17.69        43.00        11.34        21.37 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       12.76        25.02        20.22        30.61        14.56        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
        9.83        21.27        20.48        11.93        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76         8.32        17.36        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       18.21        10.78        10.98        14.14        14.70        17.82 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        24.33        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       31.07        12.07        66.38        40.21        63.19        30.31 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       14.04         1.15        22.29        19.59        13.61        14.27 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 
       13.81        14.07        14.27         3.02        14.43        14.70 
TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M 
       14.10        14.96         7.69        20.68        13.78        13.58 
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        80.91 
TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 
        4.18        58.82         1.45        74.30        45.40        33.47 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS 
      108.36        39.32         1.41        30.18       102.84        65.39 
TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
      124.04        50.37        37.25       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        38.66        52.73       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 
      131.15       108.66        57.63        17.52        52.50        12.16 
TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
      147.42       130.72       129.57        32.48       116.91        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
       41.29        95.38        66.90        82.82        77.36        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       31.50        50.33        53.06        47.38        52.50        45.53 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       48.16         7.07        44.65        45.80        19.30        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        19.59        30.51        33.60        28.73 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       37.78        29.95        13.32        11.87         8.71        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        12.36        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 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         2.99        12.30        15.19        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        13.84        19.73        12.07        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        18.97        15.68        14.14        19.63 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        16.44        16.77        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        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        11.15         7.33        12.53        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
        7.82        11.51        16.41        15.62        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        29.49        54.05        22.09        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        61.02        58.72        57.11        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       59.15        28.24         5.85         4.18         2.43         5.56 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       24.72        38.30        42.25         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       69.24        59.87        43.50         0.30        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       102.90        66.77        81.34 
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        46.06         4.08         0.89        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON 
       48.10        91.17         1.25         1.15        17.82         1.51 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        0.76         0.03         4.67        16.57        18.08         0.30 
TCGA-FY-A3W9 TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N 
        0.76         6.87         4.14         6.58         4.54         0.89 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35         1.15         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 
       10.26        16.90         9.80         9.63         2.96         8.65 
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        86.70         6.02        12.43 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
        6.74        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         0.72        16.64        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        8.71        10.98         5.19 

  AMP PEAK 30(7Q21.11) MUTATED AMP PEAK 30(7Q21.11) WILD-TYPE 
                          0.03                           0.03 
  AMP PEAK 30(7Q21.11) MUTATED AMP PEAK 30(7Q21.11) WILD-TYPE 
                         98.56                         158.83 
  AMP PEAK 30(7Q21.11) MUTATED AMP PEAK 30(7Q21.11) WILD-TYPE 
                        12.885                         16.640 
[1] "0.0 - 98.6 (12.9)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "2.3"
D28V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 30(7Q21.11) MUTATED         9        6         4        1         0
  AMP PEAK 30(7Q21.11) WILD-TYPE     271       45       105        1        45
                                vv
clus                             STAGE IVC
  AMP PEAK 30(7Q21.11) MUTATED           0
  AMP PEAK 30(7Q21.11) WILD-TYPE         6
D28V3, multiclass
           clus
vv          AMP PEAK 30(7Q21.11) MUTATED AMP PEAK 30(7Q21.11) WILD-TYPE
  STAGE I                              9                            271
  STAGE II                             6                             45
  STAGE III                            4                            105
  STAGE IV                             1                              1
  STAGE IVA                            0                             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(7Q21.11) MUTATED     6   8   5   1
  AMP PEAK 30(7Q21.11) WILD-TYPE 134 158 160  20
D28V4, multiclass
    clus
vv   AMP PEAK 30(7Q21.11) MUTATED AMP PEAK 30(7Q21.11) WILD-TYPE
  T1                            6                            134
  T2                            8                            158
  T3                            5                            160
  T4                            1                             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"
D28V5, binary
                                cls
clus                               0   1
  AMP PEAK 30(7Q21.11) MUTATED    13   2
  AMP PEAK 30(7Q21.11) WILD-TYPE 210 220
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 30(7Q21.11) MUTATED     13    2
  AMP PEAK 30(7Q21.11) WILD-TYPE  210  220
   clus
vv  AMP PEAK 30(7Q21.11) MUTATED AMP PEAK 30(7Q21.11) WILD-TYPE
  0                           13                            210
  1                            2                            220
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 30(7Q21.11) MUTATED     5   0  15
  AMP PEAK 30(7Q21.11) WILD-TYPE 268   9 197
D28V6, multiclass
    clus
vv   AMP PEAK 30(7Q21.11) MUTATED AMP PEAK 30(7Q21.11) WILD-TYPE
  M0                            5                            268
  M1                            0                              9
  MX                           15                            197
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                                cls
clus                               0   1
  AMP PEAK 30(7Q21.11) MUTATED    15   5
  AMP PEAK 30(7Q21.11) WILD-TYPE 349 126
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 30(7Q21.11) MUTATED     15    5
  AMP PEAK 30(7Q21.11) WILD-TYPE  349  126
        clus
vv       AMP PEAK 30(7Q21.11) MUTATED AMP PEAK 30(7Q21.11) WILD-TYPE
  FEMALE                           15                            349
  MALE                              5                            126
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 30(7Q21.11) MUTATED                0
  AMP PEAK 30(7Q21.11) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 30(7Q21.11) MUTATED                                              10
  AMP PEAK 30(7Q21.11) WILD-TYPE                                           343
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 30(7Q21.11) MUTATED                                                                       10
  AMP PEAK 30(7Q21.11) WILD-TYPE                                                                     88
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 30(7Q21.11) MUTATED                                                                     0
  AMP PEAK 30(7Q21.11) WILD-TYPE                                                                  35
D28V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 30(7Q21.11) 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 30(7Q21.11) WILD-TYPE
  OTHER  SPECIFY                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     343
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             88
  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"
D28V9, binary
                                cls
clus                               0   1
  AMP PEAK 30(7Q21.11) MUTATED     0  20
  AMP PEAK 30(7Q21.11) WILD-TYPE  14 461
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 30(7Q21.11) MUTATED      0   20
  AMP PEAK 30(7Q21.11) WILD-TYPE   14  461
     clus
vv    AMP PEAK 30(7Q21.11) MUTATED AMP PEAK 30(7Q21.11) WILD-TYPE
  NO                             0                             14
  YES                           20                            461
[1] 2 2
[1] FALSE
D28V10, binary
                                cls
clus                               0   1
  AMP PEAK 30(7Q21.11) MUTATED    18   0
  AMP PEAK 30(7Q21.11) WILD-TYPE 399  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 30(7Q21.11) MUTATED     18    0
  AMP PEAK 30(7Q21.11) WILD-TYPE  399   17
     clus
vv    AMP PEAK 30(7Q21.11) MUTATED AMP PEAK 30(7Q21.11) WILD-TYPE
  NO                            18                            399
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 30(7Q21.11) MUTATED              2                       0   16
  AMP PEAK 30(7Q21.11) WILD-TYPE          128                      16  312
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 30(7Q21.11) MUTATED                     1
  AMP PEAK 30(7Q21.11) WILD-TYPE                   0
D28V11, multiclass
                         clus
vv                        AMP PEAK 30(7Q21.11) MUTATED
  MINIMAL (T3)                                       2
  MODERATE/ADVANCED (T4A)                            0
  NONE                                              16
  VERY ADVANCED (T4B)                                1
                         clus
vv                        AMP PEAK 30(7Q21.11) WILD-TYPE
  MINIMAL (T3)                                       128
  MODERATE/ADVANCED (T4A)                             16
  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
  AMP PEAK 30(7Q21.11) MUTATED    15   2   0   2
  AMP PEAK 30(7Q21.11) WILD-TYPE 363  49   4  28
D28V12, multiclass
    clus
vv   AMP PEAK 30(7Q21.11) MUTATED AMP PEAK 30(7Q21.11) WILD-TYPE
  R0                           15                            363
  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"
D28V13, continuous
D28V14, binary
                                cls
clus                               0   1
  AMP PEAK 30(7Q21.11) MUTATED     8  12
  AMP PEAK 30(7Q21.11) WILD-TYPE 216 249
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 30(7Q21.11) MUTATED      8   12
  AMP PEAK 30(7Q21.11) WILD-TYPE  216  249
            clus
vv           AMP PEAK 30(7Q21.11) MUTATED AMP PEAK 30(7Q21.11) WILD-TYPE
  MULTIFOCAL                            8                            216
  UNIFOCAL                             12                            249
[1] 2 2
[1] FALSE
D28V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 30(7Q21.11) MUTATED                                  0     0
  AMP PEAK 30(7Q21.11) WILD-TYPE                                1    49
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 30(7Q21.11) MUTATED                           0    12
  AMP PEAK 30(7Q21.11) WILD-TYPE                        26   309
D28V16, multiclass
                                  clus
vv                                 AMP PEAK 30(7Q21.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                      12
                                  clus
vv                                 AMP PEAK 30(7Q21.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        49
  BLACK OR AFRICAN AMERICAN                                    26
  WHITE                                                       309
[1] 4 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 30(7Q21.11) MUTATED     0  12
  AMP PEAK 30(7Q21.11) WILD-TYPE  38 338
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 30(7Q21.11) MUTATED      0   12
  AMP PEAK 30(7Q21.11) WILD-TYPE   38  338
                        clus
vv                       AMP PEAK 30(7Q21.11) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           12
                        clus
vv                       AMP PEAK 30(7Q21.11) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            338
[1] 2 2
[1] FALSE

Clustering(29) Variable = AMP PEAK 31(7Q31.1) MUTATION ANALYSIS
D29V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 31(7Q31.1) MUTATED    20   1
  AMP PEAK 31(7Q31.1) WILD-TYPE 457  13
  AMP PEAK 31(7Q31.1) MUTATED AMP PEAK 31(7Q31.1) WILD-TYPE 
                           21                           470 
  AMP PEAK 31(7Q31.1) MUTATED AMP PEAK 31(7Q31.1) WILD-TYPE 
                            1                            13 
$`AMP PEAK 31(7Q31.1) MUTATED`
TCGA-BJ-A190 TCGA-BJ-A192 TCGA-BJ-A2N9 TCGA-BJ-A45E TCGA-DJ-A2Q0 TCGA-EL-A3T9 
       20.58         8.09        20.48         0.03         8.12         5.72 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CJ TCGA-EM-A2CO TCGA-EM-A2CQ 
       54.21        57.01        10.65        16.44         6.05        12.30 
TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N 
       17.59        17.46         9.24        13.51        12.26        98.56 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-KS-A4I3 
        1.64         0.99        12.43 

$`AMP PEAK 31(7Q31.1) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A28R TCGA-BJ-A28S 
       17.69        23.34        20.71         4.83         4.87        21.04 
TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 
        2.79         5.10        11.31        17.52         1.22        30.21 
TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ 
       22.88        18.38        16.57        18.97         7.04        16.01 
TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D 
       13.94        15.48        23.31        18.64         5.75         6.48 
TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K 
        3.45         6.35         7.82         6.18         5.06         8.98 
TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME 
        4.93         5.98         0.53         0.10         0.20         0.23 
TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ 
       11.38        10.68         0.10         0.39         0.10        20.22 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 
       15.42        36.46         5.98        15.85        18.54        18.84 
TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K 
       30.12        11.57        30.02        25.12         4.27         3.22 
TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        2.76        17.26        14.07       137.88         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       25.35        13.41        11.90        14.60         7.99        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      100.01        18.51        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45         8.88         1.02         5.95        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33         8.48        10.45         1.51         9.60        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
        8.28         7.69         5.52         8.78         8.42         9.34 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77         9.21         9.44         9.90         8.61        10.09 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
        7.07        10.36        12.43        10.85        15.88        15.09 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        12.49        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        24.23        17.69        43.00        11.34        21.37 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       12.76        25.02        20.22        30.61        14.56        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
        9.83        21.27        20.48        11.93        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76         8.32        17.36        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       18.21        10.78        10.98        14.14        14.70        17.82 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        24.33        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       31.07        12.07        66.38        40.21        63.19        30.31 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       14.04         1.15        22.29        19.59        13.61        14.27 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 
       13.81        14.07        14.27         3.02        14.43        14.70 
TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M 
       14.10        14.96         7.69        20.68        13.78        13.58 
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        80.91 
TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 
        4.18        58.82         1.45        74.30        45.40        33.47 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS 
      108.36        39.32         1.41        30.18       102.84        65.39 
TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
      124.04        50.37        37.25       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        38.66        52.73       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 
      131.15       108.66        57.63        17.52        52.50        12.16 
TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
      147.42       130.72       129.57        32.48       116.91        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
       41.29        95.38        66.90        82.82        77.36        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       31.50        50.33        53.06        47.38        52.50        45.53 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       48.16         7.07        44.65        45.80        19.30        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        19.59        30.51        33.60        28.73 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        37.78        29.95        13.32        11.87         8.71 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        12.36        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        11.74        11.15        14.24        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
       23.51         2.99        15.19        10.49        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       13.84        19.73        12.07        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        18.97        15.68        14.14        19.63        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        16.44        16.77        27.95        23.77        16.80 
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        11.15         7.33        12.53        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       11.51        16.41        15.62        12.79        70.65        16.90 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        9.01         4.83         8.61         8.38         9.80         5.03 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       37.87        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       29.49        54.05        22.09        16.08        29.19        19.76 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        58.22        13.74        71.01        80.02        65.36 
TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24         5.85         4.18         2.43         5.56        24.72 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       38.30        42.25         2.37         4.50        80.81        69.24 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       59.87        43.50         0.30        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        4.01         1.94        73.74        59.70        31.59        44.25 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       102.90        66.77        81.34        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 
       46.06         4.08         0.89        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 
       91.17         1.25         1.15        17.82         1.51         0.76 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
        0.03         4.67        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         6.87         4.14         6.58         4.54         0.89 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35         1.15         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 
       10.26        16.90         9.80         9.63         2.96         8.65 
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-A4I5 
      143.57        15.98        15.68        86.70         6.02         6.74 
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         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  AMP PEAK 31(7Q31.1) MUTATED AMP PEAK 31(7Q31.1) WILD-TYPE 
                         0.03                          0.03 
  AMP PEAK 31(7Q31.1) MUTATED AMP PEAK 31(7Q31.1) WILD-TYPE 
                        98.56                        158.83 
  AMP PEAK 31(7Q31.1) MUTATED AMP PEAK 31(7Q31.1) WILD-TYPE 
                       12.300                        16.785 
[1] "0.0 - 98.6 (12.3)"  "0.0 - 158.8 (16.8)"
[1] "hr=" "2.5"
D29V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 31(7Q31.1) MUTATED        10        6         4        1         0
  AMP PEAK 31(7Q31.1) WILD-TYPE     270       45       105        1        45
                               vv
clus                            STAGE IVC
  AMP PEAK 31(7Q31.1) MUTATED           0
  AMP PEAK 31(7Q31.1) WILD-TYPE         6
D29V3, multiclass
           clus
vv          AMP PEAK 31(7Q31.1) MUTATED AMP PEAK 31(7Q31.1) WILD-TYPE
  STAGE I                            10                           270
  STAGE II                            6                            45
  STAGE III                           4                           105
  STAGE IV                            1                             1
  STAGE IVA                           0                            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 31(7Q31.1) MUTATED     6   7   7   1
  AMP PEAK 31(7Q31.1) WILD-TYPE 134 159 158  20
D29V4, multiclass
    clus
vv   AMP PEAK 31(7Q31.1) MUTATED AMP PEAK 31(7Q31.1) WILD-TYPE
  T1                           6                           134
  T2                           7                           159
  T3                           7                           158
  T4                           1                            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"
D29V5, binary
                               cls
clus                              0   1
  AMP PEAK 31(7Q31.1) MUTATED    12   3
  AMP PEAK 31(7Q31.1) WILD-TYPE 211 219
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 31(7Q31.1) MUTATED     12    3
  AMP PEAK 31(7Q31.1) WILD-TYPE  211  219
   clus
vv  AMP PEAK 31(7Q31.1) MUTATED AMP PEAK 31(7Q31.1) WILD-TYPE
  0                          12                           211
  1                           3                           219
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK 31(7Q31.1) MUTATED     5   0  16
  AMP PEAK 31(7Q31.1) WILD-TYPE 268   9 196
D29V6, multiclass
    clus
vv   AMP PEAK 31(7Q31.1) MUTATED AMP PEAK 31(7Q31.1) WILD-TYPE
  M0                           5                           268
  M1                           0                             9
  MX                          16                           196
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                               cls
clus                              0   1
  AMP PEAK 31(7Q31.1) MUTATED    16   5
  AMP PEAK 31(7Q31.1) WILD-TYPE 348 126
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 31(7Q31.1) MUTATED     16    5
  AMP PEAK 31(7Q31.1) WILD-TYPE  348  126
        clus
vv       AMP PEAK 31(7Q31.1) MUTATED AMP PEAK 31(7Q31.1) WILD-TYPE
  FEMALE                          16                           348
  MALE                             5                           126
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 31(7Q31.1) MUTATED                0
  AMP PEAK 31(7Q31.1) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 31(7Q31.1) MUTATED                                              10
  AMP PEAK 31(7Q31.1) WILD-TYPE                                           343
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 31(7Q31.1) MUTATED                                                                       11
  AMP PEAK 31(7Q31.1) WILD-TYPE                                                                     87
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 31(7Q31.1) MUTATED                                                                     0
  AMP PEAK 31(7Q31.1) WILD-TYPE                                                                  35
D29V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 31(7Q31.1) MUTATED
  OTHER  SPECIFY                                                                                   0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   10
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          11
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                              0
                                                                        clus
vv                                                                       AMP PEAK 31(7Q31.1) WILD-TYPE
  OTHER  SPECIFY                                                                                     9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    343
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            87
  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"
D29V9, binary
                               cls
clus                              0   1
  AMP PEAK 31(7Q31.1) MUTATED     0  21
  AMP PEAK 31(7Q31.1) WILD-TYPE  14 460
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 31(7Q31.1) MUTATED      0   21
  AMP PEAK 31(7Q31.1) WILD-TYPE   14  460
     clus
vv    AMP PEAK 31(7Q31.1) MUTATED AMP PEAK 31(7Q31.1) WILD-TYPE
  NO                            0                            14
  YES                          21                           460
[1] 2 2
[1] FALSE
D29V10, binary
                               cls
clus                              0   1
  AMP PEAK 31(7Q31.1) MUTATED    19   0
  AMP PEAK 31(7Q31.1) WILD-TYPE 398  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 31(7Q31.1) MUTATED     19    0
  AMP PEAK 31(7Q31.1) WILD-TYPE  398   17
     clus
vv    AMP PEAK 31(7Q31.1) MUTATED AMP PEAK 31(7Q31.1) WILD-TYPE
  NO                           19                           398
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 31(7Q31.1) MUTATED              2                       0   16
  AMP PEAK 31(7Q31.1) WILD-TYPE          128                      16  312
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 31(7Q31.1) MUTATED                     1
  AMP PEAK 31(7Q31.1) WILD-TYPE                   0
D29V11, multiclass
                         clus
vv                        AMP PEAK 31(7Q31.1) MUTATED
  MINIMAL (T3)                                      2
  MODERATE/ADVANCED (T4A)                           0
  NONE                                             16
  VERY ADVANCED (T4B)                               1
                         clus
vv                        AMP PEAK 31(7Q31.1) WILD-TYPE
  MINIMAL (T3)                                      128
  MODERATE/ADVANCED (T4A)                            16
  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
  AMP PEAK 31(7Q31.1) MUTATED    14   3   0   3
  AMP PEAK 31(7Q31.1) WILD-TYPE 364  48   4  27
D29V12, multiclass
    clus
vv   AMP PEAK 31(7Q31.1) MUTATED AMP PEAK 31(7Q31.1) WILD-TYPE
  R0                          14                           364
  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 31(7Q31.1) MUTATED    10  11
  AMP PEAK 31(7Q31.1) WILD-TYPE 214 250
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 31(7Q31.1) MUTATED     10   11
  AMP PEAK 31(7Q31.1) WILD-TYPE  214  250
            clus
vv           AMP PEAK 31(7Q31.1) MUTATED AMP PEAK 31(7Q31.1) WILD-TYPE
  MULTIFOCAL                          10                           214
  UNIFOCAL                            11                           250
[1] 2 2
[1] FALSE
D29V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 31(7Q31.1) MUTATED                                  0     1
  AMP PEAK 31(7Q31.1) WILD-TYPE                                1    48
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 31(7Q31.1) MUTATED                           0    10
  AMP PEAK 31(7Q31.1) WILD-TYPE                        26   311
D29V16, multiclass
                                  clus
vv                                 AMP PEAK 31(7Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                     10
                                  clus
vv                                 AMP PEAK 31(7Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       48
  BLACK OR AFRICAN AMERICAN                                   26
  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"
D29V17, binary
                               cls
clus                              0   1
  AMP PEAK 31(7Q31.1) MUTATED     0   9
  AMP PEAK 31(7Q31.1) WILD-TYPE  38 341
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 31(7Q31.1) MUTATED      0    9
  AMP PEAK 31(7Q31.1) WILD-TYPE   38  341
                        clus
vv                       AMP PEAK 31(7Q31.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           9
                        clus
vv                       AMP PEAK 31(7Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           341
[1] 2 2
[1] FALSE

Clustering(30) Variable = AMP PEAK 32(7Q34) MUTATION ANALYSIS
D30V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 32(7Q34) MUTATED    20   1
  AMP PEAK 32(7Q34) WILD-TYPE 457  13
  AMP PEAK 32(7Q34) MUTATED AMP PEAK 32(7Q34) WILD-TYPE 
                         21                         470 
  AMP PEAK 32(7Q34) MUTATED AMP PEAK 32(7Q34) WILD-TYPE 
                          1                          13 
$`AMP PEAK 32(7Q34) MUTATED`
TCGA-BJ-A190 TCGA-BJ-A192 TCGA-BJ-A2N9 TCGA-BJ-A45E TCGA-DJ-A2Q0 TCGA-EL-A3T9 
       20.58         8.09        20.48         0.03         8.12         5.72 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CJ TCGA-EM-A2CO TCGA-EM-A2OY 
       54.21        57.01        10.65        16.44         6.05        17.59 
TCGA-EM-A3AI TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FY-A3I5 
       17.46         9.24        13.51        12.26        98.56         1.64 
TCGA-FY-A3NM TCGA-J8-A3O1 TCGA-KS-A4ID 
        0.99        27.19        33.24 

$`AMP PEAK 32(7Q34) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A28R TCGA-BJ-A28S 
       17.69        23.34        20.71         4.83         4.87        21.04 
TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 
        2.79         5.10        11.31        17.52         1.22        30.21 
TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ 
       22.88        18.38        16.57        18.97         7.04        16.01 
TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D 
       13.94        15.48        23.31        18.64         5.75         6.48 
TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K 
        3.45         6.35         7.82         6.18         5.06         8.98 
TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME 
        4.93         5.98         0.53         0.10         0.20         0.23 
TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ 
       11.38        10.68         0.10         0.39         0.10        20.22 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 
       15.42        36.46         5.98        15.85        18.54        18.84 
TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K 
       30.12        11.57        30.02        25.12         4.27         3.22 
TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        2.76        17.26        14.07       137.88         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       25.35        13.41        11.90        14.60         7.99        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      100.01        18.51        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45         8.88         1.02         5.95        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33         8.48        10.45         1.51         9.60        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 
        8.28         7.69         5.52         8.78         8.42         9.34 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77         9.21         9.44         9.90         8.61        10.09 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
        7.07        10.36        12.43        10.85        15.88        15.09 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR 
       31.04        12.49        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        24.23        17.69        43.00        11.34        21.37 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       12.76        25.02        20.22        30.61        14.56        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
        9.83        21.27        20.48        11.93        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76         8.32        17.36        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       18.21        10.78        10.98        14.14        14.70        17.82 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        24.33        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       31.07        12.07        66.38        40.21        63.19        30.31 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       14.04         1.15        22.29        19.59        13.61        14.27 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 
       13.81        14.07        14.27         3.02        14.43        14.70 
TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M 
       14.10        14.96         7.69        20.68        13.78        13.58 
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        80.91 
TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 
        4.18        58.82         1.45        74.30        45.40        33.47 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS 
      108.36        39.32         1.41        30.18       102.84        65.39 
TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
      124.04        50.37        37.25       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        38.66        52.73       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 
      131.15       108.66        57.63        17.52        52.50        12.16 
TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
      147.42       130.72       129.57        32.48       116.91        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
       41.29        95.38        66.90        82.82        77.36        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       31.50        50.33        53.06        47.38        52.50        45.53 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       48.16         7.07        44.65        45.80        19.30        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        19.59        30.51        33.60        28.73 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        37.78        29.95        13.32        11.87         8.71 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        12.36        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        11.74        11.15        14.24        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         2.99        12.30        15.19        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        13.84        19.73        12.07        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        18.97        15.68        14.14        19.63 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        16.44        16.77        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        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        11.15         7.33        12.53        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
        7.82        11.51        16.41        15.62        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        29.49        54.05        22.09        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        61.02        58.72        57.11        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       59.15        28.24         5.85         4.18         2.43         5.56 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       24.72        38.30        42.25         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       69.24        59.87        43.50         0.30        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       102.90        66.77        81.34 
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        46.06         4.08         0.89        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON 
       48.10        91.17         1.25         1.15        17.82         1.51 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        0.76         0.03         4.67        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         6.87         4.14         6.58         4.54 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
        0.89         1.35         1.15         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        10.26        16.90         9.80         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE 
        8.65        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        86.70         6.02        12.43 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-L6-A4EP 
        6.74        32.45        87.39        84.72        35.28        33.40 
TCGA-L6-A4EQ TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       40.37        21.83         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  AMP PEAK 32(7Q34) MUTATED AMP PEAK 32(7Q34) WILD-TYPE 
                       0.03                        0.03 
  AMP PEAK 32(7Q34) MUTATED AMP PEAK 32(7Q34) WILD-TYPE 
                      98.56                      158.83 
  AMP PEAK 32(7Q34) MUTATED AMP PEAK 32(7Q34) WILD-TYPE 
                     13.510                      16.685 
[1] "0.0 - 98.6 (13.5)"  "0.0 - 158.8 (16.7)"
[1] "hr=" "2.3"
D30V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 32(7Q34) MUTATED        10        6         4        1         0
  AMP PEAK 32(7Q34) WILD-TYPE     270       45       105        1        45
                             vv
clus                          STAGE IVC
  AMP PEAK 32(7Q34) MUTATED           0
  AMP PEAK 32(7Q34) WILD-TYPE         6
D30V3, multiclass
           clus
vv          AMP PEAK 32(7Q34) MUTATED AMP PEAK 32(7Q34) WILD-TYPE
  STAGE I                          10                         270
  STAGE II                          6                          45
  STAGE III                         4                         105
  STAGE IV                          1                           1
  STAGE IVA                         0                          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 32(7Q34) MUTATED     6   7   7   1
  AMP PEAK 32(7Q34) WILD-TYPE 134 159 158  20
D30V4, multiclass
    clus
vv   AMP PEAK 32(7Q34) MUTATED AMP PEAK 32(7Q34) WILD-TYPE
  T1                         6                         134
  T2                         7                         159
  T3                         7                         158
  T4                         1                          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"
D30V5, binary
                             cls
clus                            0   1
  AMP PEAK 32(7Q34) MUTATED    13   2
  AMP PEAK 32(7Q34) WILD-TYPE 210 220
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 32(7Q34) MUTATED     13    2
  AMP PEAK 32(7Q34) WILD-TYPE  210  220
   clus
vv  AMP PEAK 32(7Q34) MUTATED AMP PEAK 32(7Q34) WILD-TYPE
  0                        13                         210
  1                         2                         220
[1] 2 2
[1] FALSE
                             vv
clus                           M0  M1  MX
  AMP PEAK 32(7Q34) MUTATED     6   0  15
  AMP PEAK 32(7Q34) WILD-TYPE 267   9 197
D30V6, multiclass
    clus
vv   AMP PEAK 32(7Q34) MUTATED AMP PEAK 32(7Q34) WILD-TYPE
  M0                         6                         267
  M1                         0                           9
  MX                        15                         197
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                             cls
clus                            0   1
  AMP PEAK 32(7Q34) MUTATED    17   4
  AMP PEAK 32(7Q34) WILD-TYPE 347 127
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 32(7Q34) MUTATED     17    4
  AMP PEAK 32(7Q34) WILD-TYPE  347  127
        clus
vv       AMP PEAK 32(7Q34) MUTATED AMP PEAK 32(7Q34) WILD-TYPE
  FEMALE                        17                         347
  MALE                           4                         127
[1] 2 2
[1] FALSE
                             vv
clus                          OTHER  SPECIFY
  AMP PEAK 32(7Q34) MUTATED                0
  AMP PEAK 32(7Q34) WILD-TYPE              9
                             vv
clus                          THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 32(7Q34) MUTATED                                              10
  AMP PEAK 32(7Q34) WILD-TYPE                                           343
                             vv
clus                          THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 32(7Q34) MUTATED                                                                       11
  AMP PEAK 32(7Q34) WILD-TYPE                                                                     87
                             vv
clus                          THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 32(7Q34) MUTATED                                                                     0
  AMP PEAK 32(7Q34) WILD-TYPE                                                                  35
D30V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 32(7Q34) MUTATED
  OTHER  SPECIFY                                                                                 0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                 10
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                        11
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                            0
                                                                        clus
vv                                                                       AMP PEAK 32(7Q34) WILD-TYPE
  OTHER  SPECIFY                                                                                   9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  343
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          87
  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"
D30V9, binary
                             cls
clus                            0   1
  AMP PEAK 32(7Q34) MUTATED     0  21
  AMP PEAK 32(7Q34) WILD-TYPE  14 460
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 32(7Q34) MUTATED      0   21
  AMP PEAK 32(7Q34) WILD-TYPE   14  460
     clus
vv    AMP PEAK 32(7Q34) MUTATED AMP PEAK 32(7Q34) WILD-TYPE
  NO                          0                          14
  YES                        21                         460
[1] 2 2
[1] FALSE
D30V10, binary
                             cls
clus                            0   1
  AMP PEAK 32(7Q34) MUTATED    19   0
  AMP PEAK 32(7Q34) WILD-TYPE 398  17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 32(7Q34) MUTATED     19    0
  AMP PEAK 32(7Q34) WILD-TYPE  398   17
     clus
vv    AMP PEAK 32(7Q34) MUTATED AMP PEAK 32(7Q34) WILD-TYPE
  NO                         19                         398
  YES                         0                          17
[1] 2 2
[1] FALSE
                             vv
clus                          MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 32(7Q34) MUTATED              2                       0   17
  AMP PEAK 32(7Q34) WILD-TYPE          128                      16  311
                             vv
clus                          VERY ADVANCED (T4B)
  AMP PEAK 32(7Q34) MUTATED                     1
  AMP PEAK 32(7Q34) WILD-TYPE                   0
D30V11, multiclass
                         clus
vv                        AMP PEAK 32(7Q34) MUTATED AMP PEAK 32(7Q34) WILD-TYPE
  MINIMAL (T3)                                    2                         128
  MODERATE/ADVANCED (T4A)                         0                          16
  NONE                                           17                         311
  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 32(7Q34) MUTATED    15   2   0   3
  AMP PEAK 32(7Q34) WILD-TYPE 363  49   4  27
D30V12, multiclass
    clus
vv   AMP PEAK 32(7Q34) MUTATED AMP PEAK 32(7Q34) WILD-TYPE
  R0                        15                         363
  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"
D30V13, continuous
D30V14, binary
                             cls
clus                            0   1
  AMP PEAK 32(7Q34) MUTATED     9  12
  AMP PEAK 32(7Q34) WILD-TYPE 215 249
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 32(7Q34) MUTATED      9   12
  AMP PEAK 32(7Q34) WILD-TYPE  215  249
            clus
vv           AMP PEAK 32(7Q34) MUTATED AMP PEAK 32(7Q34) WILD-TYPE
  MULTIFOCAL                         9                         215
  UNIFOCAL                          12                         249
[1] 2 2
[1] FALSE
D30V15, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 32(7Q34) MUTATED                                  0     0
  AMP PEAK 32(7Q34) WILD-TYPE                                1    49
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 32(7Q34) MUTATED                           0    12
  AMP PEAK 32(7Q34) WILD-TYPE                        26   309
D30V16, multiclass
                                  clus
vv                                 AMP PEAK 32(7Q34) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                0
  WHITE                                                   12
                                  clus
vv                                 AMP PEAK 32(7Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     49
  BLACK OR AFRICAN AMERICAN                                 26
  WHITE                                                    309
[1] 4 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 32(7Q34) MUTATED     1   9
  AMP PEAK 32(7Q34) WILD-TYPE  37 341
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 32(7Q34) MUTATED      1    9
  AMP PEAK 32(7Q34) WILD-TYPE   37  341
                        clus
vv                       AMP PEAK 32(7Q34) MUTATED AMP PEAK 32(7Q34) WILD-TYPE
  HISPANIC OR LATINO                             1                          37
  NOT HISPANIC OR LATINO                         9                         341
[1] 2 2
[1] FALSE

Clustering(31) Variable = AMP PEAK 33(9Q22.31) MUTATION ANALYSIS
D31V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 33(9Q22.31) MUTATED     6   0
  AMP PEAK 33(9Q22.31) WILD-TYPE 471  14
  AMP PEAK 33(9Q22.31) MUTATED AMP PEAK 33(9Q22.31) WILD-TYPE 
                             6                            485 
  AMP PEAK 33(9Q22.31) MUTATED AMP PEAK 33(9Q22.31) WILD-TYPE 
                             0                             14 
$`AMP PEAK 33(9Q22.31) MUTATED`
TCGA-DJ-A2PW TCGA-EL-A4K9 TCGA-EM-A1YD TCGA-ET-A2N4 TCGA-ET-A40Q TCGA-FY-A3I5 
        7.69        37.78        57.01         2.66         7.17         1.64 

$`AMP PEAK 33(9Q22.31) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PX 
       10.45         1.51         9.60        12.56         8.28         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
        1.45        74.30        45.40        33.47       108.36        39.32 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        30.18       102.84        65.39       124.04        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       37.25       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        38.66        52.73       139.00       131.15       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        12.16       147.42       130.72 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       116.91        98.24        41.29        95.38 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       50.33        53.06        47.38        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        12.36        18.05        19.79        19.46        54.21 
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        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       10.49        13.15        22.16        13.84        19.73        17.59 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       12.07        17.59        17.46        17.29        14.60        17.46 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       18.97        15.68        14.14        19.63        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       16.44        16.77        27.95        23.77        16.80        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 
       11.15         7.33        12.53         9.24        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        16.41        15.62        13.51        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       29.19        19.76        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       65.36        84.89        98.56        61.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        59.15        28.24         5.85         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40R TCGA-ET-A40S 
       25.32       132.36        24.72         3.22         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       102.90        66.77        81.34 
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        46.06         4.08         0.89        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM 
       48.10        91.17         1.25         1.15        17.82         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
        1.51         0.76         0.03         4.67        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         6.87         4.14         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
        4.54         0.89         1.35         1.15         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        10.26        16.90         9.80         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        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        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        12.43         6.74        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         0.72 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       16.64        32.45         8.71        10.98         5.19 

  AMP PEAK 33(9Q22.31) MUTATED AMP PEAK 33(9Q22.31) WILD-TYPE 
                          1.64                           0.03 
  AMP PEAK 33(9Q22.31) MUTATED AMP PEAK 33(9Q22.31) WILD-TYPE 
                         57.01                         158.83 
  AMP PEAK 33(9Q22.31) MUTATED AMP PEAK 33(9Q22.31) WILD-TYPE 
                          7.43                          16.64 
[1] "1.6 - 57.0 (7.4)"   "0.0 - 158.8 (16.6)"
[1] "hr="     "9100000"
D31V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 33(9Q22.31) MUTATED         1        2         3        0         0
  AMP PEAK 33(9Q22.31) WILD-TYPE     279       49       106        2        45
                                vv
clus                             STAGE IVC
  AMP PEAK 33(9Q22.31) MUTATED           0
  AMP PEAK 33(9Q22.31) WILD-TYPE         6
D31V3, multiclass
           clus
vv          AMP PEAK 33(9Q22.31) MUTATED AMP PEAK 33(9Q22.31) WILD-TYPE
  STAGE I                              1                            279
  STAGE II                             2                             49
  STAGE III                            3                            106
  STAGE IV                             0                              2
  STAGE IVA                            0                             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(9Q22.31) MUTATED     0   2   4   0
  AMP PEAK 33(9Q22.31) WILD-TYPE 140 164 161  21
D31V4, multiclass
    clus
vv   AMP PEAK 33(9Q22.31) MUTATED AMP PEAK 33(9Q22.31) WILD-TYPE
  T1                            0                            140
  T2                            2                            164
  T3                            4                            161
  T4                            0                             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"
D31V5, binary
                                cls
clus                               0   1
  AMP PEAK 33(9Q22.31) MUTATED     4   2
  AMP PEAK 33(9Q22.31) WILD-TYPE 219 220
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 33(9Q22.31) MUTATED      4    2
  AMP PEAK 33(9Q22.31) WILD-TYPE  219  220
   clus
vv  AMP PEAK 33(9Q22.31) MUTATED AMP PEAK 33(9Q22.31) WILD-TYPE
  0                            4                            219
  1                            2                            220
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 33(9Q22.31) MUTATED     2   0   4
  AMP PEAK 33(9Q22.31) WILD-TYPE 271   9 208
D31V6, multiclass
    clus
vv   AMP PEAK 33(9Q22.31) MUTATED AMP PEAK 33(9Q22.31) WILD-TYPE
  M0                            2                            271
  M1                            0                              9
  MX                            4                            208
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                                cls
clus                               0   1
  AMP PEAK 33(9Q22.31) MUTATED     3   3
  AMP PEAK 33(9Q22.31) WILD-TYPE 361 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 33(9Q22.31) MUTATED      3    3
  AMP PEAK 33(9Q22.31) WILD-TYPE  361  128
        clus
vv       AMP PEAK 33(9Q22.31) MUTATED AMP PEAK 33(9Q22.31) WILD-TYPE
  FEMALE                            3                            361
  MALE                              3                            128
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 33(9Q22.31) MUTATED                0
  AMP PEAK 33(9Q22.31) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 33(9Q22.31) MUTATED                                               2
  AMP PEAK 33(9Q22.31) WILD-TYPE                                           351
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 33(9Q22.31) MUTATED                                                                        3
  AMP PEAK 33(9Q22.31) WILD-TYPE                                                                     95
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 33(9Q22.31) MUTATED                                                                     1
  AMP PEAK 33(9Q22.31) WILD-TYPE                                                                  34
D31V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 33(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 33(9Q22.31) WILD-TYPE
  OTHER  SPECIFY                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     351
  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"
D31V9, binary
                                cls
clus                               0   1
  AMP PEAK 33(9Q22.31) MUTATED     0   6
  AMP PEAK 33(9Q22.31) WILD-TYPE  14 475
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 33(9Q22.31) MUTATED      0    6
  AMP PEAK 33(9Q22.31) WILD-TYPE   14  475
     clus
vv    AMP PEAK 33(9Q22.31) MUTATED AMP PEAK 33(9Q22.31) WILD-TYPE
  NO                             0                             14
  YES                            6                            475
[1] 2 2
[1] FALSE
D31V10, binary
                                cls
clus                               0   1
  AMP PEAK 33(9Q22.31) MUTATED     4   1
  AMP PEAK 33(9Q22.31) WILD-TYPE 413  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 33(9Q22.31) MUTATED      4    1
  AMP PEAK 33(9Q22.31) WILD-TYPE  413   16
     clus
vv    AMP PEAK 33(9Q22.31) MUTATED AMP PEAK 33(9Q22.31) WILD-TYPE
  NO                             4                            413
  YES                            1                             16
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 33(9Q22.31) MUTATED              3                       0    3
  AMP PEAK 33(9Q22.31) WILD-TYPE          127                      16  325
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 33(9Q22.31) MUTATED                     0
  AMP PEAK 33(9Q22.31) WILD-TYPE                   1
D31V11, multiclass
                         clus
vv                        AMP PEAK 33(9Q22.31) MUTATED
  MINIMAL (T3)                                       3
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               3
  VERY ADVANCED (T4B)                                0
                         clus
vv                        AMP PEAK 33(9Q22.31) WILD-TYPE
  MINIMAL (T3)                                       127
  MODERATE/ADVANCED (T4A)                             16
  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(9Q22.31) MUTATED     5   0   0   1
  AMP PEAK 33(9Q22.31) WILD-TYPE 373  51   4  29
D31V12, multiclass
    clus
vv   AMP PEAK 33(9Q22.31) MUTATED AMP PEAK 33(9Q22.31) WILD-TYPE
  R0                            5                            373
  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"
D31V13, continuous
D31V14, binary
                                cls
clus                               0   1
  AMP PEAK 33(9Q22.31) MUTATED     5   1
  AMP PEAK 33(9Q22.31) WILD-TYPE 219 260
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 33(9Q22.31) MUTATED      5    1
  AMP PEAK 33(9Q22.31) WILD-TYPE  219  260
            clus
vv           AMP PEAK 33(9Q22.31) MUTATED AMP PEAK 33(9Q22.31) WILD-TYPE
  MULTIFOCAL                            5                            219
  UNIFOCAL                              1                            260
[1] 2 2
[1] FALSE
D31V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 33(9Q22.31) MUTATED                                  0     0
  AMP PEAK 33(9Q22.31) WILD-TYPE                                1    49
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 33(9Q22.31) MUTATED                           0     5
  AMP PEAK 33(9Q22.31) WILD-TYPE                        26   316
D31V16, multiclass
                                  clus
vv                                 AMP PEAK 33(9Q22.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       5
                                  clus
vv                                 AMP PEAK 33(9Q22.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        49
  BLACK OR AFRICAN AMERICAN                                    26
  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"
D31V17, binary
                                cls
clus                               0   1
  AMP PEAK 33(9Q22.31) MUTATED     0   5
  AMP PEAK 33(9Q22.31) WILD-TYPE  38 345
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 33(9Q22.31) MUTATED      0    5
  AMP PEAK 33(9Q22.31) WILD-TYPE   38  345
                        clus
vv                       AMP PEAK 33(9Q22.31) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            5
                        clus
vv                       AMP PEAK 33(9Q22.31) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            345
[1] 2 2
[1] FALSE

Clustering(32) Variable = AMP PEAK 34(9Q31.1) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 34(9Q31.1) MUTATED     5   1
  AMP PEAK 34(9Q31.1) WILD-TYPE 472  13
  AMP PEAK 34(9Q31.1) MUTATED AMP PEAK 34(9Q31.1) WILD-TYPE 
                            6                           485 
  AMP PEAK 34(9Q31.1) MUTATED AMP PEAK 34(9Q31.1) WILD-TYPE 
                            1                            13 
$`AMP PEAK 34(9Q31.1) MUTATED`
TCGA-DJ-A2PW TCGA-EL-A3CW TCGA-EL-A4K9 TCGA-EM-A1YD TCGA-ET-A40P TCGA-FY-A3I5 
        7.69        57.01        37.78        57.01         3.22         1.64 

$`AMP PEAK 34(9Q31.1) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PX 
       10.45         1.51         9.60        12.56         8.28         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4KD 
       19.59        30.51        33.60        28.73        41.13        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       13.32        11.87         8.71        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YE 
       12.36        18.05        19.79        19.46        54.21        54.08 
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 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT 
       23.51         6.05         2.99        12.30        15.19        10.49 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        13.84        19.73        17.59        12.07 
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        17.46        18.97 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        19.63        13.38         8.35        16.44 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       16.77        27.95        23.77        16.80        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        11.15 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33        12.53         9.24        13.91         7.82        11.51 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       16.41        15.62        13.51        12.79        70.65        16.90 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        9.01         4.83         8.61         8.38         9.80         5.03 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       37.87        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       29.49        54.05        22.09        12.26        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       65.36        84.89        98.56        61.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        59.15        28.24         5.85         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
       25.32       132.36        24.72         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       102.90        66.77        81.34 
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        46.06         4.08         0.89        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM 
       48.10        91.17         1.25         1.15        17.82         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
        1.51         0.76         0.03         4.67        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         6.87         4.14         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
        4.54         0.89         1.35         1.15         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        10.26        16.90         9.80         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        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        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        12.43         6.74        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         0.72 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       16.64        32.45         8.71        10.98         5.19 

  AMP PEAK 34(9Q31.1) MUTATED AMP PEAK 34(9Q31.1) WILD-TYPE 
                         1.64                          0.03 
  AMP PEAK 34(9Q31.1) MUTATED AMP PEAK 34(9Q31.1) WILD-TYPE 
                        57.01                        158.83 
  AMP PEAK 34(9Q31.1) MUTATED AMP PEAK 34(9Q31.1) WILD-TYPE 
                       22.735                        16.570 
[1] "1.6 - 57.0 (22.7)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "4.7"
D32V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 34(9Q31.1) MUTATED         1        2         3        0         0
  AMP PEAK 34(9Q31.1) WILD-TYPE     279       49       106        2        45
                               vv
clus                            STAGE IVC
  AMP PEAK 34(9Q31.1) MUTATED           0
  AMP PEAK 34(9Q31.1) WILD-TYPE         6
D32V3, multiclass
           clus
vv          AMP PEAK 34(9Q31.1) MUTATED AMP PEAK 34(9Q31.1) WILD-TYPE
  STAGE I                             1                           279
  STAGE II                            2                            49
  STAGE III                           3                           106
  STAGE IV                            0                             2
  STAGE IVA                           0                            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 34(9Q31.1) MUTATED     0   4   2   0
  AMP PEAK 34(9Q31.1) WILD-TYPE 140 162 163  21
D32V4, multiclass
    clus
vv   AMP PEAK 34(9Q31.1) MUTATED AMP PEAK 34(9Q31.1) WILD-TYPE
  T1                           0                           140
  T2                           4                           162
  T3                           2                           163
  T4                           0                            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"
D32V5, binary
                               cls
clus                              0   1
  AMP PEAK 34(9Q31.1) MUTATED     4   2
  AMP PEAK 34(9Q31.1) WILD-TYPE 219 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 34(9Q31.1) MUTATED      4    2
  AMP PEAK 34(9Q31.1) WILD-TYPE  219  220
   clus
vv  AMP PEAK 34(9Q31.1) MUTATED AMP PEAK 34(9Q31.1) WILD-TYPE
  0                           4                           219
  1                           2                           220
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK 34(9Q31.1) MUTATED     3   0   3
  AMP PEAK 34(9Q31.1) WILD-TYPE 270   9 209
D32V6, multiclass
    clus
vv   AMP PEAK 34(9Q31.1) MUTATED AMP PEAK 34(9Q31.1) WILD-TYPE
  M0                           3                           270
  M1                           0                             9
  MX                           3                           209
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                               cls
clus                              0   1
  AMP PEAK 34(9Q31.1) MUTATED     4   2
  AMP PEAK 34(9Q31.1) WILD-TYPE 360 129
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 34(9Q31.1) MUTATED      4    2
  AMP PEAK 34(9Q31.1) WILD-TYPE  360  129
        clus
vv       AMP PEAK 34(9Q31.1) MUTATED AMP PEAK 34(9Q31.1) WILD-TYPE
  FEMALE                           4                           360
  MALE                             2                           129
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 34(9Q31.1) MUTATED                0
  AMP PEAK 34(9Q31.1) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 34(9Q31.1) MUTATED                                               3
  AMP PEAK 34(9Q31.1) WILD-TYPE                                           350
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 34(9Q31.1) MUTATED                                                                        3
  AMP PEAK 34(9Q31.1) WILD-TYPE                                                                     95
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 34(9Q31.1) MUTATED                                                                     0
  AMP PEAK 34(9Q31.1) WILD-TYPE                                                                  35
D32V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 34(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 34(9Q31.1) WILD-TYPE
  OTHER  SPECIFY                                                                                     9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    350
  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"
D32V9, binary
                               cls
clus                              0   1
  AMP PEAK 34(9Q31.1) MUTATED     0   6
  AMP PEAK 34(9Q31.1) WILD-TYPE  14 475
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 34(9Q31.1) MUTATED      0    6
  AMP PEAK 34(9Q31.1) WILD-TYPE   14  475
     clus
vv    AMP PEAK 34(9Q31.1) MUTATED AMP PEAK 34(9Q31.1) WILD-TYPE
  NO                            0                            14
  YES                           6                           475
[1] 2 2
[1] FALSE
D32V10, binary
                               cls
clus                              0   1
  AMP PEAK 34(9Q31.1) MUTATED     5   0
  AMP PEAK 34(9Q31.1) WILD-TYPE 412  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 34(9Q31.1) MUTATED      5    0
  AMP PEAK 34(9Q31.1) WILD-TYPE  412   17
     clus
vv    AMP PEAK 34(9Q31.1) MUTATED AMP PEAK 34(9Q31.1) WILD-TYPE
  NO                            5                           412
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 34(9Q31.1) MUTATED              1                       0    5
  AMP PEAK 34(9Q31.1) WILD-TYPE          129                      16  323
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 34(9Q31.1) MUTATED                     0
  AMP PEAK 34(9Q31.1) WILD-TYPE                   1
D32V11, multiclass
                         clus
vv                        AMP PEAK 34(9Q31.1) MUTATED
  MINIMAL (T3)                                      1
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              5
  VERY ADVANCED (T4B)                               0
                         clus
vv                        AMP PEAK 34(9Q31.1) WILD-TYPE
  MINIMAL (T3)                                      129
  MODERATE/ADVANCED (T4A)                            16
  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 34(9Q31.1) MUTATED     6   0   0   0
  AMP PEAK 34(9Q31.1) WILD-TYPE 372  51   4  30
D32V12, multiclass
    clus
vv   AMP PEAK 34(9Q31.1) MUTATED AMP PEAK 34(9Q31.1) WILD-TYPE
  R0                           6                           372
  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 34(9Q31.1) MUTATED     3   3
  AMP PEAK 34(9Q31.1) WILD-TYPE 221 258
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 34(9Q31.1) MUTATED      3    3
  AMP PEAK 34(9Q31.1) WILD-TYPE  221  258
            clus
vv           AMP PEAK 34(9Q31.1) MUTATED AMP PEAK 34(9Q31.1) WILD-TYPE
  MULTIFOCAL                           3                           221
  UNIFOCAL                             3                           258
[1] 2 2
[1] FALSE
D32V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 34(9Q31.1) MUTATED                                  0     0
  AMP PEAK 34(9Q31.1) WILD-TYPE                                1    49
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 34(9Q31.1) MUTATED                           0     5
  AMP PEAK 34(9Q31.1) WILD-TYPE                        26   316
D32V16, multiclass
                                  clus
vv                                 AMP PEAK 34(9Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      5
                                  clus
vv                                 AMP PEAK 34(9Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       49
  BLACK OR AFRICAN AMERICAN                                   26
  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"
D32V17, binary
                               cls
clus                              0   1
  AMP PEAK 34(9Q31.1) MUTATED     0   5
  AMP PEAK 34(9Q31.1) WILD-TYPE  38 345
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 34(9Q31.1) MUTATED      0    5
  AMP PEAK 34(9Q31.1) WILD-TYPE   38  345
                        clus
vv                       AMP PEAK 34(9Q31.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           5
                        clus
vv                       AMP PEAK 34(9Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           345
[1] 2 2
[1] FALSE

Clustering(33) Variable = AMP PEAK 35(9Q34.3) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 35(9Q34.3) MUTATED     7   0
  AMP PEAK 35(9Q34.3) WILD-TYPE 470  14
  AMP PEAK 35(9Q34.3) MUTATED AMP PEAK 35(9Q34.3) WILD-TYPE 
                            7                           484 
  AMP PEAK 35(9Q34.3) MUTATED AMP PEAK 35(9Q34.3) WILD-TYPE 
                            0                            14 
$`AMP PEAK 35(9Q34.3) MUTATED`
TCGA-DJ-A13M TCGA-DJ-A2PW TCGA-EL-A4K9 TCGA-EM-A1YD TCGA-EM-A22Q TCGA-FE-A22Z 
       17.26         7.69        37.78        57.01        14.24        73.74 
TCGA-FY-A3I5 
        1.64 

$`AMP PEAK 35(9Q34.3) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13O 
       30.02        25.12         4.27         3.22         2.76        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PX TCGA-DJ-A2PY 
        1.51         9.60        12.56         8.28         5.52         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.42         8.12         9.34         6.77         9.21         9.44 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
        9.90         8.61        10.09         7.07        10.36        12.43 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        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        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04         1.15        22.29 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4KD 
       19.59        30.51        33.60        28.73        41.13        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       13.32        11.87         8.71        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YE 
       12.36        18.05        19.79        19.46        54.21        54.08 
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-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.74        11.15        16.44        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
        6.05         2.99        12.30        15.19        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        13.84        19.73        17.59        12.07        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        17.46        18.97        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR 
       14.14        19.63        13.38         8.35        16.44        16.77 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        16.80        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        11.15         7.33 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
       12.53         9.24        13.91         7.82        11.51        16.41 
TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       15.62        13.51        12.79        70.65        16.90         9.01 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        4.83         8.61         8.38         9.80         5.03        37.87 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       12.72         0.95        47.47        48.20        29.69        32.35 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       14.79        12.33        14.79        27.09        18.38        29.49 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       54.05        22.09        12.26        16.08        29.19        19.76 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        58.22        13.74        71.01        80.02        65.36 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       84.89        98.56        61.02        58.72        57.11        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       59.15        28.24         5.85         4.18         2.43         5.56 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       24.72        38.30        42.25         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       69.24        59.87        43.50         0.30        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        2.14         4.01         1.94        59.70        31.59        44.25 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       102.90        66.77        81.34        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 
       46.06         4.08         0.89        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON 
       91.17         1.25         1.15        17.82         0.99         1.51 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        0.76         0.03         4.67        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         6.87         4.14         6.58         4.54 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
        0.89         1.35         1.15         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        10.26        16.90         9.80         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        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        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       12.43         6.74        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         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

  AMP PEAK 35(9Q34.3) MUTATED AMP PEAK 35(9Q34.3) WILD-TYPE 
                         1.64                          0.03 
  AMP PEAK 35(9Q34.3) MUTATED AMP PEAK 35(9Q34.3) WILD-TYPE 
                        73.74                        158.83 
  AMP PEAK 35(9Q34.3) MUTATED AMP PEAK 35(9Q34.3) WILD-TYPE 
                        17.26                         16.57 
[1] "1.6 - 73.7 (17.3)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "9200000"
D33V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 35(9Q34.3) MUTATED         2        2         2        0         1
  AMP PEAK 35(9Q34.3) WILD-TYPE     278       49       107        2        44
                               vv
clus                            STAGE IVC
  AMP PEAK 35(9Q34.3) MUTATED           0
  AMP PEAK 35(9Q34.3) WILD-TYPE         6
D33V3, multiclass
           clus
vv          AMP PEAK 35(9Q34.3) MUTATED AMP PEAK 35(9Q34.3) WILD-TYPE
  STAGE I                             2                           278
  STAGE II                            2                            49
  STAGE III                           2                           107
  STAGE IV                            0                             2
  STAGE IVA                           1                            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 35(9Q34.3) MUTATED     1   2   3   1
  AMP PEAK 35(9Q34.3) WILD-TYPE 139 164 162  20
D33V4, multiclass
    clus
vv   AMP PEAK 35(9Q34.3) MUTATED AMP PEAK 35(9Q34.3) WILD-TYPE
  T1                           1                           139
  T2                           2                           164
  T3                           3                           162
  T4                           1                            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"
D33V5, binary
                               cls
clus                              0   1
  AMP PEAK 35(9Q34.3) MUTATED     5   2
  AMP PEAK 35(9Q34.3) WILD-TYPE 218 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 35(9Q34.3) MUTATED      5    2
  AMP PEAK 35(9Q34.3) WILD-TYPE  218  220
   clus
vv  AMP PEAK 35(9Q34.3) MUTATED AMP PEAK 35(9Q34.3) WILD-TYPE
  0                           5                           218
  1                           2                           220
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK 35(9Q34.3) MUTATED     3   0   4
  AMP PEAK 35(9Q34.3) WILD-TYPE 270   9 208
D33V6, multiclass
    clus
vv   AMP PEAK 35(9Q34.3) MUTATED AMP PEAK 35(9Q34.3) WILD-TYPE
  M0                           3                           270
  M1                           0                             9
  MX                           4                           208
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                               cls
clus                              0   1
  AMP PEAK 35(9Q34.3) MUTATED     4   3
  AMP PEAK 35(9Q34.3) WILD-TYPE 360 128
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 35(9Q34.3) MUTATED      4    3
  AMP PEAK 35(9Q34.3) WILD-TYPE  360  128
        clus
vv       AMP PEAK 35(9Q34.3) MUTATED AMP PEAK 35(9Q34.3) WILD-TYPE
  FEMALE                           4                           360
  MALE                             3                           128
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 35(9Q34.3) MUTATED                0
  AMP PEAK 35(9Q34.3) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 35(9Q34.3) MUTATED                                               2
  AMP PEAK 35(9Q34.3) WILD-TYPE                                           351
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 35(9Q34.3) MUTATED                                                                        5
  AMP PEAK 35(9Q34.3) WILD-TYPE                                                                     93
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 35(9Q34.3) MUTATED                                                                     0
  AMP PEAK 35(9Q34.3) WILD-TYPE                                                                  35
D33V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 35(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 35(9Q34.3) WILD-TYPE
  OTHER  SPECIFY                                                                                     9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    351
  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"
D33V9, binary
                               cls
clus                              0   1
  AMP PEAK 35(9Q34.3) MUTATED     1   6
  AMP PEAK 35(9Q34.3) WILD-TYPE  13 475
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 35(9Q34.3) MUTATED      1    6
  AMP PEAK 35(9Q34.3) WILD-TYPE   13  475
     clus
vv    AMP PEAK 35(9Q34.3) MUTATED AMP PEAK 35(9Q34.3) WILD-TYPE
  NO                            1                            13
  YES                           6                           475
[1] 2 2
[1] FALSE
D33V10, binary
                               cls
clus                              0   1
  AMP PEAK 35(9Q34.3) MUTATED     6   0
  AMP PEAK 35(9Q34.3) WILD-TYPE 411  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 35(9Q34.3) MUTATED      6    0
  AMP PEAK 35(9Q34.3) WILD-TYPE  411   17
     clus
vv    AMP PEAK 35(9Q34.3) MUTATED AMP PEAK 35(9Q34.3) WILD-TYPE
  NO                            6                           411
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 35(9Q34.3) MUTATED              1                       1    5
  AMP PEAK 35(9Q34.3) WILD-TYPE          129                      15  323
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 35(9Q34.3) MUTATED                     0
  AMP PEAK 35(9Q34.3) WILD-TYPE                   1
D33V11, multiclass
                         clus
vv                        AMP PEAK 35(9Q34.3) MUTATED
  MINIMAL (T3)                                      1
  MODERATE/ADVANCED (T4A)                           1
  NONE                                              5
  VERY ADVANCED (T4B)                               0
                         clus
vv                        AMP PEAK 35(9Q34.3) WILD-TYPE
  MINIMAL (T3)                                      129
  MODERATE/ADVANCED (T4A)                            15
  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 35(9Q34.3) MUTATED     7   0   0   0
  AMP PEAK 35(9Q34.3) WILD-TYPE 371  51   4  30
D33V12, multiclass
    clus
vv   AMP PEAK 35(9Q34.3) MUTATED AMP PEAK 35(9Q34.3) WILD-TYPE
  R0                           7                           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"
D33V13, continuous
D33V14, binary
                               cls
clus                              0   1
  AMP PEAK 35(9Q34.3) MUTATED     4   3
  AMP PEAK 35(9Q34.3) WILD-TYPE 220 258
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 35(9Q34.3) MUTATED      4    3
  AMP PEAK 35(9Q34.3) WILD-TYPE  220  258
            clus
vv           AMP PEAK 35(9Q34.3) MUTATED AMP PEAK 35(9Q34.3) WILD-TYPE
  MULTIFOCAL                           4                           220
  UNIFOCAL                             3                           258
[1] 2 2
[1] FALSE
D33V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 35(9Q34.3) MUTATED                                  0     0
  AMP PEAK 35(9Q34.3) WILD-TYPE                                1    49
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 35(9Q34.3) MUTATED                           0     5
  AMP PEAK 35(9Q34.3) WILD-TYPE                        26   316
D33V16, multiclass
                                  clus
vv                                 AMP PEAK 35(9Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      5
                                  clus
vv                                 AMP PEAK 35(9Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       49
  BLACK OR AFRICAN AMERICAN                                   26
  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"
D33V17, binary
                               cls
clus                              0   1
  AMP PEAK 35(9Q34.3) MUTATED     0   5
  AMP PEAK 35(9Q34.3) WILD-TYPE  38 345
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 35(9Q34.3) MUTATED      0    5
  AMP PEAK 35(9Q34.3) WILD-TYPE   38  345
                        clus
vv                       AMP PEAK 35(9Q34.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           5
                        clus
vv                       AMP PEAK 35(9Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           345
[1] 2 2
[1] FALSE

Clustering(34) Variable = AMP PEAK 36(10Q24.2) MUTATION ANALYSIS
D34V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 36(10Q24.2) MUTATED     3   0
  AMP PEAK 36(10Q24.2) WILD-TYPE 474  14
  AMP PEAK 36(10Q24.2) MUTATED AMP PEAK 36(10Q24.2) WILD-TYPE 
                             3                            488 
  AMP PEAK 36(10Q24.2) MUTATED AMP PEAK 36(10Q24.2) WILD-TYPE 
                             0                             14 
$`AMP PEAK 36(10Q24.2) MUTATED`
TCGA-EM-A1YC TCGA-EM-A22N TCGA-ET-A39I 
       54.21        10.65        13.74 

$`AMP PEAK 36(10Q24.2) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        5.52         8.78         8.42         8.12         9.34         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
        9.21         9.44         9.90         8.61        10.09         7.07 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       10.36        12.43        10.85        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        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 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.07        14.27         3.02        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        13.78        13.58        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        80.91         4.18 
TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 
       58.82         1.45        74.30        45.40        33.47       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
       39.32         1.41        30.18       102.84        65.39       124.04 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        37.25       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        38.66        52.73       139.00       131.15 
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        12.16       147.42 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      130.72       129.57        32.48       116.91        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
       95.38         5.72        66.90        82.82        77.36        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       31.50        50.33        53.06        47.38        52.50        45.53 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       48.16         7.07        44.65        45.80        19.30        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        19.59        30.51        33.60        28.73 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        37.78        29.95        13.32        11.87         8.71 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        12.36        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        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        10.49        13.15        22.16        13.84        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       17.59        12.07        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 
       17.46        18.97        15.68        14.14        19.63        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        16.44        16.77        27.95        23.77        16.80 
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        11.15         7.33        12.53         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        16.41        15.62        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        9.80         5.03        37.87        12.72         0.95        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39J 
       16.08        29.19        19.76         2.66        58.22        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
       80.02        65.36        84.89        98.56        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        2.43         5.56        24.72        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       59.70        31.59        44.25        24.69        68.22       102.90 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77        81.34        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        46.06         4.08         0.89 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10        91.17         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       17.82         1.64         0.99         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
        4.67        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 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
        1.15         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        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90         9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74 
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         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  AMP PEAK 36(10Q24.2) MUTATED AMP PEAK 36(10Q24.2) WILD-TYPE 
                         10.65                           0.03 
  AMP PEAK 36(10Q24.2) MUTATED AMP PEAK 36(10Q24.2) WILD-TYPE 
                         54.21                         158.83 
  AMP PEAK 36(10Q24.2) MUTATED AMP PEAK 36(10Q24.2) WILD-TYPE 
                        13.740                         16.605 
[1] "10.7 - 54.2 (13.7)" "0.0 - 158.8 (16.6)"
[1] "hr="     "3300000"
D34V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 36(10Q24.2) MUTATED         2        0         1        0         0
  AMP PEAK 36(10Q24.2) WILD-TYPE     278       51       108        2        45
                                vv
clus                             STAGE IVC
  AMP PEAK 36(10Q24.2) MUTATED           0
  AMP PEAK 36(10Q24.2) WILD-TYPE         6
D34V3, multiclass
           clus
vv          AMP PEAK 36(10Q24.2) MUTATED AMP PEAK 36(10Q24.2) WILD-TYPE
  STAGE I                              2                            278
  STAGE II                             0                             51
  STAGE III                            1                            108
  STAGE IV                             0                              2
  STAGE IVA                            0                             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 36(10Q24.2) MUTATED     2   0   1   0
  AMP PEAK 36(10Q24.2) WILD-TYPE 138 166 164  21
D34V4, multiclass
    clus
vv   AMP PEAK 36(10Q24.2) MUTATED AMP PEAK 36(10Q24.2) WILD-TYPE
  T1                            2                            138
  T2                            0                            166
  T3                            1                            164
  T4                            0                             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"
D34V5, binary
                                cls
clus                               0   1
  AMP PEAK 36(10Q24.2) MUTATED     2   0
  AMP PEAK 36(10Q24.2) WILD-TYPE 221 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 36(10Q24.2) MUTATED      2    0
  AMP PEAK 36(10Q24.2) WILD-TYPE  221  222
   clus
vv  AMP PEAK 36(10Q24.2) MUTATED AMP PEAK 36(10Q24.2) WILD-TYPE
  0                            2                            221
  1                            0                            222
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 36(10Q24.2) MUTATED     0   0   3
  AMP PEAK 36(10Q24.2) WILD-TYPE 273   9 209
D34V6, multiclass
    clus
vv   AMP PEAK 36(10Q24.2) MUTATED AMP PEAK 36(10Q24.2) WILD-TYPE
  M0                            0                            273
  M1                            0                              9
  MX                            3                            209
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                                cls
clus                               0   1
  AMP PEAK 36(10Q24.2) MUTATED     3   0
  AMP PEAK 36(10Q24.2) WILD-TYPE 361 131
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 36(10Q24.2) MUTATED      3    0
  AMP PEAK 36(10Q24.2) WILD-TYPE  361  131
        clus
vv       AMP PEAK 36(10Q24.2) MUTATED AMP PEAK 36(10Q24.2) WILD-TYPE
  FEMALE                            3                            361
  MALE                              0                            131
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 36(10Q24.2) MUTATED                0
  AMP PEAK 36(10Q24.2) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 36(10Q24.2) MUTATED                                               0
  AMP PEAK 36(10Q24.2) WILD-TYPE                                           353
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 36(10Q24.2) MUTATED                                                                        3
  AMP PEAK 36(10Q24.2) WILD-TYPE                                                                     95
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 36(10Q24.2) MUTATED                                                                     0
  AMP PEAK 36(10Q24.2) WILD-TYPE                                                                  35
D34V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 36(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 36(10Q24.2) WILD-TYPE
  OTHER  SPECIFY                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     353
  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"
D34V9, binary
                                cls
clus                               0   1
  AMP PEAK 36(10Q24.2) MUTATED     0   3
  AMP PEAK 36(10Q24.2) WILD-TYPE  14 478
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 36(10Q24.2) MUTATED      0    3
  AMP PEAK 36(10Q24.2) WILD-TYPE   14  478
     clus
vv    AMP PEAK 36(10Q24.2) MUTATED AMP PEAK 36(10Q24.2) WILD-TYPE
  NO                             0                             14
  YES                            3                            478
[1] 2 2
[1] FALSE
D34V10, binary
                                cls
clus                               0   1
  AMP PEAK 36(10Q24.2) MUTATED     3   0
  AMP PEAK 36(10Q24.2) WILD-TYPE 414  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 36(10Q24.2) MUTATED      3    0
  AMP PEAK 36(10Q24.2) WILD-TYPE  414   17
     clus
vv    AMP PEAK 36(10Q24.2) MUTATED AMP PEAK 36(10Q24.2) WILD-TYPE
  NO                             3                            414
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 36(10Q24.2) MUTATED              0                       0    3
  AMP PEAK 36(10Q24.2) WILD-TYPE          130                      16  325
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 36(10Q24.2) MUTATED                     0
  AMP PEAK 36(10Q24.2) WILD-TYPE                   1
D34V11, multiclass
                         clus
vv                        AMP PEAK 36(10Q24.2) MUTATED
  MINIMAL (T3)                                       0
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               3
  VERY ADVANCED (T4B)                                0
                         clus
vv                        AMP PEAK 36(10Q24.2) WILD-TYPE
  MINIMAL (T3)                                       130
  MODERATE/ADVANCED (T4A)                             16
  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 36(10Q24.2) MUTATED     2   0   0   1
  AMP PEAK 36(10Q24.2) WILD-TYPE 376  51   4  29
D34V12, multiclass
    clus
vv   AMP PEAK 36(10Q24.2) MUTATED AMP PEAK 36(10Q24.2) WILD-TYPE
  R0                            2                            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"
D34V13, continuous
[1] "Remove cluster labels:"       "AMP PEAK 36(10Q24.2) MUTATED"
clus
  AMP PEAK 36(10Q24.2) MUTATED AMP PEAK 36(10Q24.2) WILD-TYPE 
                             2                            389 
                    TCGA-BJ-A0Z0                     TCGA-BJ-A0Z3 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A0Z9                     TCGA-BJ-A0ZA 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A0ZB                     TCGA-BJ-A0ZH 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A0ZJ                     TCGA-BJ-A18Y 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A18Z                     TCGA-BJ-A190 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A191                     TCGA-BJ-A28R 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A28T                     TCGA-BJ-A28W 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A28X                     TCGA-BJ-A28Z 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A290                     TCGA-BJ-A291 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A2N8                     TCGA-BJ-A2N9 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A2NA                     TCGA-BJ-A3EZ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A3PR                     TCGA-BJ-A3PU 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A45C                     TCGA-BJ-A45D 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A45E                     TCGA-BJ-A45G 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A45I                     TCGA-BJ-A45J 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A45K                     TCGA-BJ-A4O8 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A4O9                     TCGA-CE-A13K 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-CE-A3MD                     TCGA-DE-A0XZ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A0Y2                     TCGA-DE-A0Y3 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A3KN                     TCGA-DE-A4M8 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A4MA                     TCGA-DE-A4MB 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A4MC                     TCGA-DE-A4MD 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A69K                     TCGA-DE-A7U5 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A13M                     TCGA-DJ-A13O 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A13P                     TCGA-DJ-A13R 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A13T                     TCGA-DJ-A13U 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A13V                     TCGA-DJ-A13W 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A13X                     TCGA-DJ-A1QG 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A1QH                     TCGA-DJ-A1QM 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PO                     TCGA-DJ-A2PP 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PQ                     TCGA-DJ-A2PR 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PS                     TCGA-DJ-A2PT 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PU                     TCGA-DJ-A2PV 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PW                     TCGA-DJ-A2PX 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PY                     TCGA-DJ-A2PZ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2Q0                     TCGA-DJ-A2Q1 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2Q2                     TCGA-DJ-A2Q3 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2Q4                     TCGA-DJ-A2Q5 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2Q6                     TCGA-DJ-A2Q7 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2Q8                     TCGA-DJ-A2Q9 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2QA                     TCGA-DJ-A2QB 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UK                     TCGA-DJ-A3UM 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UN                     TCGA-DJ-A3UO 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UP                     TCGA-DJ-A3UQ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UR                     TCGA-DJ-A3UU 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UW                     TCGA-DJ-A3UX 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UZ                     TCGA-DJ-A3V0 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3V2                     TCGA-DJ-A3V3 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3V4                     TCGA-DJ-A3V5 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3V7                     TCGA-DJ-A3V8 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3V9                     TCGA-DJ-A3VA 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3VB                     TCGA-DJ-A3VD 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3VF                     TCGA-DJ-A3VG 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3VJ                     TCGA-DJ-A3VL 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A4UL                     TCGA-DJ-A4UQ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A4UR                     TCGA-DJ-A4UW 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A4V2                     TCGA-DJ-A4V5 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DO-A1K0                     TCGA-DO-A2HM 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-E3-A3DY                     TCGA-E3-A3DZ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-E3-A3E0                     TCGA-E3-A3E1 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-E3-A3E2                     TCGA-E3-A3E3 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-E3-A3E5                     TCGA-E8-A242 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-E8-A2EA                     TCGA-E8-A2JQ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-E8-A414                     TCGA-E8-A415 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-E8-A417                     TCGA-E8-A419 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-E8-A433                     TCGA-E8-A436 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-E8-A438                     TCGA-E8-A44K 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CM                     TCGA-EL-A3CN 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CO                     TCGA-EL-A3CR 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CS                     TCGA-EL-A3CT 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CU                     TCGA-EL-A3CV 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CW                     TCGA-EL-A3CX 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CY                     TCGA-EL-A3CZ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3D0                     TCGA-EL-A3D1 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3D4                     TCGA-EL-A3D5 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3D6                     TCGA-EL-A3GO 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3GP                     TCGA-EL-A3GQ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3GS                     TCGA-EL-A3GU 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3GV                     TCGA-EL-A3GX 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3H3                     TCGA-EL-A3H4 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3H5                     TCGA-EL-A3H7 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3H8                     TCGA-EL-A3MW 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3MX                     TCGA-EL-A3MZ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3N2                     TCGA-EL-A3T0 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3T1                     TCGA-EL-A3T2 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3TB                     TCGA-EL-A3ZH 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZK                     TCGA-EL-A3ZL 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZN                     TCGA-EL-A3ZO 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZP                     TCGA-EL-A3ZS 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4JV                     TCGA-EL-A4JW 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4JX                     TCGA-EL-A4JZ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4K0                     TCGA-EL-A4K1 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4K2                     TCGA-EL-A4K4 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4K6                     TCGA-EL-A4K7 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4KD                     TCGA-EL-A4KG 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4KI                     TCGA-EM-A1CS 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A1CT                     TCGA-EM-A1CU 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A1CV                     TCGA-EM-A1CW 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A1YA                     TCGA-EM-A1YB 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A1YD                     TCGA-EM-A1YE 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A22I                     TCGA-EM-A22J 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A22K                     TCGA-EM-A22L 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A22M                     TCGA-EM-A22O 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A22P                     TCGA-EM-A22Q 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2CK                     TCGA-EM-A2CN 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2CP                     TCGA-EM-A2CQ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2CS                     TCGA-EM-A2CT 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2CU                     TCGA-EM-A2OV 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2OW                     TCGA-EM-A2OX 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2OY                     TCGA-EM-A2OZ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2P0                     TCGA-EM-A2P1 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2P2                     TCGA-EM-A2P3 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3AJ                     TCGA-EM-A3AK 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3AL                     TCGA-EM-A3AN 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3AO                     TCGA-EM-A3AQ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3AR                     TCGA-EM-A3FJ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3FK                     TCGA-EM-A3FL 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3FM                     TCGA-EM-A3FN 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3FO                     TCGA-EM-A3FP 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3FQ                     TCGA-EM-A3FR 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3O3                     TCGA-EM-A3O7 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3O8                     TCGA-EM-A3O9 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3OA                     TCGA-EM-A3OB 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3ST                     TCGA-EM-A3SU 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3SX                     TCGA-EM-A3SY 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3SZ                     TCGA-EM-A4FF 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A4FH                     TCGA-EM-A4FK 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A4FM                     TCGA-EM-A4FN 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A4FO                     TCGA-EM-A4FQ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A4FR                     TCGA-EM-A4FU 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A4FV                     TCGA-EM-A4G1 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25G                     TCGA-ET-A25I 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25J                     TCGA-ET-A25K 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25L                     TCGA-ET-A25M 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25N                     TCGA-ET-A25O 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25P                     TCGA-ET-A2MX 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A2MZ                     TCGA-ET-A2N0 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A2N1                     TCGA-ET-A2N4 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A39K                     TCGA-ET-A39L 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A39O                     TCGA-ET-A39P 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A39R                     TCGA-ET-A39S 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A39T                     TCGA-ET-A3BO 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3BP                     TCGA-ET-A3BQ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3BS                     TCGA-ET-A3BT 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3BU                     TCGA-ET-A3BV 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3BX                     TCGA-ET-A3DQ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3DR                     TCGA-ET-A3DS 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3DT                     TCGA-ET-A3DU 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3DV                     TCGA-ET-A3DW 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A40P                     TCGA-ET-A40Q 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A40R                     TCGA-ET-A40S 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A40T                     TCGA-ET-A4KN 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A22Z                     TCGA-FE-A230 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A231                     TCGA-FE-A232 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A233                     TCGA-FE-A234 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A235                     TCGA-FE-A236 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A237                     TCGA-FE-A238 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A239                     TCGA-FE-A23A 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A3PB                     TCGA-FE-A3PC 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A3PD                     TCGA-FK-A3S3 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FK-A3SB                     TCGA-FK-A3SE 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FK-A3SG                     TCGA-FK-A3SH 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FK-A4UB                     TCGA-FY-A2QD 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3I4                     TCGA-FY-A3I5 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3NM                     TCGA-FY-A3NN 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3ON                     TCGA-FY-A3R6 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3R7                     TCGA-FY-A3R9 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3TY                     TCGA-FY-A3W9 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3YR                     TCGA-FY-A40K 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A40L                     TCGA-FY-A40M 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A40N                     TCGA-FY-A4B3 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A4B4                     TCGA-GE-A2C6 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-H2-A26U                     TCGA-H2-A2K9 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-H2-A3RH                     TCGA-H2-A3RI 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-H2-A421                     TCGA-H2-A422 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-IM-A3EB                     TCGA-IM-A3ED 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-IM-A3U2                     TCGA-IM-A3U3 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-IM-A41Y                     TCGA-IM-A41Z 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-IM-A420                     TCGA-IM-A4EB 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-J8-A3NZ                     TCGA-J8-A3O0 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-J8-A3O1                     TCGA-J8-A3O2 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-J8-A3YD                     TCGA-J8-A3YE 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-J8-A3YF                     TCGA-J8-A3YG 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-J8-A3YH                     TCGA-J8-A42S 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-J8-A4HW                     TCGA-J8-A4HY 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A41F                     TCGA-KS-A41I 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A41J                     TCGA-KS-A41L 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A4I1                     TCGA-KS-A4I3 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A4I5                     TCGA-KS-A4I7 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A4I9                     TCGA-KS-A4IB 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A4IC                     TCGA-KS-A4ID 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-L6-A4EP                     TCGA-L6-A4EQ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-L6-A4EU                     TCGA-MK-A4N6 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-MK-A4N7                     TCGA-MK-A4N9 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-QD-A8IV 
"AMP PEAK 36(10Q24.2) WILD-TYPE" 
D34V14, binary
                                cls
clus                               0   1
  AMP PEAK 36(10Q24.2) MUTATED     1   2
  AMP PEAK 36(10Q24.2) WILD-TYPE 223 259
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 36(10Q24.2) MUTATED      1    2
  AMP PEAK 36(10Q24.2) WILD-TYPE  223  259
            clus
vv           AMP PEAK 36(10Q24.2) MUTATED AMP PEAK 36(10Q24.2) WILD-TYPE
  MULTIFOCAL                            1                            223
  UNIFOCAL                              2                            259
[1] 2 2
[1] FALSE
D34V15, continuous
[1] "Remove cluster labels:"       "AMP PEAK 36(10Q24.2) MUTATED"
clus
  AMP PEAK 36(10Q24.2) MUTATED AMP PEAK 36(10Q24.2) WILD-TYPE 
                             2                            395 
                    TCGA-BJ-A0Z2                     TCGA-BJ-A0Z3 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A0Z9                     TCGA-BJ-A0ZA 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A0ZB                     TCGA-BJ-A0ZC 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A0ZE                     TCGA-BJ-A0ZG 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A0ZH                     TCGA-BJ-A0ZJ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A18Y                     TCGA-BJ-A18Z 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A190                     TCGA-BJ-A191 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A192                     TCGA-BJ-A28R 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A28S                     TCGA-BJ-A28T 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A28V                     TCGA-BJ-A28W 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A28Z                     TCGA-BJ-A290 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A291                     TCGA-BJ-A2N8 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A2N9                     TCGA-BJ-A2P4 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A3PU                     TCGA-BJ-A45C 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A45D                     TCGA-BJ-A45E 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A45F                     TCGA-BJ-A45G 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A45H                     TCGA-BJ-A45I 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A45J                     TCGA-BJ-A45K 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A4O8                     TCGA-BJ-A4O9 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-CE-A13K                     TCGA-CE-A27D 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-CE-A3MD                     TCGA-CE-A3ME 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-CE-A481                     TCGA-CE-A482 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-CE-A483                     TCGA-CE-A484 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-CE-A485                     TCGA-DE-A0XZ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A0Y2                     TCGA-DE-A0Y3 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A2OL                     TCGA-DE-A3KN 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A4M8                     TCGA-DE-A4M9 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A4MA                     TCGA-DE-A4MB 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A4MC                     TCGA-DE-A4MD 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A69J                     TCGA-DE-A69K 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A7U5                     TCGA-DJ-A13M 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A13O                     TCGA-DJ-A13R 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A13S                     TCGA-DJ-A13U 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A13V                     TCGA-DJ-A13W 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A13X                     TCGA-DJ-A1QD 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A1QE                     TCGA-DJ-A1QF 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A1QG                     TCGA-DJ-A1QH 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A1QI                     TCGA-DJ-A1QL 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A1QM                     TCGA-DJ-A1QN 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A1QO                     TCGA-DJ-A1QQ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PN                     TCGA-DJ-A2PO 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PP                     TCGA-DJ-A2PQ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PR                     TCGA-DJ-A2PS 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PT                     TCGA-DJ-A2PU 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PV                     TCGA-DJ-A2PW 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PY                     TCGA-DJ-A2PZ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2Q0                     TCGA-DJ-A2Q1 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2Q2                     TCGA-DJ-A2Q3 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2Q4                     TCGA-DJ-A2Q5 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2Q6                     TCGA-DJ-A2Q7 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2Q8                     TCGA-DJ-A2Q9 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2QA                     TCGA-DJ-A2QC 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UK                     TCGA-DJ-A3UM 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UN                     TCGA-DJ-A3UO 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UP                     TCGA-DJ-A3UQ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UR                     TCGA-DJ-A3US 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UT                     TCGA-DJ-A3UU 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UW                     TCGA-DJ-A3UX 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UY                     TCGA-DJ-A3V0 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3V2                     TCGA-DJ-A3V3 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3V4                     TCGA-DJ-A3V5 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3V7                     TCGA-DJ-A3V8 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3VA                     TCGA-DJ-A3VB 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3VD                     TCGA-DJ-A3VE 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3VF                     TCGA-DJ-A3VG 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3VJ                     TCGA-DJ-A3VL 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3VM                     TCGA-DJ-A4UL 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A4UQ                     TCGA-DJ-A4UT 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A4V0                     TCGA-DJ-A4V2 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A4V4                     TCGA-DJ-A4V5 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DO-A1JZ                     TCGA-DO-A1K0 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DO-A2HM                     TCGA-E3-A3DY 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-E3-A3DZ                     TCGA-E3-A3E0 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-E3-A3E1                     TCGA-E3-A3E2 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-E3-A3E3                     TCGA-E8-A419 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CN                     TCGA-EL-A3CO 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CR                     TCGA-EL-A3CS 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CT                     TCGA-EL-A3CU 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CV                     TCGA-EL-A3CW 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CX                     TCGA-EL-A3CY 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CZ                     TCGA-EL-A3D0 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3D1                     TCGA-EL-A3D4 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3D5                     TCGA-EL-A3D6 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3GO                     TCGA-EL-A3GP 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3GQ                     TCGA-EL-A3GR 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3GS                     TCGA-EL-A3GU 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3GV                     TCGA-EL-A3GW 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3GX                     TCGA-EL-A3GY 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3GZ                     TCGA-EL-A3H2 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3H3                     TCGA-EL-A3H4 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3H5                     TCGA-EL-A3H7 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3H8                     TCGA-EL-A3MW 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3MX                     TCGA-EL-A3MY 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3MZ                     TCGA-EL-A3N2 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3N3                     TCGA-EL-A3T1 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3T2                     TCGA-EL-A3T3 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3T6                     TCGA-EL-A3T7 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3T8                     TCGA-EL-A3T9 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3TA                     TCGA-EL-A3TB 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZG                     TCGA-EL-A3ZH 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZK                     TCGA-EL-A3ZL 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZN                     TCGA-EL-A3ZO 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZP                     TCGA-EL-A3ZQ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZR                     TCGA-EL-A3ZS 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZT                     TCGA-EL-A4JV 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4JW                     TCGA-EL-A4JX 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4JZ                     TCGA-EL-A4K0 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4K1                     TCGA-EL-A4K2 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4K4                     TCGA-EL-A4K6 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4K7                     TCGA-EL-A4K9 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4KD                     TCGA-EL-A4KG 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4KH                     TCGA-EL-A4KI 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A1CS                     TCGA-EM-A1CT 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A1CU                     TCGA-EM-A1CV 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A1CW                     TCGA-EM-A1YA 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A1YB                     TCGA-EM-A1YD 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A1YE                     TCGA-EM-A22I 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A22J                     TCGA-EM-A22K 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A22L                     TCGA-EM-A22O 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A22P                     TCGA-EM-A22Q 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2CJ                     TCGA-EM-A2CK 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2CL                     TCGA-EM-A2CN 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2CO                     TCGA-EM-A2CP 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2CQ                     TCGA-EM-A2CS 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2CT                     TCGA-EM-A2CU 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2OW                     TCGA-EM-A2OX 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2OY                     TCGA-EM-A2P0 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2P1                     TCGA-EM-A2P2 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A2P3                     TCGA-EM-A3AI 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3AJ                     TCGA-EM-A3AK 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3AL                     TCGA-EM-A3AN 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3AO                     TCGA-EM-A3AP 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3AQ                     TCGA-EM-A3AR 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3FJ                     TCGA-EM-A3FM 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3FN                     TCGA-EM-A3FO 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3FP                     TCGA-EM-A3FR 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3O3                     TCGA-EM-A3O6 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3O7                     TCGA-EM-A3O8 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3O9                     TCGA-EM-A3OA 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3OB                     TCGA-EM-A3ST 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3SU                     TCGA-EM-A3SX 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A3SY                     TCGA-EM-A3SZ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A4FF                     TCGA-EM-A4FH 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A4FK                     TCGA-EM-A4FM 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A4FN                     TCGA-EM-A4FQ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A4FR                     TCGA-EM-A4FU 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EM-A4FV                     TCGA-EM-A4G1 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25G                     TCGA-ET-A25I 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25J                     TCGA-ET-A25K 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25L                     TCGA-ET-A25M 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25N                     TCGA-ET-A25O 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25P                     TCGA-ET-A25R 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A2MY                     TCGA-ET-A2MZ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A2N0                     TCGA-ET-A2N5 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A39J                     TCGA-ET-A39M 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A39N                     TCGA-ET-A39O 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A39P                     TCGA-ET-A39T 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3BN                     TCGA-ET-A3BO 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3BP                     TCGA-ET-A3BQ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3BS                     TCGA-ET-A3BT 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3BU                     TCGA-ET-A3BV 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3BW                     TCGA-ET-A3BX 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3DO                     TCGA-ET-A3DS 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3DT                     TCGA-ET-A40P 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A40Q                     TCGA-ET-A40R 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A40S                     TCGA-ET-A4KN 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A4KQ                     TCGA-FE-A22Z 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A230                     TCGA-FE-A232 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A233                     TCGA-FE-A234 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A235                     TCGA-FE-A236 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A237                     TCGA-FE-A238 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A239                     TCGA-FE-A23A 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A3PA                     TCGA-FE-A3PB 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A3PC                     TCGA-FE-A3PD 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A2QD                     TCGA-FY-A3I4 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3I5                     TCGA-FY-A3ON 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3R8                     TCGA-FY-A3TY 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3W9                     TCGA-FY-A3YR 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A40K                     TCGA-FY-A40L 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A40M                     TCGA-FY-A40N 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A4B3                     TCGA-FY-A76V 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-GE-A2C6                     TCGA-H2-A421 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-IM-A3EB                     TCGA-IM-A3ED 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-IM-A3U2                     TCGA-IM-A3U3 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-IM-A41Y                     TCGA-IM-A41Z 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-IM-A420                     TCGA-IM-A4EB 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-J8-A3O0                     TCGA-J8-A3YD 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-J8-A3YG                     TCGA-KS-A41F 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A41I                     TCGA-KS-A41J 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A41L                     TCGA-KS-A4I3 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A4I5                     TCGA-KS-A4I7 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A4I9                     TCGA-KS-A4IB 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A4IC                     TCGA-KS-A4ID 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-L6-A4EP                     TCGA-L6-A4EQ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-L6-A4ET                     TCGA-L6-A4EU 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-MK-A4N6                     TCGA-MK-A4N7 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-MK-A4N9                     TCGA-MK-A84Z 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-QD-A8IV 
"AMP PEAK 36(10Q24.2) WILD-TYPE" 
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 36(10Q24.2) MUTATED                                  0     0
  AMP PEAK 36(10Q24.2) WILD-TYPE                                1    49
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 36(10Q24.2) MUTATED                           0     1
  AMP PEAK 36(10Q24.2) WILD-TYPE                        26   320
D34V16, multiclass
[1] "Remove cluster labels:"       "AMP PEAK 36(10Q24.2) MUTATED"
clus
  AMP PEAK 36(10Q24.2) MUTATED AMP PEAK 36(10Q24.2) WILD-TYPE 
                             1                            396 
                    TCGA-BJ-A0YZ                     TCGA-BJ-A0Z2 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A0Z3                     TCGA-BJ-A0Z5 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A0Z9                     TCGA-BJ-A0ZA 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A0ZB                     TCGA-BJ-A0ZC 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A0ZE                     TCGA-BJ-A0ZG 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A0ZH                     TCGA-BJ-A0ZJ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A18Y                     TCGA-BJ-A18Z 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A190                     TCGA-BJ-A191 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A192                     TCGA-BJ-A28R 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A28S                     TCGA-BJ-A28T 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A28V                     TCGA-BJ-A28W 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A28X                     TCGA-BJ-A28Z 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A290                     TCGA-BJ-A291 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A2N7                     TCGA-BJ-A2N8 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A2N9                     TCGA-BJ-A2NA 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A2P4                     TCGA-BJ-A3EZ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A3F0                     TCGA-BJ-A3PR 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A3PT                     TCGA-BJ-A3PU 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A45C                     TCGA-BJ-A45D 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A45E                     TCGA-BJ-A45F 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A45G                     TCGA-BJ-A45H 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A45I                     TCGA-BJ-A45J 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A45K                     TCGA-BJ-A4O8 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-BJ-A4O9                     TCGA-CE-A13K 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-CE-A27D                     TCGA-CE-A3MD 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-CE-A3ME                     TCGA-CE-A481 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-CE-A482                     TCGA-CE-A483 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-CE-A484                     TCGA-CE-A485 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A0XZ                     TCGA-DE-A0Y2 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A0Y3                     TCGA-DE-A2OL 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A3KN                     TCGA-DE-A4M8 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A4M9                     TCGA-DE-A4MA 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A4MB                     TCGA-DE-A4MC 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A4MD                     TCGA-DE-A69J 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DE-A69K                     TCGA-DE-A7U5 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A13M                     TCGA-DJ-A13O 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A13P                     TCGA-DJ-A13R 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A13S                     TCGA-DJ-A13T 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A13U                     TCGA-DJ-A13W 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A1QD                     TCGA-DJ-A1QE 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A1QF                     TCGA-DJ-A1QG 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A1QH                     TCGA-DJ-A1QI 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A1QM                     TCGA-DJ-A1QO 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A1QQ                     TCGA-DJ-A2PN 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PO                     TCGA-DJ-A2PQ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PR                     TCGA-DJ-A2PT 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PU                     TCGA-DJ-A2PV 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PW                     TCGA-DJ-A2PX 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2PY                     TCGA-DJ-A2PZ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2Q0                     TCGA-DJ-A2Q1 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2Q2                     TCGA-DJ-A2Q3 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2Q4                     TCGA-DJ-A2Q5 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2Q6                     TCGA-DJ-A2Q7 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2Q9                     TCGA-DJ-A2QA 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A2QB                     TCGA-DJ-A3UK 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UM                     TCGA-DJ-A3UN 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UO                     TCGA-DJ-A3UQ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UR                     TCGA-DJ-A3US 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UT                     TCGA-DJ-A3UU 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UW                     TCGA-DJ-A3UX 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3UY                     TCGA-DJ-A3UZ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3V2                     TCGA-DJ-A3V3 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3V4                     TCGA-DJ-A3V5 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3V7                     TCGA-DJ-A3V8 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3V9                     TCGA-DJ-A3VD 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3VE                     TCGA-DJ-A3VF 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3VG                     TCGA-DJ-A3VJ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A3VL                     TCGA-DJ-A3VM 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A4UL                     TCGA-DJ-A4UQ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A4UR                     TCGA-DJ-A4UT 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A4UW                     TCGA-DJ-A4V0 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DJ-A4V4                     TCGA-DJ-A4V5 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DO-A1JZ                     TCGA-DO-A1K0 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-DO-A2HM                     TCGA-E3-A3DY 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-E3-A3DZ                     TCGA-E3-A3E0 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-E3-A3E1                     TCGA-E3-A3E2 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-E3-A3E3                     TCGA-E3-A3E5 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-E8-A242                     TCGA-E8-A2EA 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-E8-A2JQ                     TCGA-E8-A3X7 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-E8-A413                     TCGA-E8-A414 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-E8-A415                     TCGA-E8-A416 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-E8-A417                     TCGA-E8-A418 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-E8-A419                     TCGA-E8-A432 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-E8-A433                     TCGA-E8-A434 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-E8-A436                     TCGA-E8-A437 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-E8-A438                     TCGA-E8-A44K 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-E8-A44M                     TCGA-EL-A3CL 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CM                     TCGA-EL-A3CN 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CO                     TCGA-EL-A3CP 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CR                     TCGA-EL-A3CS 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CT                     TCGA-EL-A3CU 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CV                     TCGA-EL-A3CW 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CX                     TCGA-EL-A3CY 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3CZ                     TCGA-EL-A3D0 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3D1                     TCGA-EL-A3D4 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3D5                     TCGA-EL-A3D6 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3GO                     TCGA-EL-A3GP 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3GQ                     TCGA-EL-A3GR 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3GS                     TCGA-EL-A3GU 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3GV                     TCGA-EL-A3GW 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3GX                     TCGA-EL-A3GY 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3GZ                     TCGA-EL-A3H1 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3H2                     TCGA-EL-A3H3 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3H4                     TCGA-EL-A3H5 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3H7                     TCGA-EL-A3H8 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3MW                     TCGA-EL-A3MX 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3MY                     TCGA-EL-A3MZ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3N2                     TCGA-EL-A3N3 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3T0                     TCGA-EL-A3T1 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3T2                     TCGA-EL-A3T3 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3T6                     TCGA-EL-A3T7 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3T8                     TCGA-EL-A3T9 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3TA                     TCGA-EL-A3TB 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZG                     TCGA-EL-A3ZH 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZK                     TCGA-EL-A3ZL 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZN                     TCGA-EL-A3ZO 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZP                     TCGA-EL-A3ZQ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZR                     TCGA-EL-A3ZS 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A3ZT                     TCGA-EL-A4JV 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4JW                     TCGA-EL-A4JX 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4JZ                     TCGA-EL-A4K0 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4K1                     TCGA-EL-A4K2 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4K4                     TCGA-EL-A4K6 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4K7                     TCGA-EL-A4K9 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4KD                     TCGA-EL-A4KG 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-EL-A4KH                     TCGA-EL-A4KI 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25G                     TCGA-ET-A25I 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25J                     TCGA-ET-A25K 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25L                     TCGA-ET-A25M 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25N                     TCGA-ET-A25O 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A25P                     TCGA-ET-A25R 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A2MX                     TCGA-ET-A2MY 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A2MZ                     TCGA-ET-A2N0 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A2N1                     TCGA-ET-A2N3 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A2N4                     TCGA-ET-A2N5 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A39J                     TCGA-ET-A39K 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A39M                     TCGA-ET-A39N 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A39O                     TCGA-ET-A39P 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A39R                     TCGA-ET-A39S 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A39T                     TCGA-ET-A3BN 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3BO                     TCGA-ET-A3BQ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3BS                     TCGA-ET-A3BT 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3BU                     TCGA-ET-A3BV 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3BW                     TCGA-ET-A3DO 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3DP                     TCGA-ET-A3DQ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3DR                     TCGA-ET-A3DS 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3DT                     TCGA-ET-A3DU 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A3DV                     TCGA-ET-A3DW 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A40P                     TCGA-ET-A40Q 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A40R                     TCGA-ET-A40S 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A40T                     TCGA-ET-A4KN 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-ET-A4KQ                     TCGA-FE-A22Z 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A230                     TCGA-FE-A231 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A232                     TCGA-FE-A233 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A234                     TCGA-FE-A235 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A236                     TCGA-FE-A237 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A238                     TCGA-FE-A239 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A23A                     TCGA-FE-A3PA 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A3PB                     TCGA-FE-A3PC 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FE-A3PD                     TCGA-FK-A3S3 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FK-A3SB                     TCGA-FK-A3SD 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FK-A3SE                     TCGA-FK-A3SG 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FK-A3SH                     TCGA-FK-A4UB 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A2QD                     TCGA-FY-A3BL 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3I4                     TCGA-FY-A3I5 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3NM                     TCGA-FY-A3ON 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3R6                     TCGA-FY-A3R7 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3R8                     TCGA-FY-A3R9 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3RA                     TCGA-FY-A3W9 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A3WA                     TCGA-FY-A3YR 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A40K                     TCGA-FY-A40L 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A40M                     TCGA-FY-A40N 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A4B0                     TCGA-FY-A4B3 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-FY-A4B4                     TCGA-FY-A76V 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-GE-A2C6                     TCGA-H2-A26U 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-H2-A2K9                     TCGA-H2-A3RH 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-H2-A3RI                     TCGA-H2-A421 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-H2-A422                     TCGA-IM-A3EB 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-IM-A3ED                     TCGA-IM-A3U2 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-IM-A3U3                     TCGA-IM-A41Y 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-IM-A41Z                     TCGA-IM-A420 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-IM-A4EB                     TCGA-J8-A3NZ 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-J8-A3O0                     TCGA-J8-A3O1 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-J8-A3O2                     TCGA-J8-A3YD 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-J8-A3YE                     TCGA-J8-A3YF 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-J8-A3YG                     TCGA-J8-A3YH 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-J8-A42S                     TCGA-J8-A4HW 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-J8-A4HY                     TCGA-KS-A41F 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A41I                     TCGA-KS-A41J 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A41L                     TCGA-KS-A4I1 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A4I3                     TCGA-KS-A4I5 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A4I7                     TCGA-KS-A4I9 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A4IB                     TCGA-KS-A4IC 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-KS-A4ID                     TCGA-L6-A4EP 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-L6-A4EQ                     TCGA-L6-A4ET 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-L6-A4EU                     TCGA-MK-A4N6 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-MK-A4N7                     TCGA-MK-A4N9 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
                    TCGA-MK-A84Z                     TCGA-QD-A8IV 
"AMP PEAK 36(10Q24.2) WILD-TYPE" "AMP PEAK 36(10Q24.2) WILD-TYPE" 
D34V17, binary
                                cls
clus                               0   1
  AMP PEAK 36(10Q24.2) MUTATED     0   1
  AMP PEAK 36(10Q24.2) WILD-TYPE  38 349
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 36(10Q24.2) MUTATED      0    1
  AMP PEAK 36(10Q24.2) WILD-TYPE   38  349
                        clus
vv                       AMP PEAK 36(10Q24.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            1
                        clus
vv                       AMP PEAK 36(10Q24.2) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            349
[1] 2 2
[1] FALSE

Clustering(35) Variable = AMP PEAK 37(10Q25.1) MUTATION ANALYSIS
D35V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 37(10Q25.1) MUTATED     4   0
  AMP PEAK 37(10Q25.1) WILD-TYPE 473  14
  AMP PEAK 37(10Q25.1) MUTATED AMP PEAK 37(10Q25.1) WILD-TYPE 
                             4                            487 
  AMP PEAK 37(10Q25.1) MUTATED AMP PEAK 37(10Q25.1) WILD-TYPE 
                             0                             14 
$`AMP PEAK 37(10Q25.1) MUTATED`
TCGA-DJ-A3UQ TCGA-EM-A1YC TCGA-EM-A22N TCGA-ET-A2MZ 
       19.56        54.21        10.65        12.26 

$`AMP PEAK 37(10Q25.1) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        5.52         8.78         8.42         8.12         9.34         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
        9.21         9.44         9.90         8.61        10.09         7.07 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       10.36        12.43        10.85        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       12.49        31.46        16.41        36.33        32.81        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
        1.45        74.30        45.40        33.47       108.36        39.32 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        30.18       102.84        65.39       124.04        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       37.25       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        38.66        52.73       139.00       131.15       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        12.16       147.42       130.72 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       116.91        98.24        41.29        95.38 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       50.33        53.06        47.38        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       37.78        29.95        13.32        11.87         8.71        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        12.36        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        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       10.49        13.15        22.16        13.84        19.73        17.59 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       12.07        17.59        17.46        17.29        14.60        17.46 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       18.97        15.68        14.14        19.63        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       16.44        16.77        27.95        23.77        16.80        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 
       11.15         7.33        12.53         9.24        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        16.41        15.62        13.51        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        29.49        54.05        22.09        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       65.36        84.89        98.56        61.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        59.15        28.24         5.85         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        24.69        68.22       102.90        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       81.34        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        46.06         4.08         0.89        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10        91.17         1.25         1.15        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        1.64         0.99         1.51         0.76         0.03         4.67 
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         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74        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         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  AMP PEAK 37(10Q25.1) MUTATED AMP PEAK 37(10Q25.1) WILD-TYPE 
                         10.65                           0.03 
  AMP PEAK 37(10Q25.1) MUTATED AMP PEAK 37(10Q25.1) WILD-TYPE 
                         54.21                         158.83 
  AMP PEAK 37(10Q25.1) MUTATED AMP PEAK 37(10Q25.1) WILD-TYPE 
                         15.91                          16.57 
[1] "10.7 - 54.2 (15.9)" "0.0 - 158.8 (16.6)"
[1] "hr="     "3300000"
D35V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 37(10Q25.1) MUTATED         2        0         2        0         0
  AMP PEAK 37(10Q25.1) WILD-TYPE     278       51       107        2        45
                                vv
clus                             STAGE IVC
  AMP PEAK 37(10Q25.1) MUTATED           0
  AMP PEAK 37(10Q25.1) WILD-TYPE         6
D35V3, multiclass
           clus
vv          AMP PEAK 37(10Q25.1) MUTATED AMP PEAK 37(10Q25.1) WILD-TYPE
  STAGE I                              2                            278
  STAGE II                             0                             51
  STAGE III                            2                            107
  STAGE IV                             0                              2
  STAGE IVA                            0                             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 37(10Q25.1) MUTATED     2   0   2   0
  AMP PEAK 37(10Q25.1) WILD-TYPE 138 166 163  21
D35V4, multiclass
    clus
vv   AMP PEAK 37(10Q25.1) MUTATED AMP PEAK 37(10Q25.1) WILD-TYPE
  T1                            2                            138
  T2                            0                            166
  T3                            2                            163
  T4                            0                             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"
D35V5, binary
                                cls
clus                               0   1
  AMP PEAK 37(10Q25.1) MUTATED     3   1
  AMP PEAK 37(10Q25.1) WILD-TYPE 220 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 37(10Q25.1) MUTATED      3    1
  AMP PEAK 37(10Q25.1) WILD-TYPE  220  221
   clus
vv  AMP PEAK 37(10Q25.1) MUTATED AMP PEAK 37(10Q25.1) WILD-TYPE
  0                            3                            220
  1                            1                            221
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 37(10Q25.1) MUTATED     1   0   3
  AMP PEAK 37(10Q25.1) WILD-TYPE 272   9 209
D35V6, multiclass
    clus
vv   AMP PEAK 37(10Q25.1) MUTATED AMP PEAK 37(10Q25.1) WILD-TYPE
  M0                            1                            272
  M1                            0                              9
  MX                            3                            209
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                                cls
clus                               0   1
  AMP PEAK 37(10Q25.1) MUTATED     3   1
  AMP PEAK 37(10Q25.1) WILD-TYPE 361 130
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 37(10Q25.1) MUTATED      3    1
  AMP PEAK 37(10Q25.1) WILD-TYPE  361  130
        clus
vv       AMP PEAK 37(10Q25.1) MUTATED AMP PEAK 37(10Q25.1) WILD-TYPE
  FEMALE                            3                            361
  MALE                              1                            130
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 37(10Q25.1) MUTATED                0
  AMP PEAK 37(10Q25.1) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 37(10Q25.1) MUTATED                                               1
  AMP PEAK 37(10Q25.1) WILD-TYPE                                           352
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 37(10Q25.1) MUTATED                                                                        2
  AMP PEAK 37(10Q25.1) WILD-TYPE                                                                     96
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 37(10Q25.1) MUTATED                                                                     1
  AMP PEAK 37(10Q25.1) WILD-TYPE                                                                  34
D35V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 37(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 37(10Q25.1) WILD-TYPE
  OTHER  SPECIFY                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             96
  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"
D35V9, binary
                                cls
clus                               0   1
  AMP PEAK 37(10Q25.1) MUTATED     0   4
  AMP PEAK 37(10Q25.1) WILD-TYPE  14 477
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 37(10Q25.1) MUTATED      0    4
  AMP PEAK 37(10Q25.1) WILD-TYPE   14  477
     clus
vv    AMP PEAK 37(10Q25.1) MUTATED AMP PEAK 37(10Q25.1) WILD-TYPE
  NO                             0                             14
  YES                            4                            477
[1] 2 2
[1] FALSE
D35V10, binary
                                cls
clus                               0   1
  AMP PEAK 37(10Q25.1) MUTATED     4   0
  AMP PEAK 37(10Q25.1) WILD-TYPE 413  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 37(10Q25.1) MUTATED      4    0
  AMP PEAK 37(10Q25.1) WILD-TYPE  413   17
     clus
vv    AMP PEAK 37(10Q25.1) MUTATED AMP PEAK 37(10Q25.1) WILD-TYPE
  NO                             4                            413
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 37(10Q25.1) MUTATED              1                       0    3
  AMP PEAK 37(10Q25.1) WILD-TYPE          129                      16  325
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 37(10Q25.1) MUTATED                     0
  AMP PEAK 37(10Q25.1) WILD-TYPE                   1
D35V11, multiclass
                         clus
vv                        AMP PEAK 37(10Q25.1) MUTATED
  MINIMAL (T3)                                       1
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               3
  VERY ADVANCED (T4B)                                0
                         clus
vv                        AMP PEAK 37(10Q25.1) WILD-TYPE
  MINIMAL (T3)                                       129
  MODERATE/ADVANCED (T4A)                             16
  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 37(10Q25.1) MUTATED     2   0   0   2
  AMP PEAK 37(10Q25.1) WILD-TYPE 376  51   4  28
D35V12, multiclass
    clus
vv   AMP PEAK 37(10Q25.1) MUTATED AMP PEAK 37(10Q25.1) WILD-TYPE
  R0                            2                            376
  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"
D35V13, continuous
D35V14, binary
                                cls
clus                               0   1
  AMP PEAK 37(10Q25.1) MUTATED     2   2
  AMP PEAK 37(10Q25.1) WILD-TYPE 222 259
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 37(10Q25.1) MUTATED      2    2
  AMP PEAK 37(10Q25.1) WILD-TYPE  222  259
            clus
vv           AMP PEAK 37(10Q25.1) MUTATED AMP PEAK 37(10Q25.1) WILD-TYPE
  MULTIFOCAL                            2                            222
  UNIFOCAL                              2                            259
[1] 2 2
[1] FALSE
D35V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 37(10Q25.1) MUTATED                                  0     1
  AMP PEAK 37(10Q25.1) WILD-TYPE                                1    48
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 37(10Q25.1) MUTATED                           0     1
  AMP PEAK 37(10Q25.1) WILD-TYPE                        26   320
D35V16, multiclass
[1] "Remove cluster labels:"       "AMP PEAK 37(10Q25.1) MUTATED"
clus
  AMP PEAK 37(10Q25.1) MUTATED AMP PEAK 37(10Q25.1) WILD-TYPE 
                             2                            395 
                    TCGA-BJ-A0YZ                     TCGA-BJ-A0Z2 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A0Z3                     TCGA-BJ-A0Z5 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A0Z9                     TCGA-BJ-A0ZA 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A0ZB                     TCGA-BJ-A0ZC 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A0ZE                     TCGA-BJ-A0ZG 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A0ZH                     TCGA-BJ-A0ZJ 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A18Y                     TCGA-BJ-A18Z 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A190                     TCGA-BJ-A191 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A192                     TCGA-BJ-A28R 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A28S                     TCGA-BJ-A28T 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A28V                     TCGA-BJ-A28W 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A28X                     TCGA-BJ-A28Z 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A290                     TCGA-BJ-A291 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A2N7                     TCGA-BJ-A2N8 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A2N9                     TCGA-BJ-A2NA 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A2P4                     TCGA-BJ-A3EZ 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A3F0                     TCGA-BJ-A3PR 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A3PT                     TCGA-BJ-A3PU 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A45C                     TCGA-BJ-A45D 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A45E                     TCGA-BJ-A45F 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A45G                     TCGA-BJ-A45H 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A45I                     TCGA-BJ-A45J 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A45K                     TCGA-BJ-A4O8 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-BJ-A4O9                     TCGA-CE-A13K 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-CE-A27D                     TCGA-CE-A3MD 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-CE-A3ME                     TCGA-CE-A481 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-CE-A482                     TCGA-CE-A483 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-CE-A484                     TCGA-CE-A485 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DE-A0XZ                     TCGA-DE-A0Y2 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DE-A0Y3                     TCGA-DE-A2OL 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DE-A3KN                     TCGA-DE-A4M8 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DE-A4M9                     TCGA-DE-A4MA 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DE-A4MB                     TCGA-DE-A4MC 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DE-A4MD                     TCGA-DE-A69J 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DE-A69K                     TCGA-DE-A7U5 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A13M                     TCGA-DJ-A13O 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A13P                     TCGA-DJ-A13R 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A13S                     TCGA-DJ-A13T 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A13U                     TCGA-DJ-A13W 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A1QD                     TCGA-DJ-A1QE 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A1QF                     TCGA-DJ-A1QG 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A1QH                     TCGA-DJ-A1QI 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A1QM                     TCGA-DJ-A1QO 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A1QQ                     TCGA-DJ-A2PN 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A2PO                     TCGA-DJ-A2PQ 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A2PR                     TCGA-DJ-A2PT 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A2PU                     TCGA-DJ-A2PV 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A2PW                     TCGA-DJ-A2PX 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A2PY                     TCGA-DJ-A2PZ 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A2Q0                     TCGA-DJ-A2Q1 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A2Q2                     TCGA-DJ-A2Q3 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A2Q4                     TCGA-DJ-A2Q5 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A2Q6                     TCGA-DJ-A2Q7 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A2Q9                     TCGA-DJ-A2QA 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A2QB                     TCGA-DJ-A3UK 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A3UM                     TCGA-DJ-A3UN 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A3UO                     TCGA-DJ-A3UR 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A3US                     TCGA-DJ-A3UT 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A3UU                     TCGA-DJ-A3UW 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A3UX                     TCGA-DJ-A3UY 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A3UZ                     TCGA-DJ-A3V2 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A3V3                     TCGA-DJ-A3V4 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A3V5                     TCGA-DJ-A3V7 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A3V8                     TCGA-DJ-A3V9 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A3VD                     TCGA-DJ-A3VE 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A3VF                     TCGA-DJ-A3VG 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A3VJ                     TCGA-DJ-A3VL 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A3VM                     TCGA-DJ-A4UL 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A4UQ                     TCGA-DJ-A4UR 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A4UT                     TCGA-DJ-A4UW 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A4V0                     TCGA-DJ-A4V4 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DJ-A4V5                     TCGA-DO-A1JZ 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-DO-A1K0                     TCGA-DO-A2HM 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-E3-A3DY                     TCGA-E3-A3DZ 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-E3-A3E0                     TCGA-E3-A3E1 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-E3-A3E2                     TCGA-E3-A3E3 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-E3-A3E5                     TCGA-E8-A242 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-E8-A2EA                     TCGA-E8-A2JQ 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-E8-A3X7                     TCGA-E8-A413 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-E8-A414                     TCGA-E8-A415 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-E8-A416                     TCGA-E8-A417 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-E8-A418                     TCGA-E8-A419 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-E8-A432                     TCGA-E8-A433 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-E8-A434                     TCGA-E8-A436 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-E8-A437                     TCGA-E8-A438 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-E8-A44K                     TCGA-E8-A44M 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3CL                     TCGA-EL-A3CM 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3CN                     TCGA-EL-A3CO 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3CP                     TCGA-EL-A3CR 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3CS                     TCGA-EL-A3CT 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3CU                     TCGA-EL-A3CV 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3CW                     TCGA-EL-A3CX 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3CY                     TCGA-EL-A3CZ 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3D0                     TCGA-EL-A3D1 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3D4                     TCGA-EL-A3D5 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3D6                     TCGA-EL-A3GO 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3GP                     TCGA-EL-A3GQ 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3GR                     TCGA-EL-A3GS 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3GU                     TCGA-EL-A3GV 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3GW                     TCGA-EL-A3GX 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3GY                     TCGA-EL-A3GZ 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3H1                     TCGA-EL-A3H2 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3H3                     TCGA-EL-A3H4 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3H5                     TCGA-EL-A3H7 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3H8                     TCGA-EL-A3MW 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3MX                     TCGA-EL-A3MY 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3MZ                     TCGA-EL-A3N2 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3N3                     TCGA-EL-A3T0 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3T1                     TCGA-EL-A3T2 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3T3                     TCGA-EL-A3T6 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3T7                     TCGA-EL-A3T8 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3T9                     TCGA-EL-A3TA 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3TB                     TCGA-EL-A3ZG 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3ZH                     TCGA-EL-A3ZK 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3ZL                     TCGA-EL-A3ZN 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3ZO                     TCGA-EL-A3ZP 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3ZQ                     TCGA-EL-A3ZR 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A3ZS                     TCGA-EL-A3ZT 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A4JV                     TCGA-EL-A4JW 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A4JX                     TCGA-EL-A4JZ 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A4K0                     TCGA-EL-A4K1 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A4K2                     TCGA-EL-A4K4 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A4K6                     TCGA-EL-A4K7 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A4K9                     TCGA-EL-A4KD 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A4KG                     TCGA-EL-A4KH 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-EL-A4KI                     TCGA-ET-A25G 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A25I                     TCGA-ET-A25J 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A25K                     TCGA-ET-A25L 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A25M                     TCGA-ET-A25N 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A25O                     TCGA-ET-A25P 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A25R                     TCGA-ET-A2MX 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A2MY                     TCGA-ET-A2N0 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A2N1                     TCGA-ET-A2N3 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A2N4                     TCGA-ET-A2N5 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A39I                     TCGA-ET-A39J 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A39K                     TCGA-ET-A39M 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A39N                     TCGA-ET-A39O 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A39P                     TCGA-ET-A39R 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A39S                     TCGA-ET-A39T 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A3BN                     TCGA-ET-A3BO 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A3BQ                     TCGA-ET-A3BS 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A3BT                     TCGA-ET-A3BU 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A3BV                     TCGA-ET-A3BW 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A3DO                     TCGA-ET-A3DP 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A3DQ                     TCGA-ET-A3DR 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A3DS                     TCGA-ET-A3DT 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A3DU                     TCGA-ET-A3DV 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A3DW                     TCGA-ET-A40P 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A40Q                     TCGA-ET-A40R 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A40S                     TCGA-ET-A40T 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-ET-A4KN                     TCGA-ET-A4KQ 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-FE-A22Z                     TCGA-FE-A230 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-FE-A231                     TCGA-FE-A232 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-FE-A233                     TCGA-FE-A234 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-FE-A235                     TCGA-FE-A236 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-FE-A237                     TCGA-FE-A238 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-FE-A239                     TCGA-FE-A23A 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-FE-A3PA                     TCGA-FE-A3PB 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-FE-A3PC                     TCGA-FE-A3PD 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-FK-A3S3                     TCGA-FK-A3SB 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-FK-A3SD                     TCGA-FK-A3SE 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-FK-A3SG                     TCGA-FK-A3SH 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-FK-A4UB                     TCGA-FY-A2QD 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-FY-A3BL                     TCGA-FY-A3I4 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-FY-A3I5                     TCGA-FY-A3NM 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-FY-A3ON                     TCGA-FY-A3R6 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-FY-A3R7                     TCGA-FY-A3R8 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-FY-A3R9                     TCGA-FY-A3RA 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-FY-A3W9                     TCGA-FY-A3WA 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-FY-A3YR                     TCGA-FY-A40K 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-FY-A40L                     TCGA-FY-A40M 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-FY-A40N                     TCGA-FY-A4B0 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-FY-A4B3                     TCGA-FY-A4B4 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-FY-A76V                     TCGA-GE-A2C6 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-H2-A26U                     TCGA-H2-A2K9 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-H2-A3RH                     TCGA-H2-A3RI 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-H2-A421                     TCGA-H2-A422 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-IM-A3EB                     TCGA-IM-A3ED 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-IM-A3U2                     TCGA-IM-A3U3 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-IM-A41Y                     TCGA-IM-A41Z 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-IM-A420                     TCGA-IM-A4EB 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-J8-A3NZ                     TCGA-J8-A3O0 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-J8-A3O1                     TCGA-J8-A3O2 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-J8-A3YD                     TCGA-J8-A3YE 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-J8-A3YF                     TCGA-J8-A3YG 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-J8-A3YH                     TCGA-J8-A42S 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-J8-A4HW                     TCGA-J8-A4HY 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-KS-A41F                     TCGA-KS-A41I 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-KS-A41J                     TCGA-KS-A41L 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-KS-A4I1                     TCGA-KS-A4I3 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-KS-A4I5                     TCGA-KS-A4I7 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-KS-A4I9                     TCGA-KS-A4IB 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-KS-A4IC                     TCGA-KS-A4ID 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-L6-A4EP                     TCGA-L6-A4EQ 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-L6-A4ET                     TCGA-L6-A4EU 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-MK-A4N6                     TCGA-MK-A4N7 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-MK-A4N9                     TCGA-MK-A84Z 
"AMP PEAK 37(10Q25.1) WILD-TYPE" "AMP PEAK 37(10Q25.1) WILD-TYPE" 
                    TCGA-QD-A8IV 
"AMP PEAK 37(10Q25.1) WILD-TYPE" 
D35V17, binary
                                cls
clus                               0   1
  AMP PEAK 37(10Q25.1) MUTATED     0   2
  AMP PEAK 37(10Q25.1) WILD-TYPE  38 348
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 37(10Q25.1) MUTATED      0    2
  AMP PEAK 37(10Q25.1) WILD-TYPE   38  348
                        clus
vv                       AMP PEAK 37(10Q25.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            2
                        clus
vv                       AMP PEAK 37(10Q25.1) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            348
[1] 2 2
[1] FALSE

Clustering(36) Variable = AMP PEAK 38(11P13) MUTATION ANALYSIS
D36V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 38(11P13) MUTATED     8   0
  AMP PEAK 38(11P13) WILD-TYPE 469  14
  AMP PEAK 38(11P13) MUTATED AMP PEAK 38(11P13) WILD-TYPE 
                           8                          483 
  AMP PEAK 38(11P13) MUTATED AMP PEAK 38(11P13) WILD-TYPE 
                           0                           14 
$`AMP PEAK 38(11P13) MUTATED`
TCGA-DJ-A2Q7 TCGA-E8-A414 TCGA-EL-A3ZR TCGA-EM-A1YC TCGA-EM-A2P2 TCGA-EM-A3SY 
       10.09        14.27        48.16        54.21        17.29        13.51 
TCGA-ET-A2MZ TCGA-ET-A39N 
       12.26        98.56 

$`AMP PEAK 38(11P13) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        5.52         8.78         8.42         8.12         9.34         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.21         9.44         9.90         8.61         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       22.29        19.59        13.61        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT 
       53.06        47.38        52.50        45.53         7.07        44.65 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       45.80        19.30        45.96        37.94        31.04        19.59 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        33.60        28.73        41.13        37.78        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       13.32        11.87         8.71        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YD TCGA-EM-A1YE 
       12.36        18.05        19.79        19.46        57.01        54.08 
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 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT 
       23.51         6.05         2.99        12.30        15.19        10.49 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        13.84        19.73        17.59        12.07 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.59        17.46        14.60        17.46        18.97        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR 
       14.14        19.63        13.38         8.35        16.44        16.77 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        16.80        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        11.15         7.33 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
       12.53         9.24        13.91         7.82        11.51        16.41 
TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       15.62        12.79        70.65        16.90         9.01         4.83 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
        8.61         8.38         9.80         5.03        37.87        12.72 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
        0.95        47.47        48.20        29.69        32.35        14.79 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       12.33        14.79        27.09        18.38        29.49        54.05 
TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       22.09        16.08        29.19        19.76         2.66        58.22 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O 
       13.74        71.01        80.02        65.36        84.89        61.02 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       58.72        57.11        55.10        59.15        28.24         5.85 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
        4.18         2.43         5.56        24.72        38.30        42.25 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
        2.37         4.50        80.81        69.24        59.87        43.50 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
        0.30        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        59.70        31.59        44.25        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      102.90        66.77        81.34        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        46.06         4.08 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        0.89        22.03         0.92        48.10        91.17         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
        1.15        17.82         1.64         0.99         1.51         0.76 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
        0.03         4.67        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         6.87         4.14         6.58         4.54         0.89 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35         1.15         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 
       10.26        16.90         9.80         9.63         2.96         8.65 
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        86.70         6.02        12.43 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
        6.74        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         0.72        16.64        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        8.71        10.98         5.19 

  AMP PEAK 38(11P13) MUTATED AMP PEAK 38(11P13) WILD-TYPE 
                       10.09                         0.03 
  AMP PEAK 38(11P13) MUTATED AMP PEAK 38(11P13) WILD-TYPE 
                       98.56                       158.83 
  AMP PEAK 38(11P13) MUTATED AMP PEAK 38(11P13) WILD-TYPE 
                       15.78                        16.57 
[1] "10.1 - 98.6 (15.8)" "0.0 - 158.8 (16.6)"
[1] "hr="     "9300000"
D36V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 38(11P13) MUTATED         3        1         4        0         0
  AMP PEAK 38(11P13) WILD-TYPE     277       50       105        2        45
                              vv
clus                           STAGE IVC
  AMP PEAK 38(11P13) MUTATED           0
  AMP PEAK 38(11P13) WILD-TYPE         6
D36V3, multiclass
           clus
vv          AMP PEAK 38(11P13) MUTATED AMP PEAK 38(11P13) WILD-TYPE
  STAGE I                            3                          277
  STAGE II                           1                           50
  STAGE III                          4                          105
  STAGE IV                           0                            2
  STAGE IVA                          0                           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 38(11P13) MUTATED     2   2   4   0
  AMP PEAK 38(11P13) WILD-TYPE 138 164 161  21
D36V4, multiclass
    clus
vv   AMP PEAK 38(11P13) MUTATED AMP PEAK 38(11P13) WILD-TYPE
  T1                          2                          138
  T2                          2                          164
  T3                          4                          161
  T4                          0                           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"
D36V5, binary
                              cls
clus                             0   1
  AMP PEAK 38(11P13) MUTATED     5   1
  AMP PEAK 38(11P13) WILD-TYPE 218 221
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 38(11P13) MUTATED      5    1
  AMP PEAK 38(11P13) WILD-TYPE  218  221
   clus
vv  AMP PEAK 38(11P13) MUTATED AMP PEAK 38(11P13) WILD-TYPE
  0                          5                          218
  1                          1                          221
[1] 2 2
[1] FALSE
                              vv
clus                            M0  M1  MX
  AMP PEAK 38(11P13) MUTATED     3   0   5
  AMP PEAK 38(11P13) WILD-TYPE 270   9 207
D36V6, multiclass
    clus
vv   AMP PEAK 38(11P13) MUTATED AMP PEAK 38(11P13) WILD-TYPE
  M0                          3                          270
  M1                          0                            9
  MX                          5                          207
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                              cls
clus                             0   1
  AMP PEAK 38(11P13) MUTATED     5   3
  AMP PEAK 38(11P13) WILD-TYPE 359 128
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 38(11P13) MUTATED      5    3
  AMP PEAK 38(11P13) WILD-TYPE  359  128
        clus
vv       AMP PEAK 38(11P13) MUTATED AMP PEAK 38(11P13) WILD-TYPE
  FEMALE                          5                          359
  MALE                            3                          128
[1] 2 2
[1] FALSE
                              vv
clus                           OTHER  SPECIFY
  AMP PEAK 38(11P13) MUTATED                0
  AMP PEAK 38(11P13) WILD-TYPE              9
                              vv
clus                           THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 38(11P13) MUTATED                                               5
  AMP PEAK 38(11P13) WILD-TYPE                                           348
                              vv
clus                           THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 38(11P13) MUTATED                                                                        3
  AMP PEAK 38(11P13) WILD-TYPE                                                                     95
                              vv
clus                           THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 38(11P13) MUTATED                                                                     0
  AMP PEAK 38(11P13) WILD-TYPE                                                                  35
D36V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 38(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 38(11P13) WILD-TYPE
  OTHER  SPECIFY                                                                                    9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   348
  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"
D36V9, binary
                              cls
clus                             0   1
  AMP PEAK 38(11P13) MUTATED     0   8
  AMP PEAK 38(11P13) WILD-TYPE  14 473
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 38(11P13) MUTATED      0    8
  AMP PEAK 38(11P13) WILD-TYPE   14  473
     clus
vv    AMP PEAK 38(11P13) MUTATED AMP PEAK 38(11P13) WILD-TYPE
  NO                           0                           14
  YES                          8                          473
[1] 2 2
[1] FALSE
D36V10, binary
                              cls
clus                             0   1
  AMP PEAK 38(11P13) MUTATED     8   0
  AMP PEAK 38(11P13) WILD-TYPE 409  17
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 38(11P13) MUTATED      8    0
  AMP PEAK 38(11P13) WILD-TYPE  409   17
     clus
vv    AMP PEAK 38(11P13) MUTATED AMP PEAK 38(11P13) WILD-TYPE
  NO                           8                          409
  YES                          0                           17
[1] 2 2
[1] FALSE
                              vv
clus                           MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 38(11P13) MUTATED              1                       0    7
  AMP PEAK 38(11P13) WILD-TYPE          129                      16  321
                              vv
clus                           VERY ADVANCED (T4B)
  AMP PEAK 38(11P13) MUTATED                     0
  AMP PEAK 38(11P13) WILD-TYPE                   1
D36V11, multiclass
                         clus
vv                        AMP PEAK 38(11P13) MUTATED
  MINIMAL (T3)                                     1
  MODERATE/ADVANCED (T4A)                          0
  NONE                                             7
  VERY ADVANCED (T4B)                              0
                         clus
vv                        AMP PEAK 38(11P13) WILD-TYPE
  MINIMAL (T3)                                     129
  MODERATE/ADVANCED (T4A)                           16
  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
  AMP PEAK 38(11P13) MUTATED     7   0   0   1
  AMP PEAK 38(11P13) WILD-TYPE 371  51   4  29
D36V12, multiclass
    clus
vv   AMP PEAK 38(11P13) MUTATED AMP PEAK 38(11P13) WILD-TYPE
  R0                          7                          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"
D36V13, continuous
D36V14, binary
                              cls
clus                             0   1
  AMP PEAK 38(11P13) MUTATED     2   6
  AMP PEAK 38(11P13) WILD-TYPE 222 255
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 38(11P13) MUTATED      2    6
  AMP PEAK 38(11P13) WILD-TYPE  222  255
            clus
vv           AMP PEAK 38(11P13) MUTATED AMP PEAK 38(11P13) WILD-TYPE
  MULTIFOCAL                          2                          222
  UNIFOCAL                            6                          255
[1] 2 2
[1] FALSE
D36V15, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 38(11P13) MUTATED                                  0     2
  AMP PEAK 38(11P13) WILD-TYPE                                1    47
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 38(11P13) MUTATED                           0     3
  AMP PEAK 38(11P13) WILD-TYPE                        26   318
D36V16, multiclass
                                  clus
vv                                 AMP PEAK 38(11P13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                 0
  WHITE                                                     3
                                  clus
vv                                 AMP PEAK 38(11P13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      47
  BLACK OR AFRICAN AMERICAN                                  26
  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 38(11P13) MUTATED     0   5
  AMP PEAK 38(11P13) WILD-TYPE  38 345
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 38(11P13) MUTATED      0    5
  AMP PEAK 38(11P13) WILD-TYPE   38  345
                        clus
vv                       AMP PEAK 38(11P13) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                          5
                        clus
vv                       AMP PEAK 38(11P13) WILD-TYPE
  HISPANIC OR LATINO                               38
  NOT HISPANIC OR LATINO                          345
[1] 2 2
[1] FALSE

Clustering(37) Variable = AMP PEAK 39(12P11.1) MUTATION ANALYSIS
D37V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 39(12P11.1) MUTATED    16   0
  AMP PEAK 39(12P11.1) WILD-TYPE 461  14
  AMP PEAK 39(12P11.1) MUTATED AMP PEAK 39(12P11.1) WILD-TYPE 
                            16                            475 
  AMP PEAK 39(12P11.1) MUTATED AMP PEAK 39(12P11.1) WILD-TYPE 
                             0                             14 
$`AMP PEAK 39(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       100.01        54.21        57.01        10.65 
TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A2N3 
        6.05        17.59        17.46        13.51        12.26        19.76 
TCGA-ET-A39N TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3WA 
       98.56         1.64         0.99        17.06 

$`AMP PEAK 39(12P11.1) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
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        15.48        23.31        18.64         5.75 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
        6.48         0.03         3.45         6.35         7.82         6.18 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
        5.06         8.98         4.93         5.98         0.53         0.10 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
        0.20         0.23        11.38        10.68         0.10         0.39 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.10        20.22        15.42        36.46         5.98        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-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
        4.27         3.22         2.76        17.26        14.07       137.88 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
        3.39         8.71        25.35        13.41        11.90        14.60 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
        7.99        11.01        18.51        13.12         7.99        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
        7.20         1.45         8.88         1.02         5.95        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT 
        7.99         5.33         8.48        10.45         1.51         9.60 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       12.56         8.28         7.69         5.52         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
        8.12         9.34         6.77         9.21         9.44         9.90 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
        8.61        10.09         7.07        10.36        12.43        10.85 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       15.88        15.09        31.04        12.49        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        24.23        17.69        43.00 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       11.34        21.37        12.76        25.02        20.22        30.61 
TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       14.56        19.20         9.83        21.27        20.48        11.93 
TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ 
       22.92        21.01        18.97         7.76         8.32        17.36 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       17.23        27.62        18.21        10.78        10.98        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        30.31        14.04         1.15        22.29        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       14.43        14.70        14.10        14.96         7.69        20.68 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       13.78        13.58        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        80.91         4.18        58.82         1.45        74.30 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       45.40        33.47       108.36        39.32         1.41        30.18 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
      102.84        65.39       124.04        50.37        37.25       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        38.66 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       52.73       139.00       131.15       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        12.16       147.42       130.72       129.57        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      116.91        98.24        41.29        95.38         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN 
       82.82        77.36        78.97        31.50        50.33        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        52.50        45.53        48.16         7.07        44.65 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       45.80        19.30        45.96        37.94        31.04        19.59 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        33.60        28.73        41.13        37.78        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       13.32        11.87         8.71        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I 
       12.36        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        11.74        11.15 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP 
       14.24        16.44        17.88        13.18        23.51         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
       12.30        15.19        10.49        13.15        22.16        13.84 
TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       19.73        12.07        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 
       18.97        15.68        14.14        19.63        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       16.44        16.77        27.95        23.77        16.80        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 
       11.15         7.33        12.53         9.24        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       11.51        16.41        15.62        12.79        70.65        16.90 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        9.01         4.83         8.61         8.38         9.80         5.03 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       37.87        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N4 
       29.49        54.05        22.09        16.08        29.19         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       58.22        13.74        71.01        80.02        65.36        84.89 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
       61.02        58.72        57.11        55.10        59.15        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
        5.85         4.18         2.43         5.56        24.72        38.30 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       42.25         2.37         4.50        80.81        69.24        59.87 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       43.50         0.30        17.98        25.32       132.36        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
        3.22         7.17         4.80         5.03         2.14         4.01 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
        1.94        73.74        59.70        31.59        44.25        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       102.90        66.77        81.34        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        46.06 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.08         0.89        22.03         0.92        48.10        91.17 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        1.25         1.15        17.82         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3YR 
        4.67        16.57        18.08         0.30         0.76         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74        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         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  AMP PEAK 39(12P11.1) MUTATED AMP PEAK 39(12P11.1) WILD-TYPE 
                          0.99                           0.03 
  AMP PEAK 39(12P11.1) MUTATED AMP PEAK 39(12P11.1) WILD-TYPE 
                        100.01                         158.83 
  AMP PEAK 39(12P11.1) MUTATED AMP PEAK 39(12P11.1) WILD-TYPE 
                        17.525                         16.440 
[1] "1.0 - 100.0 (17.5)" "0.0 - 158.8 (16.4)"
[1] "hr="     "2.6e+07"
D37V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 39(12P11.1) MUTATED         7        5         4        0         0
  AMP PEAK 39(12P11.1) WILD-TYPE     273       46       105        2        45
                                vv
clus                             STAGE IVC
  AMP PEAK 39(12P11.1) MUTATED           0
  AMP PEAK 39(12P11.1) WILD-TYPE         6
D37V3, multiclass
           clus
vv          AMP PEAK 39(12P11.1) MUTATED AMP PEAK 39(12P11.1) WILD-TYPE
  STAGE I                              7                            273
  STAGE II                             5                             46
  STAGE III                            4                            105
  STAGE IV                             0                              2
  STAGE IVA                            0                             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 39(12P11.1) MUTATED     4   7   5   0
  AMP PEAK 39(12P11.1) WILD-TYPE 136 159 160  21
D37V4, multiclass
    clus
vv   AMP PEAK 39(12P11.1) MUTATED AMP PEAK 39(12P11.1) WILD-TYPE
  T1                            4                            136
  T2                            7                            159
  T3                            5                            160
  T4                            0                             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"
D37V5, binary
                                cls
clus                               0   1
  AMP PEAK 39(12P11.1) MUTATED    10   0
  AMP PEAK 39(12P11.1) WILD-TYPE 213 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 39(12P11.1) MUTATED     10    0
  AMP PEAK 39(12P11.1) WILD-TYPE  213  222
   clus
vv  AMP PEAK 39(12P11.1) MUTATED AMP PEAK 39(12P11.1) WILD-TYPE
  0                           10                            213
  1                            0                            222
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 39(12P11.1) MUTATED     2   0  14
  AMP PEAK 39(12P11.1) WILD-TYPE 271   9 198
D37V6, multiclass
    clus
vv   AMP PEAK 39(12P11.1) MUTATED AMP PEAK 39(12P11.1) WILD-TYPE
  M0                            2                            271
  M1                            0                              9
  MX                           14                            198
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                                cls
clus                               0   1
  AMP PEAK 39(12P11.1) MUTATED    13   3
  AMP PEAK 39(12P11.1) WILD-TYPE 351 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 39(12P11.1) MUTATED     13    3
  AMP PEAK 39(12P11.1) WILD-TYPE  351  128
        clus
vv       AMP PEAK 39(12P11.1) MUTATED AMP PEAK 39(12P11.1) WILD-TYPE
  FEMALE                           13                            351
  MALE                              3                            128
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 39(12P11.1) MUTATED                0
  AMP PEAK 39(12P11.1) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 39(12P11.1) MUTATED                                               6
  AMP PEAK 39(12P11.1) WILD-TYPE                                           347
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 39(12P11.1) MUTATED                                                                       10
  AMP PEAK 39(12P11.1) WILD-TYPE                                                                     88
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 39(12P11.1) MUTATED                                                                     0
  AMP PEAK 39(12P11.1) WILD-TYPE                                                                  35
D37V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 39(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 39(12P11.1) WILD-TYPE
  OTHER  SPECIFY                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     347
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             88
  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"
D37V9, binary
                                cls
clus                               0   1
  AMP PEAK 39(12P11.1) MUTATED     0  16
  AMP PEAK 39(12P11.1) WILD-TYPE  14 465
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 39(12P11.1) MUTATED      0   16
  AMP PEAK 39(12P11.1) WILD-TYPE   14  465
     clus
vv    AMP PEAK 39(12P11.1) MUTATED AMP PEAK 39(12P11.1) WILD-TYPE
  NO                             0                             14
  YES                           16                            465
[1] 2 2
[1] FALSE
D37V10, binary
                                cls
clus                               0   1
  AMP PEAK 39(12P11.1) MUTATED    15   0
  AMP PEAK 39(12P11.1) WILD-TYPE 402  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 39(12P11.1) MUTATED     15    0
  AMP PEAK 39(12P11.1) WILD-TYPE  402   17
     clus
vv    AMP PEAK 39(12P11.1) MUTATED AMP PEAK 39(12P11.1) WILD-TYPE
  NO                            15                            402
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 39(12P11.1) MUTATED              2                       0   14
  AMP PEAK 39(12P11.1) WILD-TYPE          128                      16  314
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 39(12P11.1) MUTATED                     0
  AMP PEAK 39(12P11.1) WILD-TYPE                   1
D37V11, multiclass
                         clus
vv                        AMP PEAK 39(12P11.1) MUTATED
  MINIMAL (T3)                                       2
  MODERATE/ADVANCED (T4A)                            0
  NONE                                              14
  VERY ADVANCED (T4B)                                0
                         clus
vv                        AMP PEAK 39(12P11.1) WILD-TYPE
  MINIMAL (T3)                                       128
  MODERATE/ADVANCED (T4A)                             16
  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(12P11.1) MUTATED    12   1   0   3
  AMP PEAK 39(12P11.1) WILD-TYPE 366  50   4  27
D37V12, multiclass
    clus
vv   AMP PEAK 39(12P11.1) MUTATED AMP PEAK 39(12P11.1) WILD-TYPE
  R0                           12                            366
  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"
D37V13, continuous
D37V14, binary
                                cls
clus                               0   1
  AMP PEAK 39(12P11.1) MUTATED     7   9
  AMP PEAK 39(12P11.1) WILD-TYPE 217 252
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 39(12P11.1) MUTATED      7    9
  AMP PEAK 39(12P11.1) WILD-TYPE  217  252
            clus
vv           AMP PEAK 39(12P11.1) MUTATED AMP PEAK 39(12P11.1) WILD-TYPE
  MULTIFOCAL                            7                            217
  UNIFOCAL                              9                            252
[1] 2 2
[1] FALSE
D37V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 39(12P11.1) MUTATED                                  0     0
  AMP PEAK 39(12P11.1) WILD-TYPE                                1    49
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 39(12P11.1) MUTATED                           0     9
  AMP PEAK 39(12P11.1) WILD-TYPE                        26   312
D37V16, multiclass
                                  clus
vv                                 AMP PEAK 39(12P11.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       9
                                  clus
vv                                 AMP PEAK 39(12P11.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        49
  BLACK OR AFRICAN AMERICAN                                    26
  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"
D37V17, binary
                                cls
clus                               0   1
  AMP PEAK 39(12P11.1) MUTATED     0   8
  AMP PEAK 39(12P11.1) WILD-TYPE  38 342
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 39(12P11.1) MUTATED      0    8
  AMP PEAK 39(12P11.1) WILD-TYPE   38  342
                        clus
vv                       AMP PEAK 39(12P11.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            8
                        clus
vv                       AMP PEAK 39(12P11.1) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            342
[1] 2 2
[1] FALSE

Clustering(38) Variable = AMP PEAK 40(12Q21.31) MUTATION ANALYSIS
D38V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 40(12Q21.31) MUTATED    17   0
  AMP PEAK 40(12Q21.31) WILD-TYPE 460  14
  AMP PEAK 40(12Q21.31) MUTATED AMP PEAK 40(12Q21.31) WILD-TYPE 
                             17                             474 
  AMP PEAK 40(12Q21.31) MUTATED AMP PEAK 40(12Q21.31) WILD-TYPE 
                              0                              14 
$`AMP PEAK 40(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        39.32        45.53        54.21        57.01 
TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3SY TCGA-ET-A2MZ 
       10.65         6.05        17.59        17.46        13.51        12.26 
TCGA-ET-A39N TCGA-ET-A3DS TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3WA 
       98.56         0.30         1.64         0.99        17.06 

$`AMP PEAK 40(12Q21.31) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
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        15.48        23.31        18.64         5.75 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
        6.48         0.03         3.45         6.35         7.82         6.18 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
        5.06         8.98         4.93         5.98         0.53         0.10 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
        0.20         0.23        11.38        10.68         0.10         0.39 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.10        20.22        15.42        36.46         5.98        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-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
        4.27         3.22         2.76        17.26        14.07       137.88 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
        3.39         8.71        25.35        13.41        11.90        14.60 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        7.99        11.01       100.01        18.51        13.12         7.99 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96         7.20         1.45         8.88         1.02         5.95 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS 
       10.09         7.99         5.33         8.48        10.45         1.51 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY 
        9.60        12.56         8.28         7.69         5.52         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.42         8.12         9.34         6.77         9.21         9.44 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
        9.90         8.61        10.09         7.07        10.36        12.43 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        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        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04         1.15        22.29 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GP TCGA-EL-A3GQ 
       74.30        45.40        33.47       108.36         1.41        30.18 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
      102.84        65.39       124.04        50.37        37.25       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        38.66 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       52.73       139.00       131.15       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        12.16       147.42       130.72       129.57        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      116.91        98.24        41.29        95.38         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN 
       82.82        77.36        78.97        31.50        50.33        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       47.38        52.50        48.16         7.07        44.65        45.80 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       19.30        45.96        37.94        31.04        19.59        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       33.60        28.73        41.13        37.78        29.95        13.32 
TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       11.87         8.71        26.86        18.18        20.91        12.36 
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        11.74        11.15        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ 
       16.44        17.88        13.18        23.51         2.99        12.30 
TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        10.49        13.15        22.16        13.84        19.73 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AJ 
       12.07        17.59        17.46        17.29        14.60        18.97 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        19.63        13.38         8.35        16.44 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       16.77        27.95        23.77        16.80        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        11.15 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33        12.53         9.24        13.91         7.82        11.51 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       16.41        15.62        12.79        70.65        16.90         9.01 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        4.83         8.61         8.38         9.80         5.03        37.87 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       12.72         0.95        47.47        48.20        29.69        32.35 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       14.79        12.33        14.79        27.09        18.38        29.49 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       54.05        22.09        16.08        29.19        19.76         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       58.22        13.74        71.01        80.02        65.36        84.89 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
       61.02        58.72        57.11        55.10        59.15        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
        5.85         4.18         2.43         5.56        24.72        38.30 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       42.25         2.37         4.50        80.81        69.24        59.87 
TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
       43.50        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        59.70        31.59        44.25        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      102.90        66.77        81.34        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        46.06         4.08 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        0.89        22.03         0.92        48.10        91.17         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        1.15        17.82         1.51         0.76         0.03         4.67 
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         6.87         4.14 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58         4.54         0.89         1.35         1.15         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        10.26        16.90         9.80 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
        9.63         2.96         8.65        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 
       86.70         6.02        12.43         6.74        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 
        0.72        16.64        32.45         8.71        10.98         5.19 

  AMP PEAK 40(12Q21.31) MUTATED AMP PEAK 40(12Q21.31) WILD-TYPE 
                           0.30                            0.03 
  AMP PEAK 40(12Q21.31) MUTATED AMP PEAK 40(12Q21.31) WILD-TYPE 
                          98.56                          158.83 
  AMP PEAK 40(12Q21.31) MUTATED AMP PEAK 40(12Q21.31) WILD-TYPE 
                         17.460                          16.505 
[1] "0.3 - 98.6 (17.5)"  "0.0 - 158.8 (16.5)"
[1] "hr="     "2.6e+07"
D38V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 40(12Q21.31) MUTATED         8        6         3        0         0
  AMP PEAK 40(12Q21.31) WILD-TYPE     272       45       106        2        45
                                 vv
clus                              STAGE IVC
  AMP PEAK 40(12Q21.31) MUTATED           0
  AMP PEAK 40(12Q21.31) WILD-TYPE         6
D38V3, multiclass
           clus
vv          AMP PEAK 40(12Q21.31) MUTATED AMP PEAK 40(12Q21.31) WILD-TYPE
  STAGE I                               8                             272
  STAGE II                              6                              45
  STAGE III                             3                             106
  STAGE IV                              0                               2
  STAGE IVA                             0                              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 40(12Q21.31) MUTATED     5   8   4   0
  AMP PEAK 40(12Q21.31) WILD-TYPE 135 158 161  21
D38V4, multiclass
    clus
vv   AMP PEAK 40(12Q21.31) MUTATED AMP PEAK 40(12Q21.31) WILD-TYPE
  T1                             5                             135
  T2                             8                             158
  T3                             4                             161
  T4                             0                              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"
D38V5, binary
                                 cls
clus                                0   1
  AMP PEAK 40(12Q21.31) MUTATED    12   0
  AMP PEAK 40(12Q21.31) WILD-TYPE 211 222
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 40(12Q21.31) MUTATED     12    0
  AMP PEAK 40(12Q21.31) WILD-TYPE  211  222
   clus
vv  AMP PEAK 40(12Q21.31) MUTATED AMP PEAK 40(12Q21.31) WILD-TYPE
  0                            12                             211
  1                             0                             222
[1] 2 2
[1] FALSE
                                 vv
clus                               M0  M1  MX
  AMP PEAK 40(12Q21.31) MUTATED     3   0  14
  AMP PEAK 40(12Q21.31) WILD-TYPE 270   9 198
D38V6, multiclass
    clus
vv   AMP PEAK 40(12Q21.31) MUTATED AMP PEAK 40(12Q21.31) WILD-TYPE
  M0                             3                             270
  M1                             0                               9
  MX                            14                             198
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                                 cls
clus                                0   1
  AMP PEAK 40(12Q21.31) MUTATED    14   3
  AMP PEAK 40(12Q21.31) WILD-TYPE 350 128
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 40(12Q21.31) MUTATED     14    3
  AMP PEAK 40(12Q21.31) WILD-TYPE  350  128
        clus
vv       AMP PEAK 40(12Q21.31) MUTATED AMP PEAK 40(12Q21.31) WILD-TYPE
  FEMALE                            14                             350
  MALE                               3                             128
[1] 2 2
[1] FALSE
                                 vv
clus                              OTHER  SPECIFY
  AMP PEAK 40(12Q21.31) MUTATED                0
  AMP PEAK 40(12Q21.31) WILD-TYPE              9
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 40(12Q21.31) MUTATED                                               8
  AMP PEAK 40(12Q21.31) WILD-TYPE                                           345
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 40(12Q21.31) MUTATED                                                                        9
  AMP PEAK 40(12Q21.31) WILD-TYPE                                                                     89
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 40(12Q21.31) MUTATED                                                                     0
  AMP PEAK 40(12Q21.31) WILD-TYPE                                                                  35
D38V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 40(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 40(12Q21.31) WILD-TYPE
  OTHER  SPECIFY                                                                                       9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      345
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                              89
  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"
D38V9, binary
                                 cls
clus                                0   1
  AMP PEAK 40(12Q21.31) MUTATED     0  17
  AMP PEAK 40(12Q21.31) WILD-TYPE  14 464
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 40(12Q21.31) MUTATED      0   17
  AMP PEAK 40(12Q21.31) WILD-TYPE   14  464
     clus
vv    AMP PEAK 40(12Q21.31) MUTATED AMP PEAK 40(12Q21.31) WILD-TYPE
  NO                              0                              14
  YES                            17                             464
[1] 2 2
[1] FALSE
D38V10, binary
                                 cls
clus                                0   1
  AMP PEAK 40(12Q21.31) MUTATED    16   0
  AMP PEAK 40(12Q21.31) WILD-TYPE 401  17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 40(12Q21.31) MUTATED     16    0
  AMP PEAK 40(12Q21.31) WILD-TYPE  401   17
     clus
vv    AMP PEAK 40(12Q21.31) MUTATED AMP PEAK 40(12Q21.31) WILD-TYPE
  NO                             16                             401
  YES                             0                              17
[1] 2 2
[1] FALSE
                                 vv
clus                              MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 40(12Q21.31) MUTATED              1                       0   16
  AMP PEAK 40(12Q21.31) WILD-TYPE          129                      16  312
                                 vv
clus                              VERY ADVANCED (T4B)
  AMP PEAK 40(12Q21.31) MUTATED                     0
  AMP PEAK 40(12Q21.31) WILD-TYPE                   1
D38V11, multiclass
                         clus
vv                        AMP PEAK 40(12Q21.31) MUTATED
  MINIMAL (T3)                                        1
  MODERATE/ADVANCED (T4A)                             0
  NONE                                               16
  VERY ADVANCED (T4B)                                 0
                         clus
vv                        AMP PEAK 40(12Q21.31) WILD-TYPE
  MINIMAL (T3)                                        129
  MODERATE/ADVANCED (T4A)                              16
  NONE                                                312
  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(12Q21.31) MUTATED    14   1   0   2
  AMP PEAK 40(12Q21.31) WILD-TYPE 364  50   4  28
D38V12, multiclass
    clus
vv   AMP PEAK 40(12Q21.31) MUTATED AMP PEAK 40(12Q21.31) WILD-TYPE
  R0                            14                             364
  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 40(12Q21.31) MUTATED     7  10
  AMP PEAK 40(12Q21.31) WILD-TYPE 217 251
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 40(12Q21.31) MUTATED      7   10
  AMP PEAK 40(12Q21.31) WILD-TYPE  217  251
            clus
vv           AMP PEAK 40(12Q21.31) MUTATED AMP PEAK 40(12Q21.31) WILD-TYPE
  MULTIFOCAL                             7                             217
  UNIFOCAL                              10                             251
[1] 2 2
[1] FALSE
D38V15, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 40(12Q21.31) MUTATED                                  0     0
  AMP PEAK 40(12Q21.31) WILD-TYPE                                1    49
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 40(12Q21.31) MUTATED                           0    10
  AMP PEAK 40(12Q21.31) WILD-TYPE                        26   311
D38V16, multiclass
                                  clus
vv                                 AMP PEAK 40(12Q21.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                    0
  WHITE                                                       10
                                  clus
vv                                 AMP PEAK 40(12Q21.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         49
  BLACK OR AFRICAN AMERICAN                                     26
  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"
D38V17, binary
                                 cls
clus                                0   1
  AMP PEAK 40(12Q21.31) MUTATED     1   9
  AMP PEAK 40(12Q21.31) WILD-TYPE  37 341
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 40(12Q21.31) MUTATED      1    9
  AMP PEAK 40(12Q21.31) WILD-TYPE   37  341
                        clus
vv                       AMP PEAK 40(12Q21.31) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                             9
                        clus
vv                       AMP PEAK 40(12Q21.31) WILD-TYPE
  HISPANIC OR LATINO                                  37
  NOT HISPANIC OR LATINO                             341
[1] 2 2
[1] FALSE

Clustering(39) Variable = AMP PEAK 41(12Q23.1) MUTATION ANALYSIS
D39V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 41(12Q23.1) MUTATED    17   0
  AMP PEAK 41(12Q23.1) WILD-TYPE 460  14
  AMP PEAK 41(12Q23.1) MUTATED AMP PEAK 41(12Q23.1) WILD-TYPE 
                            17                            474 
  AMP PEAK 41(12Q23.1) MUTATED AMP PEAK 41(12Q23.1) WILD-TYPE 
                             0                             14 
$`AMP PEAK 41(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        18.51        54.21        57.01        10.65 
TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N 
        6.05        17.59        17.46        13.51        12.26        98.56 
TCGA-ET-A3DS TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3WA TCGA-J8-A4HW 
        0.30         1.64         0.99        17.06         2.60 

$`AMP PEAK 41(12Q23.1) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
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        15.48        23.31        18.64         5.75 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
        6.48         0.03         3.45         6.35         7.82         6.18 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
        5.06         8.98         4.93         5.98         0.53         0.10 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
        0.20         0.23        11.38        10.68         0.10         0.39 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.10        20.22        15.42        36.46         5.98        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-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
        4.27         3.22         2.76        17.26        14.07       137.88 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
        3.39         8.71        25.35        13.41        11.90        14.60 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
        7.99        11.01       100.01        13.12         7.99        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
        7.20         1.45         8.88         1.02         5.95        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT 
        7.99         5.33         8.48        10.45         1.51         9.60 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       12.56         8.28         7.69         5.52         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
        8.12         9.34         6.77         9.21         9.44         9.90 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
        8.61        10.09         7.07        10.36        12.43        10.85 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       15.88        15.09        31.04        12.49        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        24.23        17.69        43.00 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       11.34        21.37        12.76        25.02        20.22        30.61 
TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       14.56        19.20         9.83        21.27        20.48        11.93 
TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ 
       22.92        21.01        18.97         7.76         8.32        17.36 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       17.23        27.62        18.21        10.78        10.98        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        30.31        14.04         1.15        22.29        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       14.43        14.70        14.10        14.96         7.69        20.68 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       13.78        13.58        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        80.91         4.18        58.82         1.45        74.30 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       45.40        33.47       108.36        39.32         1.41        30.18 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
      102.84        65.39       124.04        50.37        37.25       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        38.66 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       52.73       139.00       131.15       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        12.16       147.42       130.72       129.57        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      116.91        98.24        41.29        95.38         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN 
       82.82        77.36        78.97        31.50        50.33        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        52.50        45.53        48.16         7.07        44.65 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       45.80        19.30        45.96        37.94        31.04        19.59 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        33.60        28.73        41.13        37.78        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       13.32        11.87         8.71        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I 
       12.36        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        11.74        11.15 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP 
       14.24        16.44        17.88        13.18        23.51         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
       12.30        15.19        10.49        13.15        22.16        13.84 
TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       19.73        12.07        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 
       18.97        15.68        14.14        19.63        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       16.44        16.77        27.95        23.77        16.80        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 
       11.15         7.33        12.53         9.24        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       11.51        16.41        15.62        12.79        70.65        16.90 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        9.01         4.83         8.61         8.38         9.80         5.03 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       37.87        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       29.49        54.05        22.09        16.08        29.19        19.76 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        58.22        13.74        71.01        80.02        65.36 
TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24         5.85         4.18         2.43         5.56        24.72 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       38.30        42.25         2.37         4.50        80.81        69.24 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       59.87        43.50        17.98        25.32       132.36        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
        3.22         7.17         4.80         5.03         2.14         4.01 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
        1.94        73.74        59.70        31.59        44.25        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       102.90        66.77        81.34        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        46.06 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.08         0.89        22.03         0.92        48.10        91.17 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        1.25         1.15        17.82         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3YR 
        4.67        16.57        18.08         0.30         0.76         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        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 
       86.70         6.02        12.43         6.74        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 
        0.72        16.64        32.45         8.71        10.98         5.19 

  AMP PEAK 41(12Q23.1) MUTATED AMP PEAK 41(12Q23.1) WILD-TYPE 
                          0.30                           0.03 
  AMP PEAK 41(12Q23.1) MUTATED AMP PEAK 41(12Q23.1) WILD-TYPE 
                         98.56                         158.83 
  AMP PEAK 41(12Q23.1) MUTATED AMP PEAK 41(12Q23.1) WILD-TYPE 
                         17.06                          16.57 
[1] "0.3 - 98.6 (17.1)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "2.5e+07"
D39V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 41(12Q23.1) MUTATED         7        6         4        0         0
  AMP PEAK 41(12Q23.1) WILD-TYPE     273       45       105        2        45
                                vv
clus                             STAGE IVC
  AMP PEAK 41(12Q23.1) MUTATED           0
  AMP PEAK 41(12Q23.1) WILD-TYPE         6
D39V3, multiclass
           clus
vv          AMP PEAK 41(12Q23.1) MUTATED AMP PEAK 41(12Q23.1) WILD-TYPE
  STAGE I                              7                            273
  STAGE II                             6                             45
  STAGE III                            4                            105
  STAGE IV                             0                              2
  STAGE IVA                            0                             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 41(12Q23.1) MUTATED     5   7   4   0
  AMP PEAK 41(12Q23.1) WILD-TYPE 135 159 161  21
D39V4, multiclass
    clus
vv   AMP PEAK 41(12Q23.1) MUTATED AMP PEAK 41(12Q23.1) WILD-TYPE
  T1                            5                            135
  T2                            7                            159
  T3                            4                            161
  T4                            0                             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"
D39V5, binary
                                cls
clus                               0   1
  AMP PEAK 41(12Q23.1) MUTATED    11   1
  AMP PEAK 41(12Q23.1) WILD-TYPE 212 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 41(12Q23.1) MUTATED     11    1
  AMP PEAK 41(12Q23.1) WILD-TYPE  212  221
   clus
vv  AMP PEAK 41(12Q23.1) MUTATED AMP PEAK 41(12Q23.1) WILD-TYPE
  0                           11                            212
  1                            1                            221
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 41(12Q23.1) MUTATED     3   0  14
  AMP PEAK 41(12Q23.1) WILD-TYPE 270   9 198
D39V6, multiclass
    clus
vv   AMP PEAK 41(12Q23.1) MUTATED AMP PEAK 41(12Q23.1) WILD-TYPE
  M0                            3                            270
  M1                            0                              9
  MX                           14                            198
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                                cls
clus                               0   1
  AMP PEAK 41(12Q23.1) MUTATED    14   3
  AMP PEAK 41(12Q23.1) WILD-TYPE 350 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 41(12Q23.1) MUTATED     14    3
  AMP PEAK 41(12Q23.1) WILD-TYPE  350  128
        clus
vv       AMP PEAK 41(12Q23.1) MUTATED AMP PEAK 41(12Q23.1) WILD-TYPE
  FEMALE                           14                            350
  MALE                              3                            128
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 41(12Q23.1) MUTATED                0
  AMP PEAK 41(12Q23.1) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 41(12Q23.1) MUTATED                                               8
  AMP PEAK 41(12Q23.1) WILD-TYPE                                           345
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 41(12Q23.1) MUTATED                                                                        9
  AMP PEAK 41(12Q23.1) WILD-TYPE                                                                     89
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 41(12Q23.1) MUTATED                                                                     0
  AMP PEAK 41(12Q23.1) WILD-TYPE                                                                  35
D39V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 41(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 41(12Q23.1) WILD-TYPE
  OTHER  SPECIFY                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     345
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             89
  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"
D39V9, binary
                                cls
clus                               0   1
  AMP PEAK 41(12Q23.1) MUTATED     0  17
  AMP PEAK 41(12Q23.1) WILD-TYPE  14 464
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 41(12Q23.1) MUTATED      0   17
  AMP PEAK 41(12Q23.1) WILD-TYPE   14  464
     clus
vv    AMP PEAK 41(12Q23.1) MUTATED AMP PEAK 41(12Q23.1) WILD-TYPE
  NO                             0                             14
  YES                           17                            464
[1] 2 2
[1] FALSE
D39V10, binary
                                cls
clus                               0   1
  AMP PEAK 41(12Q23.1) MUTATED    16   0
  AMP PEAK 41(12Q23.1) WILD-TYPE 401  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 41(12Q23.1) MUTATED     16    0
  AMP PEAK 41(12Q23.1) WILD-TYPE  401   17
     clus
vv    AMP PEAK 41(12Q23.1) MUTATED AMP PEAK 41(12Q23.1) WILD-TYPE
  NO                            16                            401
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 41(12Q23.1) MUTATED              1                       0   16
  AMP PEAK 41(12Q23.1) WILD-TYPE          129                      16  312
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 41(12Q23.1) MUTATED                     0
  AMP PEAK 41(12Q23.1) WILD-TYPE                   1
D39V11, multiclass
                         clus
vv                        AMP PEAK 41(12Q23.1) MUTATED
  MINIMAL (T3)                                       1
  MODERATE/ADVANCED (T4A)                            0
  NONE                                              16
  VERY ADVANCED (T4B)                                0
                         clus
vv                        AMP PEAK 41(12Q23.1) WILD-TYPE
  MINIMAL (T3)                                       129
  MODERATE/ADVANCED (T4A)                             16
  NONE                                               312
  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(12Q23.1) MUTATED    14   1   0   2
  AMP PEAK 41(12Q23.1) WILD-TYPE 364  50   4  28
D39V12, multiclass
    clus
vv   AMP PEAK 41(12Q23.1) MUTATED AMP PEAK 41(12Q23.1) WILD-TYPE
  R0                           14                            364
  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"
D39V13, continuous
D39V14, binary
                                cls
clus                               0   1
  AMP PEAK 41(12Q23.1) MUTATED     9   8
  AMP PEAK 41(12Q23.1) WILD-TYPE 215 253
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 41(12Q23.1) MUTATED      9    8
  AMP PEAK 41(12Q23.1) WILD-TYPE  215  253
            clus
vv           AMP PEAK 41(12Q23.1) MUTATED AMP PEAK 41(12Q23.1) WILD-TYPE
  MULTIFOCAL                            9                            215
  UNIFOCAL                              8                            253
[1] 2 2
[1] FALSE
D39V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 41(12Q23.1) MUTATED                                  0     0
  AMP PEAK 41(12Q23.1) WILD-TYPE                                1    49
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 41(12Q23.1) MUTATED                           0    10
  AMP PEAK 41(12Q23.1) WILD-TYPE                        26   311
D39V16, multiclass
                                  clus
vv                                 AMP PEAK 41(12Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                      10
                                  clus
vv                                 AMP PEAK 41(12Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        49
  BLACK OR AFRICAN AMERICAN                                    26
  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"
D39V17, binary
                                cls
clus                               0   1
  AMP PEAK 41(12Q23.1) MUTATED     0   8
  AMP PEAK 41(12Q23.1) WILD-TYPE  38 342
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 41(12Q23.1) MUTATED      0    8
  AMP PEAK 41(12Q23.1) WILD-TYPE   38  342
                        clus
vv                       AMP PEAK 41(12Q23.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            8
                        clus
vv                       AMP PEAK 41(12Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            342
[1] 2 2
[1] FALSE

Clustering(40) Variable = AMP PEAK 42(13Q14.2) MUTATION ANALYSIS
D40V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 42(13Q14.2) MUTATED     6   0
  AMP PEAK 42(13Q14.2) WILD-TYPE 471  14
  AMP PEAK 42(13Q14.2) MUTATED AMP PEAK 42(13Q14.2) WILD-TYPE 
                             6                            485 
  AMP PEAK 42(13Q14.2) MUTATED AMP PEAK 42(13Q14.2) WILD-TYPE 
                             0                             14 
$`AMP PEAK 42(13Q14.2) MUTATED`
TCGA-BJ-A45E TCGA-CE-A482 TCGA-EL-A4KI TCGA-EM-A1YD TCGA-EM-A2CO TCGA-EM-A2OY 
        0.03        10.68         8.71        57.01         6.05        17.59 

$`AMP PEAK 42(13Q14.2) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
       18.64         5.75         6.48         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A483 TCGA-CE-A484 
        0.10         0.20         0.23        11.38         0.10         0.39 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.10        20.22        15.42        36.46         5.98        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-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
        4.27         3.22         2.76        17.26        14.07       137.88 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
        3.39         8.71        25.35        13.41        11.90        14.60 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        7.99        11.01       100.01        18.51        13.12         7.99 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96         7.20         1.45         8.88         1.02         5.95 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS 
       10.09         7.99         5.33         8.48        10.45         1.51 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY 
        9.60        12.56         8.28         7.69         5.52         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.42         8.12         9.34         6.77         9.21         9.44 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
        9.90         8.61        10.09         7.07        10.36        12.43 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        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        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04         1.15        22.29 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       29.95        13.32        11.87        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YE 
       12.36        18.05        19.79        19.46        54.21        54.08 
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 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         2.99        12.30        15.19        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        13.84        19.73        12.07        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        17.46        18.97        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       19.63        13.38         8.35        16.44        16.77        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        16.80        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        11.15         7.33        12.53 
TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
        9.24        13.91         7.82        11.51        16.41        15.62 
TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       13.51        12.79        70.65        16.90         9.01         4.83 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
        8.61         8.38         9.80         5.03        37.87        12.72 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
        0.95        47.47        48.20        29.69        32.35        14.79 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       12.33        14.79        27.09        18.38        29.49        54.05 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       22.09        12.26        16.08        29.19        19.76         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       58.22        13.74        71.01        80.02        65.36        84.89 
TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       98.56        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24         5.85         4.18         2.43         5.56        24.72 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       38.30        42.25         2.37         4.50        80.81        69.24 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       59.87        43.50         0.30        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        4.01         1.94        73.74        59.70        31.59        44.25 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       102.90        66.77        81.34        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 
       46.06         4.08         0.89        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
       91.17         1.25         1.15        17.82         1.64         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
        1.51         0.76         0.03         4.67        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         6.87         4.14         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
        4.54         0.89         1.35         1.15         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        10.26        16.90         9.80         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        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        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        12.43         6.74        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         0.72 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       16.64        32.45         8.71        10.98         5.19 

  AMP PEAK 42(13Q14.2) MUTATED AMP PEAK 42(13Q14.2) WILD-TYPE 
                          0.03                           0.03 
  AMP PEAK 42(13Q14.2) MUTATED AMP PEAK 42(13Q14.2) WILD-TYPE 
                         57.01                         158.83 
  AMP PEAK 42(13Q14.2) MUTATED AMP PEAK 42(13Q14.2) WILD-TYPE 
                         9.695                         16.640 
[1] "0.0 - 57.0 (9.7)"   "0.0 - 158.8 (16.6)"
[1] "hr="     "3300000"
D40V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 42(13Q14.2) MUTATED         2        3         1        0         0
  AMP PEAK 42(13Q14.2) WILD-TYPE     278       48       108        2        45
                                vv
clus                             STAGE IVC
  AMP PEAK 42(13Q14.2) MUTATED           0
  AMP PEAK 42(13Q14.2) WILD-TYPE         6
D40V3, multiclass
           clus
vv          AMP PEAK 42(13Q14.2) MUTATED AMP PEAK 42(13Q14.2) WILD-TYPE
  STAGE I                              2                            278
  STAGE II                             3                             48
  STAGE III                            1                            108
  STAGE IV                             0                              2
  STAGE IVA                            0                             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(13Q14.2) MUTATED     2   3   1   0
  AMP PEAK 42(13Q14.2) WILD-TYPE 138 163 164  21
D40V4, multiclass
    clus
vv   AMP PEAK 42(13Q14.2) MUTATED AMP PEAK 42(13Q14.2) WILD-TYPE
  T1                            2                            138
  T2                            3                            163
  T3                            1                            164
  T4                            0                             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"
D40V5, binary
                                cls
clus                               0   1
  AMP PEAK 42(13Q14.2) MUTATED     4   1
  AMP PEAK 42(13Q14.2) WILD-TYPE 219 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 42(13Q14.2) MUTATED      4    1
  AMP PEAK 42(13Q14.2) WILD-TYPE  219  221
   clus
vv  AMP PEAK 42(13Q14.2) MUTATED AMP PEAK 42(13Q14.2) WILD-TYPE
  0                            4                            219
  1                            1                            221
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 42(13Q14.2) MUTATED     2   0   4
  AMP PEAK 42(13Q14.2) WILD-TYPE 271   9 208
D40V6, multiclass
    clus
vv   AMP PEAK 42(13Q14.2) MUTATED AMP PEAK 42(13Q14.2) WILD-TYPE
  M0                            2                            271
  M1                            0                              9
  MX                            4                            208
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                                cls
clus                               0   1
  AMP PEAK 42(13Q14.2) MUTATED     5   1
  AMP PEAK 42(13Q14.2) WILD-TYPE 359 130
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 42(13Q14.2) MUTATED      5    1
  AMP PEAK 42(13Q14.2) WILD-TYPE  359  130
        clus
vv       AMP PEAK 42(13Q14.2) MUTATED AMP PEAK 42(13Q14.2) WILD-TYPE
  FEMALE                            5                            359
  MALE                              1                            130
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 42(13Q14.2) MUTATED                0
  AMP PEAK 42(13Q14.2) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 42(13Q14.2) MUTATED                                               3
  AMP PEAK 42(13Q14.2) WILD-TYPE                                           350
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 42(13Q14.2) MUTATED                                                                        3
  AMP PEAK 42(13Q14.2) WILD-TYPE                                                                     95
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 42(13Q14.2) MUTATED                                                                     0
  AMP PEAK 42(13Q14.2) WILD-TYPE                                                                  35
D40V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 42(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 42(13Q14.2) WILD-TYPE
  OTHER  SPECIFY                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     350
  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"
D40V9, binary
                                cls
clus                               0   1
  AMP PEAK 42(13Q14.2) MUTATED     0   6
  AMP PEAK 42(13Q14.2) WILD-TYPE  14 475
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 42(13Q14.2) MUTATED      0    6
  AMP PEAK 42(13Q14.2) WILD-TYPE   14  475
     clus
vv    AMP PEAK 42(13Q14.2) MUTATED AMP PEAK 42(13Q14.2) WILD-TYPE
  NO                             0                             14
  YES                            6                            475
[1] 2 2
[1] FALSE
D40V10, binary
                                cls
clus                               0   1
  AMP PEAK 42(13Q14.2) MUTATED     5   0
  AMP PEAK 42(13Q14.2) WILD-TYPE 412  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 42(13Q14.2) MUTATED      5    0
  AMP PEAK 42(13Q14.2) WILD-TYPE  412   17
     clus
vv    AMP PEAK 42(13Q14.2) MUTATED AMP PEAK 42(13Q14.2) WILD-TYPE
  NO                             5                            412
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 42(13Q14.2) MUTATED              1                       0    4
  AMP PEAK 42(13Q14.2) WILD-TYPE          129                      16  324
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 42(13Q14.2) MUTATED                     0
  AMP PEAK 42(13Q14.2) WILD-TYPE                   1
D40V11, multiclass
                         clus
vv                        AMP PEAK 42(13Q14.2) MUTATED
  MINIMAL (T3)                                       1
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               4
  VERY ADVANCED (T4B)                                0
                         clus
vv                        AMP PEAK 42(13Q14.2) WILD-TYPE
  MINIMAL (T3)                                       129
  MODERATE/ADVANCED (T4A)                             16
  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 42(13Q14.2) MUTATED     5   0   0   0
  AMP PEAK 42(13Q14.2) WILD-TYPE 373  51   4  30
D40V12, multiclass
    clus
vv   AMP PEAK 42(13Q14.2) MUTATED AMP PEAK 42(13Q14.2) WILD-TYPE
  R0                            5                            373
  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 42(13Q14.2) MUTATED     3   3
  AMP PEAK 42(13Q14.2) WILD-TYPE 221 258
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 42(13Q14.2) MUTATED      3    3
  AMP PEAK 42(13Q14.2) WILD-TYPE  221  258
            clus
vv           AMP PEAK 42(13Q14.2) MUTATED AMP PEAK 42(13Q14.2) WILD-TYPE
  MULTIFOCAL                            3                            221
  UNIFOCAL                              3                            258
[1] 2 2
[1] FALSE
D40V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 42(13Q14.2) MUTATED                                  0     1
  AMP PEAK 42(13Q14.2) WILD-TYPE                                1    48
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 42(13Q14.2) MUTATED                           0     2
  AMP PEAK 42(13Q14.2) WILD-TYPE                        26   319
D40V16, multiclass
                                  clus
vv                                 AMP PEAK 42(13Q14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       2
                                  clus
vv                                 AMP PEAK 42(13Q14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        48
  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"
D40V17, binary
                                cls
clus                               0   1
  AMP PEAK 42(13Q14.2) MUTATED     0   3
  AMP PEAK 42(13Q14.2) WILD-TYPE  38 347
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 42(13Q14.2) MUTATED      0    3
  AMP PEAK 42(13Q14.2) WILD-TYPE   38  347
                        clus
vv                       AMP PEAK 42(13Q14.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            3
                        clus
vv                       AMP PEAK 42(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            347
[1] 2 2
[1] FALSE

Clustering(41) Variable = AMP PEAK 43(13Q34) MUTATION ANALYSIS
D41V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 43(13Q34) MUTATED     7   0
  AMP PEAK 43(13Q34) WILD-TYPE 470  14
  AMP PEAK 43(13Q34) MUTATED AMP PEAK 43(13Q34) WILD-TYPE 
                           7                          484 
  AMP PEAK 43(13Q34) MUTATED AMP PEAK 43(13Q34) WILD-TYPE 
                           0                           14 
$`AMP PEAK 43(13Q34) MUTATED`
TCGA-BJ-A45E TCGA-E3-A3DY TCGA-EL-A4KI TCGA-EM-A1YD TCGA-EM-A2CO TCGA-EM-A2OY 
        0.03        31.07         8.71        57.01         6.05        17.59 
TCGA-KS-A4ID 
       33.24 

$`AMP PEAK 43(13Q34) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
       18.64         5.75         6.48         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DZ TCGA-E3-A3E0 
       24.33        54.90        21.53         2.33        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04         1.15        22.29 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       29.95        13.32        11.87        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YE 
       12.36        18.05        19.79        19.46        54.21        54.08 
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 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         2.99        12.30        15.19        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        13.84        19.73        12.07        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        17.46        18.97        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       19.63        13.38         8.35        16.44        16.77        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        16.80        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        11.15         7.33        12.53 
TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
        9.24        13.91         7.82        11.51        16.41        15.62 
TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       13.51        12.79        70.65        16.90         9.01         4.83 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
        8.61         8.38         9.80         5.03        37.87        12.72 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
        0.95        47.47        48.20        29.69        32.35        14.79 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       12.33        14.79        27.09        18.38        29.49        54.05 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       22.09        12.26        16.08        29.19        19.76         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       58.22        13.74        71.01        80.02        65.36        84.89 
TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       98.56        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24         5.85         4.18         2.43         5.56        24.72 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       38.30        42.25         2.37         4.50        80.81        69.24 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       59.87        43.50         0.30        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        4.01         1.94        73.74        59.70        31.59        44.25 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       102.90        66.77        81.34        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 
       46.06         4.08         0.89        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
       91.17         1.25         1.15        17.82         1.64         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
        1.51         0.76         0.03         4.67        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         6.87         4.14         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
        4.54         0.89         1.35         1.15         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        10.26        16.90         9.80         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        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        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        12.43         6.74        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         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

  AMP PEAK 43(13Q34) MUTATED AMP PEAK 43(13Q34) WILD-TYPE 
                        0.03                         0.03 
  AMP PEAK 43(13Q34) MUTATED AMP PEAK 43(13Q34) WILD-TYPE 
                       57.01                       158.83 
  AMP PEAK 43(13Q34) MUTATED AMP PEAK 43(13Q34) WILD-TYPE 
                       17.59                        16.57 
[1] "0.0 - 57.0 (17.6)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "9100000"
D41V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 43(13Q34) MUTATED         3        3         1        0         0
  AMP PEAK 43(13Q34) WILD-TYPE     277       48       108        2        45
                              vv
clus                           STAGE IVC
  AMP PEAK 43(13Q34) MUTATED           0
  AMP PEAK 43(13Q34) WILD-TYPE         6
D41V3, multiclass
           clus
vv          AMP PEAK 43(13Q34) MUTATED AMP PEAK 43(13Q34) WILD-TYPE
  STAGE I                            3                          277
  STAGE II                           3                           48
  STAGE III                          1                          108
  STAGE IV                           0                            2
  STAGE IVA                          0                           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 43(13Q34) MUTATED     2   3   2   0
  AMP PEAK 43(13Q34) WILD-TYPE 138 163 163  21
D41V4, multiclass
    clus
vv   AMP PEAK 43(13Q34) MUTATED AMP PEAK 43(13Q34) WILD-TYPE
  T1                          2                          138
  T2                          3                          163
  T3                          2                          163
  T4                          0                           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"
D41V5, binary
                              cls
clus                             0   1
  AMP PEAK 43(13Q34) MUTATED     5   1
  AMP PEAK 43(13Q34) WILD-TYPE 218 221
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 43(13Q34) MUTATED      5    1
  AMP PEAK 43(13Q34) WILD-TYPE  218  221
   clus
vv  AMP PEAK 43(13Q34) MUTATED AMP PEAK 43(13Q34) WILD-TYPE
  0                          5                          218
  1                          1                          221
[1] 2 2
[1] FALSE
                              vv
clus                            M0  M1  MX
  AMP PEAK 43(13Q34) MUTATED     3   0   4
  AMP PEAK 43(13Q34) WILD-TYPE 270   9 208
D41V6, multiclass
    clus
vv   AMP PEAK 43(13Q34) MUTATED AMP PEAK 43(13Q34) WILD-TYPE
  M0                          3                          270
  M1                          0                            9
  MX                          4                          208
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                              cls
clus                             0   1
  AMP PEAK 43(13Q34) MUTATED     5   2
  AMP PEAK 43(13Q34) WILD-TYPE 359 129
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 43(13Q34) MUTATED      5    2
  AMP PEAK 43(13Q34) WILD-TYPE  359  129
        clus
vv       AMP PEAK 43(13Q34) MUTATED AMP PEAK 43(13Q34) WILD-TYPE
  FEMALE                          5                          359
  MALE                            2                          129
[1] 2 2
[1] FALSE
                              vv
clus                           OTHER  SPECIFY
  AMP PEAK 43(13Q34) MUTATED                1
  AMP PEAK 43(13Q34) WILD-TYPE              8
                              vv
clus                           THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 43(13Q34) MUTATED                                               2
  AMP PEAK 43(13Q34) WILD-TYPE                                           351
                              vv
clus                           THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 43(13Q34) MUTATED                                                                        4
  AMP PEAK 43(13Q34) WILD-TYPE                                                                     94
                              vv
clus                           THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 43(13Q34) MUTATED                                                                     0
  AMP PEAK 43(13Q34) WILD-TYPE                                                                  35
D41V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 43(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 43(13Q34) WILD-TYPE
  OTHER  SPECIFY                                                                                    8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           94
  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"
D41V9, binary
                              cls
clus                             0   1
  AMP PEAK 43(13Q34) MUTATED     0   7
  AMP PEAK 43(13Q34) WILD-TYPE  14 474
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 43(13Q34) MUTATED      0    7
  AMP PEAK 43(13Q34) WILD-TYPE   14  474
     clus
vv    AMP PEAK 43(13Q34) MUTATED AMP PEAK 43(13Q34) WILD-TYPE
  NO                           0                           14
  YES                          7                          474
[1] 2 2
[1] FALSE
D41V10, binary
                              cls
clus                             0   1
  AMP PEAK 43(13Q34) MUTATED     6   0
  AMP PEAK 43(13Q34) WILD-TYPE 411  17
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 43(13Q34) MUTATED      6    0
  AMP PEAK 43(13Q34) WILD-TYPE  411   17
     clus
vv    AMP PEAK 43(13Q34) MUTATED AMP PEAK 43(13Q34) WILD-TYPE
  NO                           6                          411
  YES                          0                           17
[1] 2 2
[1] FALSE
                              vv
clus                           MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 43(13Q34) MUTATED              1                       0    5
  AMP PEAK 43(13Q34) WILD-TYPE          129                      16  323
                              vv
clus                           VERY ADVANCED (T4B)
  AMP PEAK 43(13Q34) MUTATED                     0
  AMP PEAK 43(13Q34) WILD-TYPE                   1
D41V11, multiclass
                         clus
vv                        AMP PEAK 43(13Q34) MUTATED
  MINIMAL (T3)                                     1
  MODERATE/ADVANCED (T4A)                          0
  NONE                                             5
  VERY ADVANCED (T4B)                              0
                         clus
vv                        AMP PEAK 43(13Q34) WILD-TYPE
  MINIMAL (T3)                                     129
  MODERATE/ADVANCED (T4A)                           16
  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 43(13Q34) MUTATED     6   0   0   0
  AMP PEAK 43(13Q34) WILD-TYPE 372  51   4  30
D41V12, multiclass
    clus
vv   AMP PEAK 43(13Q34) MUTATED AMP PEAK 43(13Q34) WILD-TYPE
  R0                          6                          372
  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"
D41V13, continuous
D41V14, binary
                              cls
clus                             0   1
  AMP PEAK 43(13Q34) MUTATED     4   3
  AMP PEAK 43(13Q34) WILD-TYPE 220 258
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 43(13Q34) MUTATED      4    3
  AMP PEAK 43(13Q34) WILD-TYPE  220  258
            clus
vv           AMP PEAK 43(13Q34) MUTATED AMP PEAK 43(13Q34) WILD-TYPE
  MULTIFOCAL                          4                          220
  UNIFOCAL                            3                          258
[1] 2 2
[1] FALSE
D41V15, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 43(13Q34) MUTATED                                  0     0
  AMP PEAK 43(13Q34) WILD-TYPE                                1    49
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 43(13Q34) MUTATED                           0     4
  AMP PEAK 43(13Q34) WILD-TYPE                        26   317
D41V16, multiclass
                                  clus
vv                                 AMP PEAK 43(13Q34) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     0
  BLACK OR AFRICAN AMERICAN                                 0
  WHITE                                                     4
                                  clus
vv                                 AMP PEAK 43(13Q34) 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"
D41V17, binary
                              cls
clus                             0   1
  AMP PEAK 43(13Q34) MUTATED     0   3
  AMP PEAK 43(13Q34) WILD-TYPE  38 347
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 43(13Q34) MUTATED      0    3
  AMP PEAK 43(13Q34) WILD-TYPE   38  347
                        clus
vv                       AMP PEAK 43(13Q34) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                          3
                        clus
vv                       AMP PEAK 43(13Q34) WILD-TYPE
  HISPANIC OR LATINO                               38
  NOT HISPANIC OR LATINO                          347
[1] 2 2
[1] FALSE

Clustering(42) Variable = AMP PEAK 44(14Q12) MUTATION ANALYSIS
D42V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 44(14Q12) MUTATED    13   0
  AMP PEAK 44(14Q12) WILD-TYPE 464  14
  AMP PEAK 44(14Q12) MUTATED AMP PEAK 44(14Q12) WILD-TYPE 
                          13                          478 
  AMP PEAK 44(14Q12) MUTATED AMP PEAK 44(14Q12) WILD-TYPE 
                           0                           14 
$`AMP PEAK 44(14Q12) MUTATED`
TCGA-DJ-A4V5 TCGA-EL-A3ZR TCGA-EL-A4KI TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO 
       24.33        48.16         8.71        57.01        10.65         6.05 
TCGA-EM-A2OY TCGA-EM-A3AI TCGA-ET-A39N TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-J8-A3YG 
       17.59        17.46        98.56         1.64         0.99        22.29 
TCGA-KS-A4I9 
       87.39 

$`AMP PEAK 44(14Q12) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        5.52         8.78         8.42         8.12         9.34         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
        9.21         9.44         9.90         8.61        10.09         7.07 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       10.36        12.43        10.85        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        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 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       15.81        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
        1.45        74.30        45.40        33.47       108.36        39.32 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        30.18       102.84        65.39       124.04        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       37.25       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        38.66        52.73       139.00       131.15       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        12.16       147.42       130.72 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       116.91        98.24        41.29        95.38 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS 
       50.33        53.06        47.38        52.50        45.53         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       29.95        13.32        11.87        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YE 
       12.36        18.05        19.79        19.46        54.21        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        11.74 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.15        14.24        16.44        17.88        13.18        23.51 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        2.99        12.30        15.19        10.49        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       13.84        19.73        12.07        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        18.97        15.68        14.14        19.63        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        16.44        16.77        27.95        23.77        16.80 
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        11.15         7.33        12.53         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        16.41        15.62        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        9.80         5.03        37.87        12.72         0.95        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
       71.01        80.02        65.36        84.89        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        2.43         5.56        24.72        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       59.70        31.59        44.25        24.69        68.22       102.90 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77        81.34        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        46.06         4.08         0.89 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10        91.17         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
       17.82         1.51         0.76         0.03         4.67        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         6.87         4.14 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58         4.54         0.89         1.35         1.15         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        10.26        16.90         9.80 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
        9.63         2.96         8.65        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        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4IB TCGA-KS-A4IC 
        6.02        12.43         6.74        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         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

  AMP PEAK 44(14Q12) MUTATED AMP PEAK 44(14Q12) WILD-TYPE 
                        0.99                         0.03 
  AMP PEAK 44(14Q12) MUTATED AMP PEAK 44(14Q12) WILD-TYPE 
                       98.56                       158.83 
  AMP PEAK 44(14Q12) MUTATED AMP PEAK 44(14Q12) WILD-TYPE 
                      17.590                       16.505 
[1] "1.0 - 98.6 (17.6)"  "0.0 - 158.8 (16.5)"
[1] "hr="     "2.6e+07"
D42V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 44(14Q12) MUTATED         3        5         4        0         1
  AMP PEAK 44(14Q12) WILD-TYPE     277       46       105        2        44
                              vv
clus                           STAGE IVC
  AMP PEAK 44(14Q12) MUTATED           0
  AMP PEAK 44(14Q12) WILD-TYPE         6
D42V3, multiclass
           clus
vv          AMP PEAK 44(14Q12) MUTATED AMP PEAK 44(14Q12) WILD-TYPE
  STAGE I                            3                          277
  STAGE II                           5                           46
  STAGE III                          4                          105
  STAGE IV                           0                            2
  STAGE IVA                          1                           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 44(14Q12) MUTATED     2   6   5   0
  AMP PEAK 44(14Q12) WILD-TYPE 138 160 160  21
D42V4, multiclass
    clus
vv   AMP PEAK 44(14Q12) MUTATED AMP PEAK 44(14Q12) WILD-TYPE
  T1                          2                          138
  T2                          6                          160
  T3                          5                          160
  T4                          0                           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"
D42V5, binary
                              cls
clus                             0   1
  AMP PEAK 44(14Q12) MUTATED     8   2
  AMP PEAK 44(14Q12) WILD-TYPE 215 220
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 44(14Q12) MUTATED      8    2
  AMP PEAK 44(14Q12) WILD-TYPE  215  220
   clus
vv  AMP PEAK 44(14Q12) MUTATED AMP PEAK 44(14Q12) WILD-TYPE
  0                          8                          215
  1                          2                          220
[1] 2 2
[1] FALSE
                              vv
clus                            M0  M1  MX
  AMP PEAK 44(14Q12) MUTATED     4   0   9
  AMP PEAK 44(14Q12) WILD-TYPE 269   9 203
D42V6, multiclass
    clus
vv   AMP PEAK 44(14Q12) MUTATED AMP PEAK 44(14Q12) WILD-TYPE
  M0                          4                          269
  M1                          0                            9
  MX                          9                          203
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                              cls
clus                             0   1
  AMP PEAK 44(14Q12) MUTATED    11   2
  AMP PEAK 44(14Q12) WILD-TYPE 353 129
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 44(14Q12) MUTATED     11    2
  AMP PEAK 44(14Q12) WILD-TYPE  353  129
        clus
vv       AMP PEAK 44(14Q12) MUTATED AMP PEAK 44(14Q12) WILD-TYPE
  FEMALE                         11                          353
  MALE                            2                          129
[1] 2 2
[1] FALSE
                              vv
clus                           OTHER  SPECIFY
  AMP PEAK 44(14Q12) MUTATED                0
  AMP PEAK 44(14Q12) WILD-TYPE              9
                              vv
clus                           THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 44(14Q12) MUTATED                                               7
  AMP PEAK 44(14Q12) WILD-TYPE                                           346
                              vv
clus                           THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 44(14Q12) MUTATED                                                                        6
  AMP PEAK 44(14Q12) WILD-TYPE                                                                     92
                              vv
clus                           THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 44(14Q12) MUTATED                                                                     0
  AMP PEAK 44(14Q12) WILD-TYPE                                                                  35
D42V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 44(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 44(14Q12) WILD-TYPE
  OTHER  SPECIFY                                                                                    9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   346
  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"
D42V9, binary
                              cls
clus                             0   1
  AMP PEAK 44(14Q12) MUTATED     0  13
  AMP PEAK 44(14Q12) WILD-TYPE  14 468
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 44(14Q12) MUTATED      0   13
  AMP PEAK 44(14Q12) WILD-TYPE   14  468
     clus
vv    AMP PEAK 44(14Q12) MUTATED AMP PEAK 44(14Q12) WILD-TYPE
  NO                           0                           14
  YES                         13                          468
[1] 2 2
[1] FALSE
D42V10, binary
                              cls
clus                             0   1
  AMP PEAK 44(14Q12) MUTATED    11   0
  AMP PEAK 44(14Q12) WILD-TYPE 406  17
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 44(14Q12) MUTATED     11    0
  AMP PEAK 44(14Q12) WILD-TYPE  406   17
     clus
vv    AMP PEAK 44(14Q12) MUTATED AMP PEAK 44(14Q12) WILD-TYPE
  NO                          11                          406
  YES                          0                           17
[1] 2 2
[1] FALSE
                              vv
clus                           MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 44(14Q12) MUTATED              3                       0   10
  AMP PEAK 44(14Q12) WILD-TYPE          127                      16  318
                              vv
clus                           VERY ADVANCED (T4B)
  AMP PEAK 44(14Q12) MUTATED                     0
  AMP PEAK 44(14Q12) WILD-TYPE                   1
D42V11, multiclass
                         clus
vv                        AMP PEAK 44(14Q12) MUTATED
  MINIMAL (T3)                                     3
  MODERATE/ADVANCED (T4A)                          0
  NONE                                            10
  VERY ADVANCED (T4B)                              0
                         clus
vv                        AMP PEAK 44(14Q12) WILD-TYPE
  MINIMAL (T3)                                     127
  MODERATE/ADVANCED (T4A)                           16
  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
  AMP PEAK 44(14Q12) MUTATED    12   0   0   1
  AMP PEAK 44(14Q12) WILD-TYPE 366  51   4  29
D42V12, multiclass
    clus
vv   AMP PEAK 44(14Q12) MUTATED AMP PEAK 44(14Q12) WILD-TYPE
  R0                         12                          366
  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 44(14Q12) MUTATED     8   5
  AMP PEAK 44(14Q12) WILD-TYPE 216 256
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 44(14Q12) MUTATED      8    5
  AMP PEAK 44(14Q12) WILD-TYPE  216  256
            clus
vv           AMP PEAK 44(14Q12) MUTATED AMP PEAK 44(14Q12) WILD-TYPE
  MULTIFOCAL                          8                          216
  UNIFOCAL                            5                          256
[1] 2 2
[1] FALSE
D42V15, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 44(14Q12) MUTATED                                  0     0
  AMP PEAK 44(14Q12) WILD-TYPE                                1    49
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 44(14Q12) MUTATED                           1     7
  AMP PEAK 44(14Q12) WILD-TYPE                        25   314
D42V16, multiclass
                                  clus
vv                                 AMP PEAK 44(14Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     0
  BLACK OR AFRICAN AMERICAN                                 1
  WHITE                                                     7
                                  clus
vv                                 AMP PEAK 44(14Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      49
  BLACK OR AFRICAN AMERICAN                                  25
  WHITE                                                     314
[1] 4 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 44(14Q12) MUTATED     0   6
  AMP PEAK 44(14Q12) WILD-TYPE  38 344
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 44(14Q12) MUTATED      0    6
  AMP PEAK 44(14Q12) WILD-TYPE   38  344
                        clus
vv                       AMP PEAK 44(14Q12) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                          6
                        clus
vv                       AMP PEAK 44(14Q12) WILD-TYPE
  HISPANIC OR LATINO                               38
  NOT HISPANIC OR LATINO                          344
[1] 2 2
[1] FALSE

Clustering(43) Variable = AMP PEAK 45(14Q32.31) MUTATION ANALYSIS
D43V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 45(14Q32.31) MUTATED    13   0
  AMP PEAK 45(14Q32.31) WILD-TYPE 464  14
  AMP PEAK 45(14Q32.31) MUTATED AMP PEAK 45(14Q32.31) WILD-TYPE 
                             13                             478 
  AMP PEAK 45(14Q32.31) MUTATED AMP PEAK 45(14Q32.31) WILD-TYPE 
                              0                              14 
$`AMP PEAK 45(14Q32.31) MUTATED`
TCGA-EL-A3ZR TCGA-EL-A4KI TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A2CO TCGA-EM-A2OY 
       48.16         8.71        57.01        10.65         6.05        17.59 
TCGA-EM-A2P2 TCGA-EM-A3AI TCGA-ET-A39N TCGA-ET-A4KN TCGA-FY-A3I5 TCGA-FY-A3NM 
       17.29        17.46        98.56         4.01         1.64         0.99 
TCGA-J8-A3YG 
       22.29 

$`AMP PEAK 45(14Q32.31) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        5.52         8.78         8.42         8.12         9.34         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
        9.21         9.44         9.90         8.61        10.09         7.07 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       10.36        12.43        10.85        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        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 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.07        14.27         3.02        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        13.78        13.58        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        80.91         4.18 
TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 
       58.82         1.45        74.30        45.40        33.47       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
       39.32         1.41        30.18       102.84        65.39       124.04 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        37.25       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        38.66        52.73       139.00       131.15 
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        12.16       147.42 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      130.72       129.57        32.48       116.91        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
       95.38         5.72        66.90        82.82        77.36        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       31.50        50.33        53.06        47.38        52.50        45.53 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT 
       37.78        29.95        13.32        11.87        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        12.36        18.05        19.79        19.46        54.21 
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 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         2.99        12.30        15.19        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        13.84        19.73        12.07        17.59        17.46 
TCGA-EM-A2P3 TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       14.60        18.97        15.68        14.14        19.63        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        16.44        16.77        27.95        23.77        16.80 
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        11.15         7.33        12.53         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        16.41        15.62        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        9.80         5.03        37.87        12.72         0.95        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
       71.01        80.02        65.36        84.89        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        2.43         5.56        24.72        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        4.80         5.03         2.14         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        24.69        68.22       102.90        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       81.34        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        46.06         4.08         0.89        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10        91.17         1.25         1.15        17.82 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
        1.51         0.76         0.03         4.67        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         6.87         4.14         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
        4.54         0.89         1.35         1.15         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        10.26        16.90         9.80         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        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        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       12.43         6.74        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         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

  AMP PEAK 45(14Q32.31) MUTATED AMP PEAK 45(14Q32.31) WILD-TYPE 
                           0.99                            0.03 
  AMP PEAK 45(14Q32.31) MUTATED AMP PEAK 45(14Q32.31) WILD-TYPE 
                          98.56                          158.83 
  AMP PEAK 45(14Q32.31) MUTATED AMP PEAK 45(14Q32.31) WILD-TYPE 
                          17.29                           16.57 
[1] "1.0 - 98.6 (17.3)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "2.5e+07"
D43V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 45(14Q32.31) MUTATED         2        5         6        0         0
  AMP PEAK 45(14Q32.31) WILD-TYPE     278       46       103        2        45
                                 vv
clus                              STAGE IVC
  AMP PEAK 45(14Q32.31) MUTATED           0
  AMP PEAK 45(14Q32.31) WILD-TYPE         6
D43V3, multiclass
           clus
vv          AMP PEAK 45(14Q32.31) MUTATED AMP PEAK 45(14Q32.31) WILD-TYPE
  STAGE I                               2                             278
  STAGE II                              5                              46
  STAGE III                             6                             103
  STAGE IV                              0                               2
  STAGE IVA                             0                              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 45(14Q32.31) MUTATED     1   6   6   0
  AMP PEAK 45(14Q32.31) WILD-TYPE 139 160 159  21
D43V4, multiclass
    clus
vv   AMP PEAK 45(14Q32.31) MUTATED AMP PEAK 45(14Q32.31) WILD-TYPE
  T1                             1                             139
  T2                             6                             160
  T3                             6                             159
  T4                             0                              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"
D43V5, binary
                                 cls
clus                                0   1
  AMP PEAK 45(14Q32.31) MUTATED     9   1
  AMP PEAK 45(14Q32.31) WILD-TYPE 214 221
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 45(14Q32.31) MUTATED      9    1
  AMP PEAK 45(14Q32.31) WILD-TYPE  214  221
   clus
vv  AMP PEAK 45(14Q32.31) MUTATED AMP PEAK 45(14Q32.31) WILD-TYPE
  0                             9                             214
  1                             1                             221
[1] 2 2
[1] FALSE
                                 vv
clus                               M0  M1  MX
  AMP PEAK 45(14Q32.31) MUTATED     2   0  11
  AMP PEAK 45(14Q32.31) WILD-TYPE 271   9 201
D43V6, multiclass
    clus
vv   AMP PEAK 45(14Q32.31) MUTATED AMP PEAK 45(14Q32.31) WILD-TYPE
  M0                             2                             271
  M1                             0                               9
  MX                            11                             201
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                                 cls
clus                                0   1
  AMP PEAK 45(14Q32.31) MUTATED    11   2
  AMP PEAK 45(14Q32.31) WILD-TYPE 353 129
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 45(14Q32.31) MUTATED     11    2
  AMP PEAK 45(14Q32.31) WILD-TYPE  353  129
        clus
vv       AMP PEAK 45(14Q32.31) MUTATED AMP PEAK 45(14Q32.31) WILD-TYPE
  FEMALE                            11                             353
  MALE                               2                             129
[1] 2 2
[1] FALSE
                                 vv
clus                              OTHER  SPECIFY
  AMP PEAK 45(14Q32.31) MUTATED                0
  AMP PEAK 45(14Q32.31) WILD-TYPE              9
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 45(14Q32.31) MUTATED                                               5
  AMP PEAK 45(14Q32.31) WILD-TYPE                                           348
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 45(14Q32.31) MUTATED                                                                        7
  AMP PEAK 45(14Q32.31) WILD-TYPE                                                                     91
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 45(14Q32.31) MUTATED                                                                     1
  AMP PEAK 45(14Q32.31) WILD-TYPE                                                                  34
D43V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 45(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 45(14Q32.31) WILD-TYPE
  OTHER  SPECIFY                                                                                       9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      348
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                              91
  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"
D43V9, binary
                                 cls
clus                                0   1
  AMP PEAK 45(14Q32.31) MUTATED     0  13
  AMP PEAK 45(14Q32.31) WILD-TYPE  14 468
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 45(14Q32.31) MUTATED      0   13
  AMP PEAK 45(14Q32.31) WILD-TYPE   14  468
     clus
vv    AMP PEAK 45(14Q32.31) MUTATED AMP PEAK 45(14Q32.31) WILD-TYPE
  NO                              0                              14
  YES                            13                             468
[1] 2 2
[1] FALSE
D43V10, binary
                                 cls
clus                                0   1
  AMP PEAK 45(14Q32.31) MUTATED    12   0
  AMP PEAK 45(14Q32.31) WILD-TYPE 405  17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 45(14Q32.31) MUTATED     12    0
  AMP PEAK 45(14Q32.31) WILD-TYPE  405   17
     clus
vv    AMP PEAK 45(14Q32.31) MUTATED AMP PEAK 45(14Q32.31) WILD-TYPE
  NO                             12                             405
  YES                             0                              17
[1] 2 2
[1] FALSE
                                 vv
clus                              MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 45(14Q32.31) MUTATED              3                       0   10
  AMP PEAK 45(14Q32.31) WILD-TYPE          127                      16  318
                                 vv
clus                              VERY ADVANCED (T4B)
  AMP PEAK 45(14Q32.31) MUTATED                     0
  AMP PEAK 45(14Q32.31) WILD-TYPE                   1
D43V11, multiclass
                         clus
vv                        AMP PEAK 45(14Q32.31) MUTATED
  MINIMAL (T3)                                        3
  MODERATE/ADVANCED (T4A)                             0
  NONE                                               10
  VERY ADVANCED (T4B)                                 0
                         clus
vv                        AMP PEAK 45(14Q32.31) WILD-TYPE
  MINIMAL (T3)                                        127
  MODERATE/ADVANCED (T4A)                              16
  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
  AMP PEAK 45(14Q32.31) MUTATED    12   0   0   1
  AMP PEAK 45(14Q32.31) WILD-TYPE 366  51   4  29
D43V12, multiclass
    clus
vv   AMP PEAK 45(14Q32.31) MUTATED AMP PEAK 45(14Q32.31) WILD-TYPE
  R0                            12                             366
  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 45(14Q32.31) MUTATED     9   4
  AMP PEAK 45(14Q32.31) WILD-TYPE 215 257
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 45(14Q32.31) MUTATED      9    4
  AMP PEAK 45(14Q32.31) WILD-TYPE  215  257
            clus
vv           AMP PEAK 45(14Q32.31) MUTATED AMP PEAK 45(14Q32.31) WILD-TYPE
  MULTIFOCAL                             9                             215
  UNIFOCAL                               4                             257
[1] 2 2
[1] FALSE
D43V15, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 45(14Q32.31) MUTATED                                  0     0
  AMP PEAK 45(14Q32.31) WILD-TYPE                                1    49
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 45(14Q32.31) MUTATED                           0     7
  AMP PEAK 45(14Q32.31) WILD-TYPE                        26   314
D43V16, multiclass
                                  clus
vv                                 AMP PEAK 45(14Q32.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                    0
  WHITE                                                        7
                                  clus
vv                                 AMP PEAK 45(14Q32.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         49
  BLACK OR AFRICAN AMERICAN                                     26
  WHITE                                                        314
[1] 4 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 45(14Q32.31) MUTATED     0   5
  AMP PEAK 45(14Q32.31) WILD-TYPE  38 345
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 45(14Q32.31) MUTATED      0    5
  AMP PEAK 45(14Q32.31) WILD-TYPE   38  345
                        clus
vv                       AMP PEAK 45(14Q32.31) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                             5
                        clus
vv                       AMP PEAK 45(14Q32.31) WILD-TYPE
  HISPANIC OR LATINO                                  38
  NOT HISPANIC OR LATINO                             345
[1] 2 2
[1] FALSE

Clustering(44) Variable = AMP PEAK 48(18Q12.1) MUTATION ANALYSIS
D44V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 48(18Q12.1) MUTATED     7   0
  AMP PEAK 48(18Q12.1) WILD-TYPE 470  14
  AMP PEAK 48(18Q12.1) MUTATED AMP PEAK 48(18Q12.1) WILD-TYPE 
                             7                            484 
  AMP PEAK 48(18Q12.1) MUTATED AMP PEAK 48(18Q12.1) WILD-TYPE 
                             0                             14 
$`AMP PEAK 48(18Q12.1) MUTATED`
TCGA-BJ-A45E TCGA-CE-A484 TCGA-EL-A3ZR TCGA-EL-A4KI TCGA-ET-A2MZ TCGA-ET-A39N 
        0.03         0.39        48.16         8.71        12.26        98.56 
TCGA-FY-A3I5 
        1.64 

$`AMP PEAK 48(18Q12.1) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
       18.64         5.75         6.48         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.10        20.22        15.42        36.46         5.98        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-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
        4.27         3.22         2.76        17.26        14.07       137.88 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
        3.39         8.71        25.35        13.41        11.90        14.60 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        7.99        11.01       100.01        18.51        13.12         7.99 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96         7.20         1.45         8.88         1.02         5.95 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS 
       10.09         7.99         5.33         8.48        10.45         1.51 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY 
        9.60        12.56         8.28         7.69         5.52         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.42         8.12         9.34         6.77         9.21         9.44 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
        9.90         8.61        10.09         7.07        10.36        12.43 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        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        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04         1.15        22.29 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT 
       53.06        47.38        52.50        45.53         7.07        44.65 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       45.80        19.30        45.96        37.94        31.04        19.59 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        33.60        28.73        41.13        37.78        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       13.32        11.87        26.86        18.18        20.91        12.36 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
       18.05        19.79        19.46        54.21        57.01        54.08 
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 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT 
       23.51         6.05         2.99        12.30        15.19        10.49 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        13.84        19.73        17.59        12.07 
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        17.46        18.97 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        19.63        13.38         8.35        16.44 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       16.77        27.95        23.77        16.80        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        11.15 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33        12.53         9.24        13.91         7.82        11.51 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       16.41        15.62        13.51        12.79        70.65        16.90 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        9.01         4.83         8.61         8.38         9.80         5.03 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       37.87        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       29.49        54.05        22.09        16.08        29.19        19.76 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        58.22        13.74        71.01        80.02        65.36 
TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24         5.85         4.18         2.43         5.56        24.72 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       38.30        42.25         2.37         4.50        80.81        69.24 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       59.87        43.50         0.30        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        4.01         1.94        73.74        59.70        31.59        44.25 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       102.90        66.77        81.34        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 
       46.06         4.08         0.89        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON 
       91.17         1.25         1.15        17.82         0.99         1.51 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        0.76         0.03         4.67        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         6.87         4.14         6.58         4.54 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
        0.89         1.35         1.15         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        10.26        16.90         9.80         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        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        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       12.43         6.74        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         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

  AMP PEAK 48(18Q12.1) MUTATED AMP PEAK 48(18Q12.1) WILD-TYPE 
                          0.03                           0.03 
  AMP PEAK 48(18Q12.1) MUTATED AMP PEAK 48(18Q12.1) WILD-TYPE 
                         98.56                         158.83 
  AMP PEAK 48(18Q12.1) MUTATED AMP PEAK 48(18Q12.1) WILD-TYPE 
                         8.710                         16.685 
[1] "0.0 - 98.6 (8.7)"   "0.0 - 158.8 (16.7)"
[1] "hr="     "9200000"
D44V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 48(18Q12.1) MUTATED         4        1         2        0         0
  AMP PEAK 48(18Q12.1) WILD-TYPE     276       50       107        2        45
                                vv
clus                             STAGE IVC
  AMP PEAK 48(18Q12.1) MUTATED           0
  AMP PEAK 48(18Q12.1) WILD-TYPE         6
D44V3, multiclass
           clus
vv          AMP PEAK 48(18Q12.1) MUTATED AMP PEAK 48(18Q12.1) WILD-TYPE
  STAGE I                              4                            276
  STAGE II                             1                             50
  STAGE III                            2                            107
  STAGE IV                             0                              2
  STAGE IVA                            0                             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 48(18Q12.1) MUTATED     2   2   3   0
  AMP PEAK 48(18Q12.1) WILD-TYPE 138 164 162  21
D44V4, multiclass
    clus
vv   AMP PEAK 48(18Q12.1) MUTATED AMP PEAK 48(18Q12.1) WILD-TYPE
  T1                            2                            138
  T2                            2                            164
  T3                            3                            162
  T4                            0                             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"
D44V5, binary
                                cls
clus                               0   1
  AMP PEAK 48(18Q12.1) MUTATED     5   1
  AMP PEAK 48(18Q12.1) WILD-TYPE 218 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 48(18Q12.1) MUTATED      5    1
  AMP PEAK 48(18Q12.1) WILD-TYPE  218  221
   clus
vv  AMP PEAK 48(18Q12.1) MUTATED AMP PEAK 48(18Q12.1) WILD-TYPE
  0                            5                            218
  1                            1                            221
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 48(18Q12.1) MUTATED     3   0   4
  AMP PEAK 48(18Q12.1) WILD-TYPE 270   9 208
D44V6, multiclass
    clus
vv   AMP PEAK 48(18Q12.1) MUTATED AMP PEAK 48(18Q12.1) WILD-TYPE
  M0                            3                            270
  M1                            0                              9
  MX                            4                            208
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                                cls
clus                               0   1
  AMP PEAK 48(18Q12.1) MUTATED     5   2
  AMP PEAK 48(18Q12.1) WILD-TYPE 359 129
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 48(18Q12.1) MUTATED      5    2
  AMP PEAK 48(18Q12.1) WILD-TYPE  359  129
        clus
vv       AMP PEAK 48(18Q12.1) MUTATED AMP PEAK 48(18Q12.1) WILD-TYPE
  FEMALE                            5                            359
  MALE                              2                            129
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 48(18Q12.1) MUTATED                0
  AMP PEAK 48(18Q12.1) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 48(18Q12.1) MUTATED                                               6
  AMP PEAK 48(18Q12.1) WILD-TYPE                                           347
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 48(18Q12.1) MUTATED                                                                        1
  AMP PEAK 48(18Q12.1) WILD-TYPE                                                                     97
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 48(18Q12.1) MUTATED                                                                     0
  AMP PEAK 48(18Q12.1) WILD-TYPE                                                                  35
D44V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 48(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 48(18Q12.1) WILD-TYPE
  OTHER  SPECIFY                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     347
  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"
D44V9, binary
                                cls
clus                               0   1
  AMP PEAK 48(18Q12.1) MUTATED     0   7
  AMP PEAK 48(18Q12.1) WILD-TYPE  14 474
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 48(18Q12.1) MUTATED      0    7
  AMP PEAK 48(18Q12.1) WILD-TYPE   14  474
     clus
vv    AMP PEAK 48(18Q12.1) MUTATED AMP PEAK 48(18Q12.1) WILD-TYPE
  NO                             0                             14
  YES                            7                            474
[1] 2 2
[1] FALSE
D44V10, binary
                                cls
clus                               0   1
  AMP PEAK 48(18Q12.1) MUTATED     5   0
  AMP PEAK 48(18Q12.1) WILD-TYPE 412  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 48(18Q12.1) MUTATED      5    0
  AMP PEAK 48(18Q12.1) WILD-TYPE  412   17
     clus
vv    AMP PEAK 48(18Q12.1) MUTATED AMP PEAK 48(18Q12.1) WILD-TYPE
  NO                             5                            412
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 48(18Q12.1) MUTATED              1                       0    5
  AMP PEAK 48(18Q12.1) WILD-TYPE          129                      16  323
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 48(18Q12.1) MUTATED                     0
  AMP PEAK 48(18Q12.1) WILD-TYPE                   1
D44V11, multiclass
                         clus
vv                        AMP PEAK 48(18Q12.1) MUTATED
  MINIMAL (T3)                                       1
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               5
  VERY ADVANCED (T4B)                                0
                         clus
vv                        AMP PEAK 48(18Q12.1) WILD-TYPE
  MINIMAL (T3)                                       129
  MODERATE/ADVANCED (T4A)                             16
  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 48(18Q12.1) MUTATED     5   0   0   1
  AMP PEAK 48(18Q12.1) WILD-TYPE 373  51   4  29
D44V12, multiclass
    clus
vv   AMP PEAK 48(18Q12.1) MUTATED AMP PEAK 48(18Q12.1) WILD-TYPE
  R0                            5                            373
  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"
D44V13, continuous
D44V14, binary
                                cls
clus                               0   1
  AMP PEAK 48(18Q12.1) MUTATED     2   5
  AMP PEAK 48(18Q12.1) WILD-TYPE 222 256
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 48(18Q12.1) MUTATED      2    5
  AMP PEAK 48(18Q12.1) WILD-TYPE  222  256
            clus
vv           AMP PEAK 48(18Q12.1) MUTATED AMP PEAK 48(18Q12.1) WILD-TYPE
  MULTIFOCAL                            2                            222
  UNIFOCAL                              5                            256
[1] 2 2
[1] FALSE
D44V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 48(18Q12.1) MUTATED                                  0     1
  AMP PEAK 48(18Q12.1) WILD-TYPE                                1    48
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 48(18Q12.1) MUTATED                           0     6
  AMP PEAK 48(18Q12.1) WILD-TYPE                        26   315
D44V16, multiclass
                                  clus
vv                                 AMP PEAK 48(18Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       6
                                  clus
vv                                 AMP PEAK 48(18Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        48
  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"
D44V17, binary
                                cls
clus                               0   1
  AMP PEAK 48(18Q12.1) MUTATED     0   7
  AMP PEAK 48(18Q12.1) WILD-TYPE  38 343
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 48(18Q12.1) MUTATED      0    7
  AMP PEAK 48(18Q12.1) WILD-TYPE   38  343
                        clus
vv                       AMP PEAK 48(18Q12.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            7
                        clus
vv                       AMP PEAK 48(18Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            343
[1] 2 2
[1] FALSE

Clustering(45) Variable = AMP PEAK 49(18Q22.1) MUTATION ANALYSIS
D45V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 49(18Q22.1) MUTATED     7   0
  AMP PEAK 49(18Q22.1) WILD-TYPE 470  14
  AMP PEAK 49(18Q22.1) MUTATED AMP PEAK 49(18Q22.1) WILD-TYPE 
                             7                            484 
  AMP PEAK 49(18Q22.1) MUTATED AMP PEAK 49(18Q22.1) WILD-TYPE 
                             0                             14 
$`AMP PEAK 49(18Q22.1) MUTATED`
TCGA-BJ-A45E TCGA-EL-A3ZR TCGA-EL-A4KI TCGA-EM-A3AN TCGA-ET-A2MZ TCGA-ET-A39N 
        0.03        48.16         8.71        19.63        12.26        98.56 
TCGA-FY-A3I5 
        1.64 

$`AMP PEAK 49(18Q22.1) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
       18.64         5.75         6.48         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
        1.45        74.30        45.40        33.47       108.36        39.32 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        30.18       102.84        65.39       124.04        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       37.25       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        38.66        52.73       139.00       131.15       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        12.16       147.42       130.72 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       116.91        98.24        41.29        95.38 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS 
       50.33        53.06        47.38        52.50        45.53         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       29.95        13.32        11.87        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
       12.36        18.05        19.79        19.46        54.21        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        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       10.49        13.15        22.16        13.84        19.73        17.59 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       12.07        17.59        17.46        17.29        14.60        17.46 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       18.97        15.68        14.14        13.38         8.35        16.44 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       16.77        27.95        23.77        16.80        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        11.15 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33        12.53         9.24        13.91         7.82        11.51 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       16.41        15.62        13.51        12.79        70.65        16.90 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        9.01         4.83         8.61         8.38         9.80         5.03 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       37.87        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       29.49        54.05        22.09        16.08        29.19        19.76 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        58.22        13.74        71.01        80.02        65.36 
TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24         5.85         4.18         2.43         5.56        24.72 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       38.30        42.25         2.37         4.50        80.81        69.24 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       59.87        43.50         0.30        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        4.01         1.94        73.74        59.70        31.59        44.25 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       102.90        66.77        81.34        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 
       46.06         4.08         0.89        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON 
       91.17         1.25         1.15        17.82         0.99         1.51 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        0.76         0.03         4.67        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         6.87         4.14         6.58         4.54 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
        0.89         1.35         1.15         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        10.26        16.90         9.80         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        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        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       12.43         6.74        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         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

  AMP PEAK 49(18Q22.1) MUTATED AMP PEAK 49(18Q22.1) WILD-TYPE 
                          0.03                           0.03 
  AMP PEAK 49(18Q22.1) MUTATED AMP PEAK 49(18Q22.1) WILD-TYPE 
                         98.56                         158.83 
  AMP PEAK 49(18Q22.1) MUTATED AMP PEAK 49(18Q22.1) WILD-TYPE 
                        12.260                         16.605 
[1] "0.0 - 98.6 (12.3)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "9200000"
D45V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 49(18Q22.1) MUTATED         4        1         2        0         0
  AMP PEAK 49(18Q22.1) WILD-TYPE     276       50       107        2        45
                                vv
clus                             STAGE IVC
  AMP PEAK 49(18Q22.1) MUTATED           0
  AMP PEAK 49(18Q22.1) WILD-TYPE         6
D45V3, multiclass
           clus
vv          AMP PEAK 49(18Q22.1) MUTATED AMP PEAK 49(18Q22.1) WILD-TYPE
  STAGE I                              4                            276
  STAGE II                             1                             50
  STAGE III                            2                            107
  STAGE IV                             0                              2
  STAGE IVA                            0                             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 49(18Q22.1) MUTATED     3   1   3   0
  AMP PEAK 49(18Q22.1) WILD-TYPE 137 165 162  21
D45V4, multiclass
    clus
vv   AMP PEAK 49(18Q22.1) MUTATED AMP PEAK 49(18Q22.1) WILD-TYPE
  T1                            3                            137
  T2                            1                            165
  T3                            3                            162
  T4                            0                             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"
D45V5, binary
                                cls
clus                               0   1
  AMP PEAK 49(18Q22.1) MUTATED     5   1
  AMP PEAK 49(18Q22.1) WILD-TYPE 218 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 49(18Q22.1) MUTATED      5    1
  AMP PEAK 49(18Q22.1) WILD-TYPE  218  221
   clus
vv  AMP PEAK 49(18Q22.1) MUTATED AMP PEAK 49(18Q22.1) WILD-TYPE
  0                            5                            218
  1                            1                            221
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 49(18Q22.1) MUTATED     2   0   5
  AMP PEAK 49(18Q22.1) WILD-TYPE 271   9 207
D45V6, multiclass
    clus
vv   AMP PEAK 49(18Q22.1) MUTATED AMP PEAK 49(18Q22.1) WILD-TYPE
  M0                            2                            271
  M1                            0                              9
  MX                            5                            207
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                                cls
clus                               0   1
  AMP PEAK 49(18Q22.1) MUTATED     5   2
  AMP PEAK 49(18Q22.1) WILD-TYPE 359 129
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 49(18Q22.1) MUTATED      5    2
  AMP PEAK 49(18Q22.1) WILD-TYPE  359  129
        clus
vv       AMP PEAK 49(18Q22.1) MUTATED AMP PEAK 49(18Q22.1) WILD-TYPE
  FEMALE                            5                            359
  MALE                              2                            129
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 49(18Q22.1) MUTATED                0
  AMP PEAK 49(18Q22.1) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 49(18Q22.1) MUTATED                                               6
  AMP PEAK 49(18Q22.1) WILD-TYPE                                           347
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 49(18Q22.1) MUTATED                                                                        1
  AMP PEAK 49(18Q22.1) WILD-TYPE                                                                     97
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 49(18Q22.1) MUTATED                                                                     0
  AMP PEAK 49(18Q22.1) WILD-TYPE                                                                  35
D45V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 49(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 49(18Q22.1) WILD-TYPE
  OTHER  SPECIFY                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     347
  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"
D45V9, binary
                                cls
clus                               0   1
  AMP PEAK 49(18Q22.1) MUTATED     0   7
  AMP PEAK 49(18Q22.1) WILD-TYPE  14 474
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 49(18Q22.1) MUTATED      0    7
  AMP PEAK 49(18Q22.1) WILD-TYPE   14  474
     clus
vv    AMP PEAK 49(18Q22.1) MUTATED AMP PEAK 49(18Q22.1) WILD-TYPE
  NO                             0                             14
  YES                            7                            474
[1] 2 2
[1] FALSE
D45V10, binary
                                cls
clus                               0   1
  AMP PEAK 49(18Q22.1) MUTATED     5   0
  AMP PEAK 49(18Q22.1) WILD-TYPE 412  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 49(18Q22.1) MUTATED      5    0
  AMP PEAK 49(18Q22.1) WILD-TYPE  412   17
     clus
vv    AMP PEAK 49(18Q22.1) MUTATED AMP PEAK 49(18Q22.1) WILD-TYPE
  NO                             5                            412
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 49(18Q22.1) MUTATED              1                       0    5
  AMP PEAK 49(18Q22.1) WILD-TYPE          129                      16  323
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 49(18Q22.1) MUTATED                     0
  AMP PEAK 49(18Q22.1) WILD-TYPE                   1
D45V11, multiclass
                         clus
vv                        AMP PEAK 49(18Q22.1) MUTATED
  MINIMAL (T3)                                       1
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               5
  VERY ADVANCED (T4B)                                0
                         clus
vv                        AMP PEAK 49(18Q22.1) WILD-TYPE
  MINIMAL (T3)                                       129
  MODERATE/ADVANCED (T4A)                             16
  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 49(18Q22.1) MUTATED     4   1   0   1
  AMP PEAK 49(18Q22.1) WILD-TYPE 374  50   4  29
D45V12, multiclass
    clus
vv   AMP PEAK 49(18Q22.1) MUTATED AMP PEAK 49(18Q22.1) WILD-TYPE
  R0                            4                            374
  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"
D45V13, continuous
D45V14, binary
                                cls
clus                               0   1
  AMP PEAK 49(18Q22.1) MUTATED     3   4
  AMP PEAK 49(18Q22.1) WILD-TYPE 221 257
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 49(18Q22.1) MUTATED      3    4
  AMP PEAK 49(18Q22.1) WILD-TYPE  221  257
            clus
vv           AMP PEAK 49(18Q22.1) MUTATED AMP PEAK 49(18Q22.1) WILD-TYPE
  MULTIFOCAL                            3                            221
  UNIFOCAL                              4                            257
[1] 2 2
[1] FALSE
D45V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 49(18Q22.1) MUTATED                                  0     0
  AMP PEAK 49(18Q22.1) WILD-TYPE                                1    49
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 49(18Q22.1) MUTATED                           0     6
  AMP PEAK 49(18Q22.1) WILD-TYPE                        26   315
D45V16, multiclass
                                  clus
vv                                 AMP PEAK 49(18Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       6
                                  clus
vv                                 AMP PEAK 49(18Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        49
  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"
D45V17, binary
                                cls
clus                               0   1
  AMP PEAK 49(18Q22.1) MUTATED     0   6
  AMP PEAK 49(18Q22.1) WILD-TYPE  38 344
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 49(18Q22.1) MUTATED      0    6
  AMP PEAK 49(18Q22.1) WILD-TYPE   38  344
                        clus
vv                       AMP PEAK 49(18Q22.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            6
                        clus
vv                       AMP PEAK 49(18Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            344
[1] 2 2
[1] FALSE

Clustering(46) Variable = AMP PEAK 50(18Q22.3) MUTATION ANALYSIS
D46V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 50(18Q22.3) MUTATED     8   0
  AMP PEAK 50(18Q22.3) WILD-TYPE 469  14
  AMP PEAK 50(18Q22.3) MUTATED AMP PEAK 50(18Q22.3) WILD-TYPE 
                             8                            483 
  AMP PEAK 50(18Q22.3) MUTATED AMP PEAK 50(18Q22.3) WILD-TYPE 
                             0                             14 
$`AMP PEAK 50(18Q22.3) MUTATED`
TCGA-BJ-A45E TCGA-EL-A3ZR TCGA-EL-A4KI TCGA-EM-A2CT TCGA-ET-A2MZ TCGA-ET-A39N 
        0.03        48.16         8.71        10.49        12.26        98.56 
TCGA-FY-A3I5 TCGA-KS-A4ID 
        1.64        33.24 

$`AMP PEAK 50(18Q22.3) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
       18.64         5.75         6.48         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
        1.45        74.30        45.40        33.47       108.36        39.32 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        30.18       102.84        65.39       124.04        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       37.25       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        38.66        52.73       139.00       131.15       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        12.16       147.42       130.72 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       116.91        98.24        41.29        95.38 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS 
       50.33        53.06        47.38        52.50        45.53         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       29.95        13.32        11.87        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
       12.36        18.05        19.79        19.46        54.21        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        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        13.84        19.73        17.59        12.07 
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        17.46        18.97 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        19.63        13.38         8.35        16.44 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       16.77        27.95        23.77        16.80        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        11.15 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33        12.53         9.24        13.91         7.82        11.51 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       16.41        15.62        13.51        12.79        70.65        16.90 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        9.01         4.83         8.61         8.38         9.80         5.03 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       37.87        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       29.49        54.05        22.09        16.08        29.19        19.76 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        58.22        13.74        71.01        80.02        65.36 
TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24         5.85         4.18         2.43         5.56        24.72 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       38.30        42.25         2.37         4.50        80.81        69.24 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       59.87        43.50         0.30        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        4.01         1.94        73.74        59.70        31.59        44.25 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       102.90        66.77        81.34        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 
       46.06         4.08         0.89        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON 
       91.17         1.25         1.15        17.82         0.99         1.51 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        0.76         0.03         4.67        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         6.87         4.14         6.58         4.54 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
        0.89         1.35         1.15         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        10.26        16.90         9.80         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        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        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       12.43         6.74        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         0.72        16.64        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        8.71        10.98         5.19 

  AMP PEAK 50(18Q22.3) MUTATED AMP PEAK 50(18Q22.3) WILD-TYPE 
                          0.03                           0.03 
  AMP PEAK 50(18Q22.3) MUTATED AMP PEAK 50(18Q22.3) WILD-TYPE 
                         98.56                         158.83 
  AMP PEAK 50(18Q22.3) MUTATED AMP PEAK 50(18Q22.3) WILD-TYPE 
                        11.375                         16.640 
[1] "0.0 - 98.6 (11.4)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "9200000"
D46V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 50(18Q22.3) MUTATED         5        1         2        0         0
  AMP PEAK 50(18Q22.3) WILD-TYPE     275       50       107        2        45
                                vv
clus                             STAGE IVC
  AMP PEAK 50(18Q22.3) MUTATED           0
  AMP PEAK 50(18Q22.3) WILD-TYPE         6
D46V3, multiclass
           clus
vv          AMP PEAK 50(18Q22.3) MUTATED AMP PEAK 50(18Q22.3) WILD-TYPE
  STAGE I                              5                            275
  STAGE II                             1                             50
  STAGE III                            2                            107
  STAGE IV                             0                              2
  STAGE IVA                            0                             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 50(18Q22.3) MUTATED     4   1   3   0
  AMP PEAK 50(18Q22.3) WILD-TYPE 136 165 162  21
D46V4, multiclass
    clus
vv   AMP PEAK 50(18Q22.3) MUTATED AMP PEAK 50(18Q22.3) WILD-TYPE
  T1                            4                            136
  T2                            1                            165
  T3                            3                            162
  T4                            0                             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"
D46V5, binary
                                cls
clus                               0   1
  AMP PEAK 50(18Q22.3) MUTATED     7   0
  AMP PEAK 50(18Q22.3) WILD-TYPE 216 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 50(18Q22.3) MUTATED      7    0
  AMP PEAK 50(18Q22.3) WILD-TYPE  216  222
   clus
vv  AMP PEAK 50(18Q22.3) MUTATED AMP PEAK 50(18Q22.3) WILD-TYPE
  0                            7                            216
  1                            0                            222
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 50(18Q22.3) MUTATED     3   0   5
  AMP PEAK 50(18Q22.3) WILD-TYPE 270   9 207
D46V6, multiclass
    clus
vv   AMP PEAK 50(18Q22.3) MUTATED AMP PEAK 50(18Q22.3) WILD-TYPE
  M0                            3                            270
  M1                            0                              9
  MX                            5                            207
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                                cls
clus                               0   1
  AMP PEAK 50(18Q22.3) MUTATED     6   2
  AMP PEAK 50(18Q22.3) WILD-TYPE 358 129
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 50(18Q22.3) MUTATED      6    2
  AMP PEAK 50(18Q22.3) WILD-TYPE  358  129
        clus
vv       AMP PEAK 50(18Q22.3) MUTATED AMP PEAK 50(18Q22.3) WILD-TYPE
  FEMALE                            6                            358
  MALE                              2                            129
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 50(18Q22.3) MUTATED                0
  AMP PEAK 50(18Q22.3) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 50(18Q22.3) MUTATED                                               5
  AMP PEAK 50(18Q22.3) WILD-TYPE                                           348
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 50(18Q22.3) MUTATED                                                                        3
  AMP PEAK 50(18Q22.3) WILD-TYPE                                                                     95
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 50(18Q22.3) MUTATED                                                                     0
  AMP PEAK 50(18Q22.3) WILD-TYPE                                                                  35
D46V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 50(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 50(18Q22.3) WILD-TYPE
  OTHER  SPECIFY                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     348
  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"
D46V9, binary
                                cls
clus                               0   1
  AMP PEAK 50(18Q22.3) MUTATED     0   8
  AMP PEAK 50(18Q22.3) WILD-TYPE  14 473
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 50(18Q22.3) MUTATED      0    8
  AMP PEAK 50(18Q22.3) WILD-TYPE   14  473
     clus
vv    AMP PEAK 50(18Q22.3) MUTATED AMP PEAK 50(18Q22.3) WILD-TYPE
  NO                             0                             14
  YES                            8                            473
[1] 2 2
[1] FALSE
D46V10, binary
                                cls
clus                               0   1
  AMP PEAK 50(18Q22.3) MUTATED     6   0
  AMP PEAK 50(18Q22.3) WILD-TYPE 411  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 50(18Q22.3) MUTATED      6    0
  AMP PEAK 50(18Q22.3) WILD-TYPE  411   17
     clus
vv    AMP PEAK 50(18Q22.3) MUTATED AMP PEAK 50(18Q22.3) WILD-TYPE
  NO                             6                            411
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 50(18Q22.3) MUTATED              1                       0    6
  AMP PEAK 50(18Q22.3) WILD-TYPE          129                      16  322
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 50(18Q22.3) MUTATED                     0
  AMP PEAK 50(18Q22.3) WILD-TYPE                   1
D46V11, multiclass
                         clus
vv                        AMP PEAK 50(18Q22.3) MUTATED
  MINIMAL (T3)                                       1
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               6
  VERY ADVANCED (T4B)                                0
                         clus
vv                        AMP PEAK 50(18Q22.3) WILD-TYPE
  MINIMAL (T3)                                       129
  MODERATE/ADVANCED (T4A)                             16
  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
  AMP PEAK 50(18Q22.3) MUTATED     6   0   0   1
  AMP PEAK 50(18Q22.3) WILD-TYPE 372  51   4  29
D46V12, multiclass
    clus
vv   AMP PEAK 50(18Q22.3) MUTATED AMP PEAK 50(18Q22.3) WILD-TYPE
  R0                            6                            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"
D46V13, continuous
D46V14, binary
                                cls
clus                               0   1
  AMP PEAK 50(18Q22.3) MUTATED     2   6
  AMP PEAK 50(18Q22.3) WILD-TYPE 222 255
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 50(18Q22.3) MUTATED      2    6
  AMP PEAK 50(18Q22.3) WILD-TYPE  222  255
            clus
vv           AMP PEAK 50(18Q22.3) MUTATED AMP PEAK 50(18Q22.3) WILD-TYPE
  MULTIFOCAL                            2                            222
  UNIFOCAL                              6                            255
[1] 2 2
[1] FALSE
D46V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 50(18Q22.3) MUTATED                                  0     0
  AMP PEAK 50(18Q22.3) WILD-TYPE                                1    49
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 50(18Q22.3) MUTATED                           0     7
  AMP PEAK 50(18Q22.3) WILD-TYPE                        26   314
D46V16, multiclass
                                  clus
vv                                 AMP PEAK 50(18Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       7
                                  clus
vv                                 AMP PEAK 50(18Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        49
  BLACK OR AFRICAN AMERICAN                                    26
  WHITE                                                       314
[1] 4 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 50(18Q22.3) MUTATED     0   6
  AMP PEAK 50(18Q22.3) WILD-TYPE  38 344
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 50(18Q22.3) MUTATED      0    6
  AMP PEAK 50(18Q22.3) WILD-TYPE   38  344
                        clus
vv                       AMP PEAK 50(18Q22.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            6
                        clus
vv                       AMP PEAK 50(18Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            344
[1] 2 2
[1] FALSE

Clustering(47) Variable = AMP PEAK 51(19P13.3) MUTATION ANALYSIS
D47V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 51(19P13.3) MUTATED     8   0
  AMP PEAK 51(19P13.3) WILD-TYPE 469  14
  AMP PEAK 51(19P13.3) MUTATED AMP PEAK 51(19P13.3) WILD-TYPE 
                             8                            483 
  AMP PEAK 51(19P13.3) MUTATED AMP PEAK 51(19P13.3) WILD-TYPE 
                             0                             14 
$`AMP PEAK 51(19P13.3) MUTATED`
TCGA-DE-A4MA TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A22N TCGA-EM-A2OY TCGA-EM-A3O9 
       30.12         8.71        54.21        10.65        17.59         9.24 
TCGA-EM-A3SY TCGA-FY-A3I5 
       13.51         1.64 

$`AMP PEAK 51(19P13.3) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MB TCGA-DE-A4MC 
        5.98        15.85        18.54        18.84        11.57        30.02 
TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
        1.45        74.30        45.40        33.47       108.36        39.32 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        30.18       102.84        65.39       124.04        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       37.25       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        38.66        52.73       139.00       131.15       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        12.16       147.42       130.72 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       116.91        98.24        41.29        95.38 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       50.33        53.06        47.38        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT 
       37.78        29.95        13.32        11.87        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YD 
       20.91        12.36        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-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT 
       23.51         6.05         2.99        12.30        15.19        10.49 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 
       13.15        22.16        13.84        19.73        12.07        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        17.46        18.97        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR 
       14.14        19.63        13.38         8.35        16.44        16.77 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        16.80        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        11.15         7.33 
TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
       12.53        13.91         7.82        11.51        16.41        15.62 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        70.65        16.90         9.01         4.83         8.61 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
        8.38         9.80         5.03        37.87        12.72         0.95 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       47.47        48.20        29.69        32.35        14.79        12.33 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       14.79        27.09        18.38        29.49        54.05        22.09 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       12.26        16.08        29.19        19.76         2.66        58.22 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
       13.74        71.01        80.02        65.36        84.89        98.56 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
       61.02        58.72        57.11        55.10        59.15        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
        5.85         4.18         2.43         5.56        24.72        38.30 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       42.25         2.37         4.50        80.81        69.24        59.87 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       43.50         0.30        17.98        25.32       132.36        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
        3.22         7.17         4.80         5.03         2.14         4.01 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
        1.94        73.74        59.70        31.59        44.25        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       102.90        66.77        81.34        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        46.06 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.08         0.89        22.03         0.92        48.10        91.17 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25         1.15        17.82         0.99         1.51         0.76 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
        0.03         4.67        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         6.87         4.14         6.58         4.54         0.89 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35         1.15         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 
       10.26        16.90         9.80         9.63         2.96         8.65 
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        86.70         6.02        12.43 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
        6.74        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         0.72        16.64        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        8.71        10.98         5.19 

  AMP PEAK 51(19P13.3) MUTATED AMP PEAK 51(19P13.3) WILD-TYPE 
                          1.64                           0.03 
  AMP PEAK 51(19P13.3) MUTATED AMP PEAK 51(19P13.3) WILD-TYPE 
                         54.21                         158.83 
  AMP PEAK 51(19P13.3) MUTATED AMP PEAK 51(19P13.3) WILD-TYPE 
                         12.08                          16.64 
[1] "1.6 - 54.2 (12.1)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "3300000"
D47V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 51(19P13.3) MUTATED         3        1         4        0         0
  AMP PEAK 51(19P13.3) WILD-TYPE     277       50       105        2        45
                                vv
clus                             STAGE IVC
  AMP PEAK 51(19P13.3) MUTATED           0
  AMP PEAK 51(19P13.3) WILD-TYPE         6
D47V3, multiclass
           clus
vv          AMP PEAK 51(19P13.3) MUTATED AMP PEAK 51(19P13.3) WILD-TYPE
  STAGE I                              3                            277
  STAGE II                             1                             50
  STAGE III                            4                            105
  STAGE IV                             0                              2
  STAGE IVA                            0                             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 51(19P13.3) MUTATED     2   1   5   0
  AMP PEAK 51(19P13.3) WILD-TYPE 138 165 160  21
D47V4, multiclass
    clus
vv   AMP PEAK 51(19P13.3) MUTATED AMP PEAK 51(19P13.3) WILD-TYPE
  T1                            2                            138
  T2                            1                            165
  T3                            5                            160
  T4                            0                             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"
D47V5, binary
                                cls
clus                               0   1
  AMP PEAK 51(19P13.3) MUTATED     6   1
  AMP PEAK 51(19P13.3) WILD-TYPE 217 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 51(19P13.3) MUTATED      6    1
  AMP PEAK 51(19P13.3) WILD-TYPE  217  221
   clus
vv  AMP PEAK 51(19P13.3) MUTATED AMP PEAK 51(19P13.3) WILD-TYPE
  0                            6                            217
  1                            1                            221
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 51(19P13.3) MUTATED     1   0   7
  AMP PEAK 51(19P13.3) WILD-TYPE 272   9 205
D47V6, multiclass
    clus
vv   AMP PEAK 51(19P13.3) MUTATED AMP PEAK 51(19P13.3) WILD-TYPE
  M0                            1                            272
  M1                            0                              9
  MX                            7                            205
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                                cls
clus                               0   1
  AMP PEAK 51(19P13.3) MUTATED     5   3
  AMP PEAK 51(19P13.3) WILD-TYPE 359 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 51(19P13.3) MUTATED      5    3
  AMP PEAK 51(19P13.3) WILD-TYPE  359  128
        clus
vv       AMP PEAK 51(19P13.3) MUTATED AMP PEAK 51(19P13.3) WILD-TYPE
  FEMALE                            5                            359
  MALE                              3                            128
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 51(19P13.3) MUTATED                0
  AMP PEAK 51(19P13.3) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 51(19P13.3) MUTATED                                               2
  AMP PEAK 51(19P13.3) WILD-TYPE                                           351
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 51(19P13.3) MUTATED                                                                        6
  AMP PEAK 51(19P13.3) WILD-TYPE                                                                     92
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 51(19P13.3) MUTATED                                                                     0
  AMP PEAK 51(19P13.3) WILD-TYPE                                                                  35
D47V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 51(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 51(19P13.3) WILD-TYPE
  OTHER  SPECIFY                                                                                      9
  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"
D47V9, binary
                                cls
clus                               0   1
  AMP PEAK 51(19P13.3) MUTATED     0   8
  AMP PEAK 51(19P13.3) WILD-TYPE  14 473
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 51(19P13.3) MUTATED      0    8
  AMP PEAK 51(19P13.3) WILD-TYPE   14  473
     clus
vv    AMP PEAK 51(19P13.3) MUTATED AMP PEAK 51(19P13.3) WILD-TYPE
  NO                             0                             14
  YES                            8                            473
[1] 2 2
[1] FALSE
D47V10, binary
                                cls
clus                               0   1
  AMP PEAK 51(19P13.3) MUTATED     7   0
  AMP PEAK 51(19P13.3) WILD-TYPE 410  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 51(19P13.3) MUTATED      7    0
  AMP PEAK 51(19P13.3) WILD-TYPE  410   17
     clus
vv    AMP PEAK 51(19P13.3) MUTATED AMP PEAK 51(19P13.3) WILD-TYPE
  NO                             7                            410
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 51(19P13.3) MUTATED              2                       0    6
  AMP PEAK 51(19P13.3) WILD-TYPE          128                      16  322
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 51(19P13.3) MUTATED                     0
  AMP PEAK 51(19P13.3) WILD-TYPE                   1
D47V11, multiclass
                         clus
vv                        AMP PEAK 51(19P13.3) MUTATED
  MINIMAL (T3)                                       2
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               6
  VERY ADVANCED (T4B)                                0
                         clus
vv                        AMP PEAK 51(19P13.3) WILD-TYPE
  MINIMAL (T3)                                       128
  MODERATE/ADVANCED (T4A)                             16
  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
  AMP PEAK 51(19P13.3) MUTATED     7   0   0   1
  AMP PEAK 51(19P13.3) WILD-TYPE 371  51   4  29
D47V12, multiclass
    clus
vv   AMP PEAK 51(19P13.3) MUTATED AMP PEAK 51(19P13.3) WILD-TYPE
  R0                            7                            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"
D47V13, continuous
D47V14, binary
                                cls
clus                               0   1
  AMP PEAK 51(19P13.3) MUTATED     5   3
  AMP PEAK 51(19P13.3) WILD-TYPE 219 258
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 51(19P13.3) MUTATED      5    3
  AMP PEAK 51(19P13.3) WILD-TYPE  219  258
            clus
vv           AMP PEAK 51(19P13.3) MUTATED AMP PEAK 51(19P13.3) WILD-TYPE
  MULTIFOCAL                            5                            219
  UNIFOCAL                              3                            258
[1] 2 2
[1] FALSE
D47V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 51(19P13.3) MUTATED                                  0     0
  AMP PEAK 51(19P13.3) WILD-TYPE                                1    49
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 51(19P13.3) MUTATED                           1     2
  AMP PEAK 51(19P13.3) WILD-TYPE                        25   319
D47V16, multiclass
                                  clus
vv                                 AMP PEAK 51(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                       2
                                  clus
vv                                 AMP PEAK 51(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        49
  BLACK OR AFRICAN AMERICAN                                    25
  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"
D47V17, binary
                                cls
clus                               0   1
  AMP PEAK 51(19P13.3) MUTATED     0   3
  AMP PEAK 51(19P13.3) WILD-TYPE  38 347
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 51(19P13.3) MUTATED      0    3
  AMP PEAK 51(19P13.3) WILD-TYPE   38  347
                        clus
vv                       AMP PEAK 51(19P13.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            3
                        clus
vv                       AMP PEAK 51(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            347
[1] 2 2
[1] FALSE

Clustering(48) Variable = AMP PEAK 52(20P13) MUTATION ANALYSIS
D48V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 52(20P13) MUTATED    13   1
  AMP PEAK 52(20P13) WILD-TYPE 464  13
  AMP PEAK 52(20P13) MUTATED AMP PEAK 52(20P13) WILD-TYPE 
                          14                          477 
  AMP PEAK 52(20P13) MUTATED AMP PEAK 52(20P13) WILD-TYPE 
                           1                           13 
$`AMP PEAK 52(20P13) MUTATED`
TCGA-BJ-A192 TCGA-EL-A3GO TCGA-EL-A3T9 TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A1YD 
        8.09        39.32         5.72         8.71        54.21        57.01 
TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A2MZ 
        6.05        17.59        17.46         9.24        13.51        12.26 
TCGA-ET-A39N TCGA-FY-A3I5 
       98.56         1.64 

$`AMP PEAK 52(20P13) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A28R 
       17.69        23.34        20.71        20.58         4.83         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
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        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GP 
        1.45        74.30        45.40        33.47       108.36         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA 
       32.48       116.91        98.24        41.29        95.38        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN 
       82.82        77.36        78.97        31.50        50.33        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        52.50        45.53        48.16         7.07        44.65 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       45.80        19.30        45.96        37.94        31.04        19.59 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        33.60        28.73        41.13        37.78        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       13.32        11.87        26.86        18.18        20.91        12.36 
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-A22N TCGA-EM-A22O TCGA-EM-A22P 
       15.75        10.45        14.53        10.65        11.74        11.15 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP 
       14.24        16.44        17.88        13.18        23.51         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
       12.30        15.19        10.49        13.15        22.16        13.84 
TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       19.73        12.07        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 
       18.97        15.68        14.14        19.63        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       16.44        16.77        27.95        23.77        16.80        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 
       11.15         7.33        12.53        13.91         7.82        11.51 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       16.41        15.62        12.79        70.65        16.90         9.01 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        4.83         8.61         8.38         9.80         5.03        37.87 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       12.72         0.95        47.47        48.20        29.69        32.35 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       14.79        12.33        14.79        27.09        18.38        29.49 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       54.05        22.09        16.08        29.19        19.76         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       58.22        13.74        71.01        80.02        65.36        84.89 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
       61.02        58.72        57.11        55.10        59.15        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
        5.85         4.18         2.43         5.56        24.72        38.30 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       42.25         2.37         4.50        80.81        69.24        59.87 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       43.50         0.30        17.98        25.32       132.36        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
        3.22         7.17         4.80         5.03         2.14         4.01 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
        1.94        73.74        59.70        31.59        44.25        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       102.90        66.77        81.34        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        46.06 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.08         0.89        22.03         0.92        48.10        91.17 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25         1.15        17.82         0.99         1.51         0.76 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
        0.03         4.67        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         6.87         4.14         6.58         4.54         0.89 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35         1.15         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 
       10.26        16.90         9.80         9.63         2.96         8.65 
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        86.70         6.02        12.43 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
        6.74        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         0.72        16.64        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        8.71        10.98         5.19 

  AMP PEAK 52(20P13) MUTATED AMP PEAK 52(20P13) WILD-TYPE 
                        1.64                         0.03 
  AMP PEAK 52(20P13) MUTATED AMP PEAK 52(20P13) WILD-TYPE 
                       98.56                       158.83 
  AMP PEAK 52(20P13) MUTATED AMP PEAK 52(20P13) WILD-TYPE 
                      12.885                       16.640 
[1] "1.6 - 98.6 (12.9)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "2.5"
D48V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 52(20P13) MUTATED         5        4         4        1         0
  AMP PEAK 52(20P13) WILD-TYPE     275       47       105        1        45
                              vv
clus                           STAGE IVC
  AMP PEAK 52(20P13) MUTATED           0
  AMP PEAK 52(20P13) WILD-TYPE         6
D48V3, multiclass
           clus
vv          AMP PEAK 52(20P13) MUTATED AMP PEAK 52(20P13) WILD-TYPE
  STAGE I                            5                          275
  STAGE II                           4                           47
  STAGE III                          4                          105
  STAGE IV                           1                            1
  STAGE IVA                          0                           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(20P13) MUTATED     2   5   6   1
  AMP PEAK 52(20P13) WILD-TYPE 138 161 159  20
D48V4, multiclass
    clus
vv   AMP PEAK 52(20P13) MUTATED AMP PEAK 52(20P13) WILD-TYPE
  T1                          2                          138
  T2                          5                          161
  T3                          6                          159
  T4                          1                           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"
D48V5, binary
                              cls
clus                             0   1
  AMP PEAK 52(20P13) MUTATED     8   1
  AMP PEAK 52(20P13) WILD-TYPE 215 221
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 52(20P13) MUTATED      8    1
  AMP PEAK 52(20P13) WILD-TYPE  215  221
   clus
vv  AMP PEAK 52(20P13) MUTATED AMP PEAK 52(20P13) WILD-TYPE
  0                          8                          215
  1                          1                          221
[1] 2 2
[1] FALSE
                              vv
clus                            M0  M1  MX
  AMP PEAK 52(20P13) MUTATED     2   0  12
  AMP PEAK 52(20P13) WILD-TYPE 271   9 200
D48V6, multiclass
    clus
vv   AMP PEAK 52(20P13) MUTATED AMP PEAK 52(20P13) WILD-TYPE
  M0                          2                          271
  M1                          0                            9
  MX                         12                          200
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                              cls
clus                             0   1
  AMP PEAK 52(20P13) MUTATED    10   4
  AMP PEAK 52(20P13) WILD-TYPE 354 127
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 52(20P13) MUTATED     10    4
  AMP PEAK 52(20P13) WILD-TYPE  354  127
        clus
vv       AMP PEAK 52(20P13) MUTATED AMP PEAK 52(20P13) WILD-TYPE
  FEMALE                         10                          354
  MALE                            4                          127
[1] 2 2
[1] FALSE
                              vv
clus                           OTHER  SPECIFY
  AMP PEAK 52(20P13) MUTATED                0
  AMP PEAK 52(20P13) WILD-TYPE              9
                              vv
clus                           THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 52(20P13) MUTATED                                               6
  AMP PEAK 52(20P13) WILD-TYPE                                           347
                              vv
clus                           THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 52(20P13) MUTATED                                                                        8
  AMP PEAK 52(20P13) WILD-TYPE                                                                     90
                              vv
clus                           THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 52(20P13) MUTATED                                                                     0
  AMP PEAK 52(20P13) WILD-TYPE                                                                  35
D48V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 52(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 52(20P13) WILD-TYPE
  OTHER  SPECIFY                                                                                    9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                   347
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           90
  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"
D48V9, binary
                              cls
clus                             0   1
  AMP PEAK 52(20P13) MUTATED     0  14
  AMP PEAK 52(20P13) WILD-TYPE  14 467
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 52(20P13) MUTATED      0   14
  AMP PEAK 52(20P13) WILD-TYPE   14  467
     clus
vv    AMP PEAK 52(20P13) MUTATED AMP PEAK 52(20P13) WILD-TYPE
  NO                           0                           14
  YES                         14                          467
[1] 2 2
[1] FALSE
D48V10, binary
                              cls
clus                             0   1
  AMP PEAK 52(20P13) MUTATED    13   0
  AMP PEAK 52(20P13) WILD-TYPE 404  17
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 52(20P13) MUTATED     13    0
  AMP PEAK 52(20P13) WILD-TYPE  404   17
     clus
vv    AMP PEAK 52(20P13) MUTATED AMP PEAK 52(20P13) WILD-TYPE
  NO                          13                          404
  YES                          0                           17
[1] 2 2
[1] FALSE
                              vv
clus                           MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 52(20P13) MUTATED              2                       0   11
  AMP PEAK 52(20P13) WILD-TYPE          128                      16  317
                              vv
clus                           VERY ADVANCED (T4B)
  AMP PEAK 52(20P13) MUTATED                     1
  AMP PEAK 52(20P13) WILD-TYPE                   0
D48V11, multiclass
                         clus
vv                        AMP PEAK 52(20P13) MUTATED
  MINIMAL (T3)                                     2
  MODERATE/ADVANCED (T4A)                          0
  NONE                                            11
  VERY ADVANCED (T4B)                              1
                         clus
vv                        AMP PEAK 52(20P13) WILD-TYPE
  MINIMAL (T3)                                     128
  MODERATE/ADVANCED (T4A)                           16
  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 52(20P13) MUTATED    11   1   0   2
  AMP PEAK 52(20P13) WILD-TYPE 367  50   4  28
D48V12, multiclass
    clus
vv   AMP PEAK 52(20P13) MUTATED AMP PEAK 52(20P13) WILD-TYPE
  R0                         11                          367
  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"
D48V13, continuous
D48V14, binary
                              cls
clus                             0   1
  AMP PEAK 52(20P13) MUTATED     6   8
  AMP PEAK 52(20P13) WILD-TYPE 218 253
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 52(20P13) MUTATED      6    8
  AMP PEAK 52(20P13) WILD-TYPE  218  253
            clus
vv           AMP PEAK 52(20P13) MUTATED AMP PEAK 52(20P13) WILD-TYPE
  MULTIFOCAL                          6                          218
  UNIFOCAL                            8                          253
[1] 2 2
[1] FALSE
D48V15, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 52(20P13) MUTATED                                  0     0
  AMP PEAK 52(20P13) WILD-TYPE                                1    49
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 52(20P13) MUTATED                           0     7
  AMP PEAK 52(20P13) WILD-TYPE                        26   314
D48V16, multiclass
                                  clus
vv                                 AMP PEAK 52(20P13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     0
  BLACK OR AFRICAN AMERICAN                                 0
  WHITE                                                     7
                                  clus
vv                                 AMP PEAK 52(20P13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      49
  BLACK OR AFRICAN AMERICAN                                  26
  WHITE                                                     314
[1] 4 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 52(20P13) MUTATED     1   5
  AMP PEAK 52(20P13) WILD-TYPE  37 345
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 52(20P13) MUTATED      1    5
  AMP PEAK 52(20P13) WILD-TYPE   37  345
                        clus
vv                       AMP PEAK 52(20P13) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                          5
                        clus
vv                       AMP PEAK 52(20P13) WILD-TYPE
  HISPANIC OR LATINO                               37
  NOT HISPANIC OR LATINO                          345
[1] 2 2
[1] FALSE

Clustering(49) Variable = AMP PEAK 53(20Q13.11) MUTATION ANALYSIS
D49V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 53(20Q13.11) MUTATED    13   1
  AMP PEAK 53(20Q13.11) WILD-TYPE 464  13
  AMP PEAK 53(20Q13.11) MUTATED AMP PEAK 53(20Q13.11) WILD-TYPE 
                             14                             477 
  AMP PEAK 53(20Q13.11) MUTATED AMP PEAK 53(20Q13.11) WILD-TYPE 
                              1                              13 
$`AMP PEAK 53(20Q13.11) MUTATED`
TCGA-DJ-A3UP TCGA-EL-A3GO TCGA-EL-A3T9 TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A1YD 
       16.41        39.32         5.72         8.71        54.21        57.01 
TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A2MZ 
        6.05        17.59        17.46         9.24        13.51        12.26 
TCGA-ET-A39N TCGA-FY-A3I5 
       98.56         1.64 

$`AMP PEAK 53(20Q13.11) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        5.52         8.78         8.42         8.12         9.34         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
        9.21         9.44         9.90         8.61        10.09         7.07 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       10.36        12.43        10.85        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       12.49        31.46        19.56        36.33        32.81        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GP 
        1.45        74.30        45.40        33.47       108.36         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA 
       32.48       116.91        98.24        41.29        95.38        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN 
       82.82        77.36        78.97        31.50        50.33        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        52.50        45.53        48.16         7.07        44.65 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       45.80        19.30        45.96        37.94        31.04        19.59 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        33.60        28.73        41.13        37.78        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       13.32        11.87        26.86        18.18        20.91        12.36 
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-A22N TCGA-EM-A22O TCGA-EM-A22P 
       15.75        10.45        14.53        10.65        11.74        11.15 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP 
       14.24        16.44        17.88        13.18        23.51         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
       12.30        15.19        10.49        13.15        22.16        13.84 
TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       19.73        12.07        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 
       18.97        15.68        14.14        19.63        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       16.44        16.77        27.95        23.77        16.80        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 
       11.15         7.33        12.53        13.91         7.82        11.51 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       16.41        15.62        12.79        70.65        16.90         9.01 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        4.83         8.61         8.38         9.80         5.03        37.87 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       12.72         0.95        47.47        48.20        29.69        32.35 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       14.79        12.33        14.79        27.09        18.38        29.49 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       54.05        22.09        16.08        29.19        19.76         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       58.22        13.74        71.01        80.02        65.36        84.89 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
       61.02        58.72        57.11        55.10        59.15        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
        5.85         4.18         2.43         5.56        24.72        38.30 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       42.25         2.37         4.50        80.81        69.24        59.87 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       43.50         0.30        17.98        25.32       132.36        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
        3.22         7.17         4.80         5.03         2.14         4.01 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
        1.94        73.74        59.70        31.59        44.25        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       102.90        66.77        81.34        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        46.06 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.08         0.89        22.03         0.92        48.10        91.17 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25         1.15        17.82         0.99         1.51         0.76 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
        0.03         4.67        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         6.87         4.14         6.58         4.54         0.89 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35         1.15         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 
       10.26        16.90         9.80         9.63         2.96         8.65 
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        86.70         6.02        12.43 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
        6.74        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         0.72        16.64        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        8.71        10.98         5.19 

  AMP PEAK 53(20Q13.11) MUTATED AMP PEAK 53(20Q13.11) WILD-TYPE 
                           1.64                            0.03 
  AMP PEAK 53(20Q13.11) MUTATED AMP PEAK 53(20Q13.11) WILD-TYPE 
                          98.56                          158.83 
  AMP PEAK 53(20Q13.11) MUTATED AMP PEAK 53(20Q13.11) WILD-TYPE 
                          14.96                           16.64 
[1] "1.6 - 98.6 (15.0)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "2.5"
D49V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 53(20Q13.11) MUTATED         6        4         3        1         0
  AMP PEAK 53(20Q13.11) WILD-TYPE     274       47       106        1        45
                                 vv
clus                              STAGE IVC
  AMP PEAK 53(20Q13.11) MUTATED           0
  AMP PEAK 53(20Q13.11) WILD-TYPE         6
D49V3, multiclass
           clus
vv          AMP PEAK 53(20Q13.11) MUTATED AMP PEAK 53(20Q13.11) WILD-TYPE
  STAGE I                               6                             274
  STAGE II                              4                              47
  STAGE III                             3                             106
  STAGE IV                              1                               1
  STAGE IVA                             0                              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 53(20Q13.11) MUTATED     2   6   5   1
  AMP PEAK 53(20Q13.11) WILD-TYPE 138 160 160  20
D49V4, multiclass
    clus
vv   AMP PEAK 53(20Q13.11) MUTATED AMP PEAK 53(20Q13.11) WILD-TYPE
  T1                             2                             138
  T2                             6                             160
  T3                             5                             160
  T4                             1                              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"
D49V5, binary
                                 cls
clus                                0   1
  AMP PEAK 53(20Q13.11) MUTATED     9   1
  AMP PEAK 53(20Q13.11) WILD-TYPE 214 221
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 53(20Q13.11) MUTATED      9    1
  AMP PEAK 53(20Q13.11) WILD-TYPE  214  221
   clus
vv  AMP PEAK 53(20Q13.11) MUTATED AMP PEAK 53(20Q13.11) WILD-TYPE
  0                             9                             214
  1                             1                             221
[1] 2 2
[1] FALSE
                                 vv
clus                               M0  M1  MX
  AMP PEAK 53(20Q13.11) MUTATED     2   0  12
  AMP PEAK 53(20Q13.11) WILD-TYPE 271   9 200
D49V6, multiclass
    clus
vv   AMP PEAK 53(20Q13.11) MUTATED AMP PEAK 53(20Q13.11) WILD-TYPE
  M0                             2                             271
  M1                             0                               9
  MX                            12                             200
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                                 cls
clus                                0   1
  AMP PEAK 53(20Q13.11) MUTATED    10   4
  AMP PEAK 53(20Q13.11) WILD-TYPE 354 127
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 53(20Q13.11) MUTATED     10    4
  AMP PEAK 53(20Q13.11) WILD-TYPE  354  127
        clus
vv       AMP PEAK 53(20Q13.11) MUTATED AMP PEAK 53(20Q13.11) WILD-TYPE
  FEMALE                            10                             354
  MALE                               4                             127
[1] 2 2
[1] FALSE
                                 vv
clus                              OTHER  SPECIFY
  AMP PEAK 53(20Q13.11) MUTATED                0
  AMP PEAK 53(20Q13.11) WILD-TYPE              9
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 53(20Q13.11) MUTATED                                               5
  AMP PEAK 53(20Q13.11) WILD-TYPE                                           348
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 53(20Q13.11) MUTATED                                                                        9
  AMP PEAK 53(20Q13.11) WILD-TYPE                                                                     89
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 53(20Q13.11) MUTATED                                                                     0
  AMP PEAK 53(20Q13.11) WILD-TYPE                                                                  35
D49V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 53(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 53(20Q13.11) WILD-TYPE
  OTHER  SPECIFY                                                                                       9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      348
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                              89
  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"
D49V9, binary
                                 cls
clus                                0   1
  AMP PEAK 53(20Q13.11) MUTATED     0  14
  AMP PEAK 53(20Q13.11) WILD-TYPE  14 467
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 53(20Q13.11) MUTATED      0   14
  AMP PEAK 53(20Q13.11) WILD-TYPE   14  467
     clus
vv    AMP PEAK 53(20Q13.11) MUTATED AMP PEAK 53(20Q13.11) WILD-TYPE
  NO                              0                              14
  YES                            14                             467
[1] 2 2
[1] FALSE
D49V10, binary
                                 cls
clus                                0   1
  AMP PEAK 53(20Q13.11) MUTATED    13   0
  AMP PEAK 53(20Q13.11) WILD-TYPE 404  17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 53(20Q13.11) MUTATED     13    0
  AMP PEAK 53(20Q13.11) WILD-TYPE  404   17
     clus
vv    AMP PEAK 53(20Q13.11) MUTATED AMP PEAK 53(20Q13.11) WILD-TYPE
  NO                             13                             404
  YES                             0                              17
[1] 2 2
[1] FALSE
                                 vv
clus                              MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 53(20Q13.11) MUTATED              1                       0   12
  AMP PEAK 53(20Q13.11) WILD-TYPE          129                      16  316
                                 vv
clus                              VERY ADVANCED (T4B)
  AMP PEAK 53(20Q13.11) MUTATED                     1
  AMP PEAK 53(20Q13.11) WILD-TYPE                   0
D49V11, multiclass
                         clus
vv                        AMP PEAK 53(20Q13.11) MUTATED
  MINIMAL (T3)                                        1
  MODERATE/ADVANCED (T4A)                             0
  NONE                                               12
  VERY ADVANCED (T4B)                                 1
                         clus
vv                        AMP PEAK 53(20Q13.11) 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 53(20Q13.11) MUTATED    12   1   0   1
  AMP PEAK 53(20Q13.11) WILD-TYPE 366  50   4  29
D49V12, multiclass
    clus
vv   AMP PEAK 53(20Q13.11) MUTATED AMP PEAK 53(20Q13.11) WILD-TYPE
  R0                            12                             366
  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 53(20Q13.11) MUTATED     6   8
  AMP PEAK 53(20Q13.11) WILD-TYPE 218 253
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 53(20Q13.11) MUTATED      6    8
  AMP PEAK 53(20Q13.11) WILD-TYPE  218  253
            clus
vv           AMP PEAK 53(20Q13.11) MUTATED AMP PEAK 53(20Q13.11) WILD-TYPE
  MULTIFOCAL                             6                             218
  UNIFOCAL                               8                             253
[1] 2 2
[1] FALSE
D49V15, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 53(20Q13.11) MUTATED                                  0     0
  AMP PEAK 53(20Q13.11) WILD-TYPE                                1    49
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 53(20Q13.11) MUTATED                           0     6
  AMP PEAK 53(20Q13.11) WILD-TYPE                        26   315
D49V16, multiclass
                                  clus
vv                                 AMP PEAK 53(20Q13.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                    0
  WHITE                                                        6
                                  clus
vv                                 AMP PEAK 53(20Q13.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         49
  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"
D49V17, binary
                                 cls
clus                                0   1
  AMP PEAK 53(20Q13.11) MUTATED     2   5
  AMP PEAK 53(20Q13.11) WILD-TYPE  36 345
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 53(20Q13.11) MUTATED      2    5
  AMP PEAK 53(20Q13.11) WILD-TYPE   36  345
                        clus
vv                       AMP PEAK 53(20Q13.11) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                             5
                        clus
vv                       AMP PEAK 53(20Q13.11) WILD-TYPE
  HISPANIC OR LATINO                                  36
  NOT HISPANIC OR LATINO                             345
[1] 2 2
[1] FALSE

Clustering(50) Variable = AMP PEAK 54(20Q13.2) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 54(20Q13.2) MUTATED    13   1
  AMP PEAK 54(20Q13.2) WILD-TYPE 464  13
  AMP PEAK 54(20Q13.2) MUTATED AMP PEAK 54(20Q13.2) WILD-TYPE 
                            14                            477 
  AMP PEAK 54(20Q13.2) MUTATED AMP PEAK 54(20Q13.2) WILD-TYPE 
                             1                             13 
$`AMP PEAK 54(20Q13.2) MUTATED`
TCGA-DE-A4MD TCGA-DJ-A1QG TCGA-EL-A3T9 TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A1YD 
       25.12        13.12         5.72         8.71        54.21        57.01 
TCGA-EM-A2CO TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A2MZ 
        6.05        17.59        17.46         9.24        13.51        12.26 
TCGA-ET-A39N TCGA-FY-A3I5 
       98.56         1.64 

$`AMP PEAK 54(20Q13.2) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        15.85        18.54        18.84        30.12        11.57 
TCGA-DE-A4MC TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O 
       30.02         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QH 
       14.60         7.99        11.01       100.01        18.51         7.99 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96         7.20         1.45         8.88         1.02         5.95 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS 
       10.09         7.99         5.33         8.48        10.45         1.51 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY 
        9.60        12.56         8.28         7.69         5.52         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.42         8.12         9.34         6.77         9.21         9.44 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
        9.90         8.61        10.09         7.07        10.36        12.43 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        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        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04         1.15        22.29 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA 
       32.48       116.91        98.24        41.29        95.38        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN 
       82.82        77.36        78.97        31.50        50.33        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        52.50        45.53        48.16         7.07        44.65 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       45.80        19.30        45.96        37.94        31.04        19.59 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        33.60        28.73        41.13        37.78        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       13.32        11.87        26.86        18.18        20.91        12.36 
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-A22N TCGA-EM-A22O TCGA-EM-A22P 
       15.75        10.45        14.53        10.65        11.74        11.15 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP 
       14.24        16.44        17.88        13.18        23.51         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
       12.30        15.19        10.49        13.15        22.16        13.84 
TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       19.73        12.07        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 
       18.97        15.68        14.14        19.63        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       16.44        16.77        27.95        23.77        16.80        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 
       11.15         7.33        12.53        13.91         7.82        11.51 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       16.41        15.62        12.79        70.65        16.90         9.01 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        4.83         8.61         8.38         9.80         5.03        37.87 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       12.72         0.95        47.47        48.20        29.69        32.35 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       14.79        12.33        14.79        27.09        18.38        29.49 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       54.05        22.09        16.08        29.19        19.76         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       58.22        13.74        71.01        80.02        65.36        84.89 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
       61.02        58.72        57.11        55.10        59.15        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
        5.85         4.18         2.43         5.56        24.72        38.30 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       42.25         2.37         4.50        80.81        69.24        59.87 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       43.50         0.30        17.98        25.32       132.36        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
        3.22         7.17         4.80         5.03         2.14         4.01 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
        1.94        73.74        59.70        31.59        44.25        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       102.90        66.77        81.34        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        46.06 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.08         0.89        22.03         0.92        48.10        91.17 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25         1.15        17.82         0.99         1.51         0.76 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
        0.03         4.67        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         6.87         4.14         6.58         4.54         0.89 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35         1.15         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 
       10.26        16.90         9.80         9.63         2.96         8.65 
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        86.70         6.02        12.43 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
        6.74        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         0.72        16.64        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        8.71        10.98         5.19 

  AMP PEAK 54(20Q13.2) MUTATED AMP PEAK 54(20Q13.2) WILD-TYPE 
                          1.64                           0.03 
  AMP PEAK 54(20Q13.2) MUTATED AMP PEAK 54(20Q13.2) WILD-TYPE 
                         98.56                         158.83 
  AMP PEAK 54(20Q13.2) MUTATED AMP PEAK 54(20Q13.2) WILD-TYPE 
                        13.315                         16.640 
[1] "1.6 - 98.6 (13.3)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "2.7"
D50V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 54(20Q13.2) MUTATED         5        4         3        1         1
  AMP PEAK 54(20Q13.2) WILD-TYPE     275       47       106        1        44
                                vv
clus                             STAGE IVC
  AMP PEAK 54(20Q13.2) MUTATED           0
  AMP PEAK 54(20Q13.2) WILD-TYPE         6
D50V3, multiclass
           clus
vv          AMP PEAK 54(20Q13.2) MUTATED AMP PEAK 54(20Q13.2) WILD-TYPE
  STAGE I                              5                            275
  STAGE II                             4                             47
  STAGE III                            3                            106
  STAGE IV                             1                              1
  STAGE IVA                            1                             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 54(20Q13.2) MUTATED     3   4   6   1
  AMP PEAK 54(20Q13.2) WILD-TYPE 137 162 159  20
D50V4, multiclass
    clus
vv   AMP PEAK 54(20Q13.2) MUTATED AMP PEAK 54(20Q13.2) WILD-TYPE
  T1                            3                            137
  T2                            4                            162
  T3                            6                            159
  T4                            1                             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"
D50V5, binary
                                cls
clus                               0   1
  AMP PEAK 54(20Q13.2) MUTATED     8   2
  AMP PEAK 54(20Q13.2) WILD-TYPE 215 220
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 54(20Q13.2) MUTATED      8    2
  AMP PEAK 54(20Q13.2) WILD-TYPE  215  220
   clus
vv  AMP PEAK 54(20Q13.2) MUTATED AMP PEAK 54(20Q13.2) WILD-TYPE
  0                            8                            215
  1                            2                            220
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 54(20Q13.2) MUTATED     2   0  12
  AMP PEAK 54(20Q13.2) WILD-TYPE 271   9 200
D50V6, multiclass
    clus
vv   AMP PEAK 54(20Q13.2) MUTATED AMP PEAK 54(20Q13.2) WILD-TYPE
  M0                            2                            271
  M1                            0                              9
  MX                           12                            200
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                                cls
clus                               0   1
  AMP PEAK 54(20Q13.2) MUTATED     8   6
  AMP PEAK 54(20Q13.2) WILD-TYPE 356 125
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 54(20Q13.2) MUTATED      8    6
  AMP PEAK 54(20Q13.2) WILD-TYPE  356  125
        clus
vv       AMP PEAK 54(20Q13.2) MUTATED AMP PEAK 54(20Q13.2) WILD-TYPE
  FEMALE                            8                            356
  MALE                              6                            125
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 54(20Q13.2) MUTATED                0
  AMP PEAK 54(20Q13.2) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 54(20Q13.2) MUTATED                                               5
  AMP PEAK 54(20Q13.2) WILD-TYPE                                           348
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 54(20Q13.2) MUTATED                                                                        9
  AMP PEAK 54(20Q13.2) WILD-TYPE                                                                     89
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 54(20Q13.2) MUTATED                                                                     0
  AMP PEAK 54(20Q13.2) WILD-TYPE                                                                  35
D50V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 54(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 54(20Q13.2) WILD-TYPE
  OTHER  SPECIFY                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     348
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             89
  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"
D50V9, binary
                                cls
clus                               0   1
  AMP PEAK 54(20Q13.2) MUTATED     0  14
  AMP PEAK 54(20Q13.2) WILD-TYPE  14 467
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 54(20Q13.2) MUTATED      0   14
  AMP PEAK 54(20Q13.2) WILD-TYPE   14  467
     clus
vv    AMP PEAK 54(20Q13.2) MUTATED AMP PEAK 54(20Q13.2) WILD-TYPE
  NO                             0                             14
  YES                           14                            467
[1] 2 2
[1] FALSE
D50V10, binary
                                cls
clus                               0   1
  AMP PEAK 54(20Q13.2) MUTATED    13   0
  AMP PEAK 54(20Q13.2) WILD-TYPE 404  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 54(20Q13.2) MUTATED     13    0
  AMP PEAK 54(20Q13.2) WILD-TYPE  404   17
     clus
vv    AMP PEAK 54(20Q13.2) MUTATED AMP PEAK 54(20Q13.2) WILD-TYPE
  NO                            13                            404
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 54(20Q13.2) MUTATED              1                       0   12
  AMP PEAK 54(20Q13.2) WILD-TYPE          129                      16  316
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 54(20Q13.2) MUTATED                     1
  AMP PEAK 54(20Q13.2) WILD-TYPE                   0
D50V11, multiclass
                         clus
vv                        AMP PEAK 54(20Q13.2) MUTATED
  MINIMAL (T3)                                       1
  MODERATE/ADVANCED (T4A)                            0
  NONE                                              12
  VERY ADVANCED (T4B)                                1
                         clus
vv                        AMP PEAK 54(20Q13.2) 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 54(20Q13.2) MUTATED    12   1   0   1
  AMP PEAK 54(20Q13.2) WILD-TYPE 366  50   4  29
D50V12, multiclass
    clus
vv   AMP PEAK 54(20Q13.2) MUTATED AMP PEAK 54(20Q13.2) WILD-TYPE
  R0                           12                            366
  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"
D50V13, continuous
D50V14, binary
                                cls
clus                               0   1
  AMP PEAK 54(20Q13.2) MUTATED     7   7
  AMP PEAK 54(20Q13.2) WILD-TYPE 217 254
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 54(20Q13.2) MUTATED      7    7
  AMP PEAK 54(20Q13.2) WILD-TYPE  217  254
            clus
vv           AMP PEAK 54(20Q13.2) MUTATED AMP PEAK 54(20Q13.2) WILD-TYPE
  MULTIFOCAL                            7                            217
  UNIFOCAL                              7                            254
[1] 2 2
[1] FALSE
D50V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 54(20Q13.2) MUTATED                                  0     0
  AMP PEAK 54(20Q13.2) WILD-TYPE                                1    49
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 54(20Q13.2) MUTATED                           0     7
  AMP PEAK 54(20Q13.2) WILD-TYPE                        26   314
D50V16, multiclass
                                  clus
vv                                 AMP PEAK 54(20Q13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       7
                                  clus
vv                                 AMP PEAK 54(20Q13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        49
  BLACK OR AFRICAN AMERICAN                                    26
  WHITE                                                       314
[1] 4 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 54(20Q13.2) MUTATED     0   7
  AMP PEAK 54(20Q13.2) WILD-TYPE  38 343
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 54(20Q13.2) MUTATED      0    7
  AMP PEAK 54(20Q13.2) WILD-TYPE   38  343
                        clus
vv                       AMP PEAK 54(20Q13.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            7
                        clus
vv                       AMP PEAK 54(20Q13.2) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            343
[1] 2 2
[1] FALSE

Clustering(51) Variable = AMP PEAK 55(20Q13.2) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 55(20Q13.2) MUTATED    12   1
  AMP PEAK 55(20Q13.2) WILD-TYPE 465  13
  AMP PEAK 55(20Q13.2) MUTATED AMP PEAK 55(20Q13.2) WILD-TYPE 
                            13                            478 
  AMP PEAK 55(20Q13.2) MUTATED AMP PEAK 55(20Q13.2) WILD-TYPE 
                             1                             13 
$`AMP PEAK 55(20Q13.2) MUTATED`
TCGA-EL-A3T9 TCGA-EL-A4KI TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A2CO TCGA-EM-A2OY 
        5.72         8.71        54.21        57.01         6.05        17.59 
TCGA-EM-A3AI TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N TCGA-FY-A3I5 
       17.46         9.24        13.51        12.26        98.56         1.64 
TCGA-L6-A4EU 
        0.72 

$`AMP PEAK 55(20Q13.2) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        5.52         8.78         8.42         8.12         9.34         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
        9.21         9.44         9.90         8.61        10.09         7.07 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       10.36        12.43        10.85        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        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 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.07        14.27         3.02        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        13.78        13.58        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        80.91         4.18 
TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 
       58.82         1.45        74.30        45.40        33.47       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
       39.32         1.41        30.18       102.84        65.39       124.04 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        37.25       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        38.66        52.73       139.00       131.15 
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        12.16       147.42 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      130.72       129.57        32.48       116.91        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
       95.38        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       50.33        53.06        47.38        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT 
       37.78        29.95        13.32        11.87        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE 
       20.91        12.36        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-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 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         2.99        12.30        15.19        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        13.84        19.73        12.07        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        18.97        15.68        14.14        19.63 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        16.44        16.77        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        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        11.15         7.33        12.53        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
        7.82        11.51        16.41        15.62        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 
       18.38        29.49        54.05        22.09        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        61.02        58.72        57.11        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       59.15        28.24         5.85         4.18         2.43         5.56 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       24.72        38.30        42.25         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       69.24        59.87        43.50         0.30        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       102.90        66.77        81.34 
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        46.06         4.08         0.89        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM 
       48.10        91.17         1.25         1.15        17.82         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
        1.51         0.76         0.03         4.67        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         6.87         4.14         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
        4.54         0.89         1.35         1.15         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        10.26        16.90         9.80         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        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        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        12.43         6.74        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        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

  AMP PEAK 55(20Q13.2) MUTATED AMP PEAK 55(20Q13.2) WILD-TYPE 
                          0.72                           0.03 
  AMP PEAK 55(20Q13.2) MUTATED AMP PEAK 55(20Q13.2) WILD-TYPE 
                         98.56                         158.83 
  AMP PEAK 55(20Q13.2) MUTATED AMP PEAK 55(20Q13.2) WILD-TYPE 
                        12.260                         16.685 
[1] "0.7 - 98.6 (12.3)"  "0.0 - 158.8 (16.7)"
[1] "hr=" "2.8"
D51V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 55(20Q13.2) MUTATED         4        4         4        1         0
  AMP PEAK 55(20Q13.2) WILD-TYPE     276       47       105        1        45
                                vv
clus                             STAGE IVC
  AMP PEAK 55(20Q13.2) MUTATED           0
  AMP PEAK 55(20Q13.2) WILD-TYPE         6
D51V3, multiclass
           clus
vv          AMP PEAK 55(20Q13.2) MUTATED AMP PEAK 55(20Q13.2) WILD-TYPE
  STAGE I                              4                            276
  STAGE II                             4                             47
  STAGE III                            4                            105
  STAGE IV                             1                              1
  STAGE IVA                            0                             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 55(20Q13.2) MUTATED     2   4   6   1
  AMP PEAK 55(20Q13.2) WILD-TYPE 138 162 159  20
D51V4, multiclass
    clus
vv   AMP PEAK 55(20Q13.2) MUTATED AMP PEAK 55(20Q13.2) WILD-TYPE
  T1                            2                            138
  T2                            4                            162
  T3                            6                            159
  T4                            1                             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"
D51V5, binary
                                cls
clus                               0   1
  AMP PEAK 55(20Q13.2) MUTATED     7   2
  AMP PEAK 55(20Q13.2) WILD-TYPE 216 220
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 55(20Q13.2) MUTATED      7    2
  AMP PEAK 55(20Q13.2) WILD-TYPE  216  220
   clus
vv  AMP PEAK 55(20Q13.2) MUTATED AMP PEAK 55(20Q13.2) WILD-TYPE
  0                            7                            216
  1                            2                            220
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 55(20Q13.2) MUTATED     1   0  12
  AMP PEAK 55(20Q13.2) WILD-TYPE 272   9 200
D51V6, multiclass
    clus
vv   AMP PEAK 55(20Q13.2) MUTATED AMP PEAK 55(20Q13.2) WILD-TYPE
  M0                            1                            272
  M1                            0                              9
  MX                           12                            200
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, binary
                                cls
clus                               0   1
  AMP PEAK 55(20Q13.2) MUTATED     9   4
  AMP PEAK 55(20Q13.2) WILD-TYPE 355 127
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 55(20Q13.2) MUTATED      9    4
  AMP PEAK 55(20Q13.2) WILD-TYPE  355  127
        clus
vv       AMP PEAK 55(20Q13.2) MUTATED AMP PEAK 55(20Q13.2) WILD-TYPE
  FEMALE                            9                            355
  MALE                              4                            127
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 55(20Q13.2) MUTATED                0
  AMP PEAK 55(20Q13.2) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 55(20Q13.2) MUTATED                                               4
  AMP PEAK 55(20Q13.2) WILD-TYPE                                           349
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 55(20Q13.2) MUTATED                                                                        8
  AMP PEAK 55(20Q13.2) WILD-TYPE                                                                     90
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 55(20Q13.2) MUTATED                                                                     1
  AMP PEAK 55(20Q13.2) WILD-TYPE                                                                  34
D51V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 55(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 55(20Q13.2) WILD-TYPE
  OTHER  SPECIFY                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     349
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             90
  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"
D51V9, binary
                                cls
clus                               0   1
  AMP PEAK 55(20Q13.2) MUTATED     0  13
  AMP PEAK 55(20Q13.2) WILD-TYPE  14 468
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 55(20Q13.2) MUTATED      0   13
  AMP PEAK 55(20Q13.2) WILD-TYPE   14  468
     clus
vv    AMP PEAK 55(20Q13.2) MUTATED AMP PEAK 55(20Q13.2) WILD-TYPE
  NO                             0                             14
  YES                           13                            468
[1] 2 2
[1] FALSE
D51V10, binary
                                cls
clus                               0   1
  AMP PEAK 55(20Q13.2) MUTATED    12   0
  AMP PEAK 55(20Q13.2) WILD-TYPE 405  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 55(20Q13.2) MUTATED     12    0
  AMP PEAK 55(20Q13.2) WILD-TYPE  405   17
     clus
vv    AMP PEAK 55(20Q13.2) MUTATED AMP PEAK 55(20Q13.2) WILD-TYPE
  NO                            12                            405
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 55(20Q13.2) MUTATED              2                       0   10
  AMP PEAK 55(20Q13.2) WILD-TYPE          128                      16  318
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 55(20Q13.2) MUTATED                     1
  AMP PEAK 55(20Q13.2) WILD-TYPE                   0
D51V11, multiclass
                         clus
vv                        AMP PEAK 55(20Q13.2) MUTATED
  MINIMAL (T3)                                       2
  MODERATE/ADVANCED (T4A)                            0
  NONE                                              10
  VERY ADVANCED (T4B)                                1
                         clus
vv                        AMP PEAK 55(20Q13.2) WILD-TYPE
  MINIMAL (T3)                                       128
  MODERATE/ADVANCED (T4A)                             16
  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 55(20Q13.2) MUTATED    10   2   0   1
  AMP PEAK 55(20Q13.2) WILD-TYPE 368  49   4  29
D51V12, multiclass
    clus
vv   AMP PEAK 55(20Q13.2) MUTATED AMP PEAK 55(20Q13.2) WILD-TYPE
  R0                           10                            368
  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"
D51V13, continuous
D51V14, binary
                                cls
clus                               0   1
  AMP PEAK 55(20Q13.2) MUTATED     7   6
  AMP PEAK 55(20Q13.2) WILD-TYPE 217 255
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 55(20Q13.2) MUTATED      7    6
  AMP PEAK 55(20Q13.2) WILD-TYPE  217  255
            clus
vv           AMP PEAK 55(20Q13.2) MUTATED AMP PEAK 55(20Q13.2) WILD-TYPE
  MULTIFOCAL                            7                            217
  UNIFOCAL                              6                            255
[1] 2 2
[1] FALSE
D51V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 55(20Q13.2) MUTATED                                  0     0
  AMP PEAK 55(20Q13.2) WILD-TYPE                                1    49
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 55(20Q13.2) MUTATED                           1     5
  AMP PEAK 55(20Q13.2) WILD-TYPE                        25   316
D51V16, multiclass
                                  clus
vv                                 AMP PEAK 55(20Q13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                       5
                                  clus
vv                                 AMP PEAK 55(20Q13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        49
  BLACK OR AFRICAN AMERICAN                                    25
  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"
D51V17, binary
                                cls
clus                               0   1
  AMP PEAK 55(20Q13.2) MUTATED     0   6
  AMP PEAK 55(20Q13.2) WILD-TYPE  38 344
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 55(20Q13.2) MUTATED      0    6
  AMP PEAK 55(20Q13.2) WILD-TYPE   38  344
                        clus
vv                       AMP PEAK 55(20Q13.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            6
                        clus
vv                       AMP PEAK 55(20Q13.2) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            344
[1] 2 2
[1] FALSE

Clustering(52) Variable = AMP PEAK 56(21Q21.3) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 56(21Q21.3) MUTATED     6   0
  AMP PEAK 56(21Q21.3) WILD-TYPE 471  14
  AMP PEAK 56(21Q21.3) MUTATED AMP PEAK 56(21Q21.3) WILD-TYPE 
                             6                            485 
  AMP PEAK 56(21Q21.3) MUTATED AMP PEAK 56(21Q21.3) WILD-TYPE 
                             0                             14 
$`AMP PEAK 56(21Q21.3) MUTATED`
TCGA-BJ-A45E TCGA-E8-A242 TCGA-EL-A3ZR TCGA-EM-A3SY TCGA-ET-A2MZ TCGA-ET-A39N 
        0.03         1.15        48.16        13.51        12.26        98.56 

$`AMP PEAK 56(21Q21.3) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
       18.64         5.75         6.48         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A2EA 
       66.38        40.21        63.19        30.31        14.04        22.29 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT 
       53.06        47.38        52.50        45.53         7.07        44.65 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       45.80        19.30        45.96        37.94        31.04        19.59 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        33.60        28.73        41.13        37.78        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       13.32        11.87         8.71        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
       12.36        18.05        19.79        19.46        54.21        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        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       10.49        13.15        22.16        13.84        19.73        17.59 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       12.07        17.59        17.46        17.29        14.60        17.46 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       18.97        15.68        14.14        19.63        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       16.44        16.77        27.95        23.77        16.80        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 
       11.15         7.33        12.53         9.24        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       11.51        16.41        15.62        12.79        70.65        16.90 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        9.01         4.83         8.61         8.38         9.80         5.03 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       37.87        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       29.49        54.05        22.09        16.08        29.19        19.76 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        58.22        13.74        71.01        80.02        65.36 
TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24         5.85         4.18         2.43         5.56        24.72 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       38.30        42.25         2.37         4.50        80.81        69.24 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       59.87        43.50         0.30        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        4.01         1.94        73.74        59.70        31.59        44.25 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       102.90        66.77        81.34        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 
       46.06         4.08         0.89        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
       91.17         1.25         1.15        17.82         1.64         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
        1.51         0.76         0.03         4.67        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         6.87         4.14         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
        4.54         0.89         1.35         1.15         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        10.26        16.90         9.80         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        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        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        12.43         6.74        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         0.72 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       16.64        32.45         8.71        10.98         5.19 

  AMP PEAK 56(21Q21.3) MUTATED AMP PEAK 56(21Q21.3) WILD-TYPE 
                          0.03                           0.03 
  AMP PEAK 56(21Q21.3) MUTATED AMP PEAK 56(21Q21.3) WILD-TYPE 
                         98.56                         158.83 
  AMP PEAK 56(21Q21.3) MUTATED AMP PEAK 56(21Q21.3) WILD-TYPE 
                        12.885                         16.640 
[1] "0.0 - 98.6 (12.9)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "9200000"
D52V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 56(21Q21.3) MUTATED         4        1         1        0         0
  AMP PEAK 56(21Q21.3) WILD-TYPE     276       50       108        2        45
                                vv
clus                             STAGE IVC
  AMP PEAK 56(21Q21.3) MUTATED           0
  AMP PEAK 56(21Q21.3) WILD-TYPE         6
D52V3, multiclass
           clus
vv          AMP PEAK 56(21Q21.3) MUTATED AMP PEAK 56(21Q21.3) WILD-TYPE
  STAGE I                              4                            276
  STAGE II                             1                             50
  STAGE III                            1                            108
  STAGE IV                             0                              2
  STAGE IVA                            0                             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(21Q21.3) MUTATED     3   1   2   0
  AMP PEAK 56(21Q21.3) WILD-TYPE 137 165 163  21
D52V4, multiclass
    clus
vv   AMP PEAK 56(21Q21.3) MUTATED AMP PEAK 56(21Q21.3) WILD-TYPE
  T1                            3                            137
  T2                            1                            165
  T3                            2                            163
  T4                            0                             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"
D52V5, binary
                                cls
clus                               0   1
  AMP PEAK 56(21Q21.3) MUTATED     4   0
  AMP PEAK 56(21Q21.3) WILD-TYPE 219 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 56(21Q21.3) MUTATED      4    0
  AMP PEAK 56(21Q21.3) WILD-TYPE  219  222
   clus
vv  AMP PEAK 56(21Q21.3) MUTATED AMP PEAK 56(21Q21.3) WILD-TYPE
  0                            4                            219
  1                            0                            222
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 56(21Q21.3) MUTATED     2   0   4
  AMP PEAK 56(21Q21.3) WILD-TYPE 271   9 208
D52V6, multiclass
    clus
vv   AMP PEAK 56(21Q21.3) MUTATED AMP PEAK 56(21Q21.3) WILD-TYPE
  M0                            2                            271
  M1                            0                              9
  MX                            4                            208
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                                cls
clus                               0   1
  AMP PEAK 56(21Q21.3) MUTATED     4   2
  AMP PEAK 56(21Q21.3) WILD-TYPE 360 129
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 56(21Q21.3) MUTATED      4    2
  AMP PEAK 56(21Q21.3) WILD-TYPE  360  129
        clus
vv       AMP PEAK 56(21Q21.3) MUTATED AMP PEAK 56(21Q21.3) WILD-TYPE
  FEMALE                            4                            360
  MALE                              2                            129
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 56(21Q21.3) MUTATED                0
  AMP PEAK 56(21Q21.3) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 56(21Q21.3) MUTATED                                               5
  AMP PEAK 56(21Q21.3) WILD-TYPE                                           348
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 56(21Q21.3) MUTATED                                                                        1
  AMP PEAK 56(21Q21.3) WILD-TYPE                                                                     97
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 56(21Q21.3) MUTATED                                                                     0
  AMP PEAK 56(21Q21.3) WILD-TYPE                                                                  35
D52V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 56(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 56(21Q21.3) WILD-TYPE
  OTHER  SPECIFY                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     348
  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"
D52V9, binary
                                cls
clus                               0   1
  AMP PEAK 56(21Q21.3) MUTATED     0   6
  AMP PEAK 56(21Q21.3) WILD-TYPE  14 475
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 56(21Q21.3) MUTATED      0    6
  AMP PEAK 56(21Q21.3) WILD-TYPE   14  475
     clus
vv    AMP PEAK 56(21Q21.3) MUTATED AMP PEAK 56(21Q21.3) WILD-TYPE
  NO                             0                             14
  YES                            6                            475
[1] 2 2
[1] FALSE
D52V10, binary
                                cls
clus                               0   1
  AMP PEAK 56(21Q21.3) MUTATED     5   0
  AMP PEAK 56(21Q21.3) WILD-TYPE 412  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 56(21Q21.3) MUTATED      5    0
  AMP PEAK 56(21Q21.3) WILD-TYPE  412   17
     clus
vv    AMP PEAK 56(21Q21.3) MUTATED AMP PEAK 56(21Q21.3) WILD-TYPE
  NO                             5                            412
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 56(21Q21.3) MUTATED              1                       0    4
  AMP PEAK 56(21Q21.3) WILD-TYPE          129                      16  324
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 56(21Q21.3) MUTATED                     0
  AMP PEAK 56(21Q21.3) WILD-TYPE                   1
D52V11, multiclass
                         clus
vv                        AMP PEAK 56(21Q21.3) MUTATED
  MINIMAL (T3)                                       1
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               4
  VERY ADVANCED (T4B)                                0
                         clus
vv                        AMP PEAK 56(21Q21.3) WILD-TYPE
  MINIMAL (T3)                                       129
  MODERATE/ADVANCED (T4A)                             16
  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 56(21Q21.3) MUTATED     3   1   0   1
  AMP PEAK 56(21Q21.3) WILD-TYPE 375  50   4  29
D52V12, multiclass
    clus
vv   AMP PEAK 56(21Q21.3) MUTATED AMP PEAK 56(21Q21.3) WILD-TYPE
  R0                            3                            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"
D52V13, continuous
D52V14, binary
                                cls
clus                               0   1
  AMP PEAK 56(21Q21.3) MUTATED     0   6
  AMP PEAK 56(21Q21.3) WILD-TYPE 224 255
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 56(21Q21.3) MUTATED      0    6
  AMP PEAK 56(21Q21.3) WILD-TYPE  224  255
            clus
vv           AMP PEAK 56(21Q21.3) MUTATED AMP PEAK 56(21Q21.3) WILD-TYPE
  MULTIFOCAL                            0                            224
  UNIFOCAL                              6                            255
[1] 2 2
[1] FALSE
D52V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 56(21Q21.3) MUTATED                                  0     0
  AMP PEAK 56(21Q21.3) WILD-TYPE                                1    49
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 56(21Q21.3) MUTATED                           0     5
  AMP PEAK 56(21Q21.3) WILD-TYPE                        26   316
D52V16, multiclass
                                  clus
vv                                 AMP PEAK 56(21Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       5
                                  clus
vv                                 AMP PEAK 56(21Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        49
  BLACK OR AFRICAN AMERICAN                                    26
  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"
D52V17, binary
                                cls
clus                               0   1
  AMP PEAK 56(21Q21.3) MUTATED     0   5
  AMP PEAK 56(21Q21.3) WILD-TYPE  38 345
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 56(21Q21.3) MUTATED      0    5
  AMP PEAK 56(21Q21.3) WILD-TYPE   38  345
                        clus
vv                       AMP PEAK 56(21Q21.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            5
                        clus
vv                       AMP PEAK 56(21Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            345
[1] 2 2
[1] FALSE

Clustering(53) Variable = AMP PEAK 57(22Q11.21) MUTATION ANALYSIS
D53V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 57(22Q11.21) MUTATED     7   0
  AMP PEAK 57(22Q11.21) WILD-TYPE 470  14
  AMP PEAK 57(22Q11.21) MUTATED AMP PEAK 57(22Q11.21) WILD-TYPE 
                              7                             484 
  AMP PEAK 57(22Q11.21) MUTATED AMP PEAK 57(22Q11.21) WILD-TYPE 
                              0                              14 
$`AMP PEAK 57(22Q11.21) MUTATED`
TCGA-BJ-A45E TCGA-DJ-A3UP TCGA-EM-A22K TCGA-EM-A22N TCGA-ET-A3DT TCGA-FY-A3W9 
        0.03        16.41        15.75        10.65        17.98         0.76 
TCGA-QD-A8IV 
        5.19 

$`AMP PEAK 57(22Q11.21) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
       18.64         5.75         6.48         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
TCGA-DJ-A3UO TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU 
       31.46        19.56        36.33        32.81        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04         1.15        22.29 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        12.36        18.05        19.79        19.46        54.21 
TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22L TCGA-EM-A22M 
       57.01        54.08        14.73        14.50        10.45        14.53 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT 
       23.51         6.05         2.99        12.30        15.19        10.49 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        13.84        19.73        17.59        12.07 
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        17.46        18.97 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        19.63        13.38         8.35        16.44 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       16.77        27.95        23.77        16.80        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        11.15 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33        12.53         9.24        13.91         7.82        11.51 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       16.41        15.62        13.51        12.79        70.65        16.90 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        9.01         4.83         8.61         8.38         9.80         5.03 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       37.87        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       29.49        54.05        22.09        12.26        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       65.36        84.89        98.56        61.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        59.15        28.24         5.85         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DU 
       80.81        69.24        59.87        43.50         0.30        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       102.90        66.77        81.34 
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        46.06         4.08         0.89        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 
       48.10        91.17         1.25         1.15        17.82         1.64 
TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
        0.99         1.51         0.76         0.03         4.67        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         6.87         4.14         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
        4.54         0.89         1.35         1.15         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        10.26        16.90         9.80         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        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        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        12.43         6.74        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         0.72 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z 
       16.64        32.45         8.71        10.98 

  AMP PEAK 57(22Q11.21) MUTATED AMP PEAK 57(22Q11.21) WILD-TYPE 
                           0.03                            0.03 
  AMP PEAK 57(22Q11.21) MUTATED AMP PEAK 57(22Q11.21) WILD-TYPE 
                          17.98                          158.83 
  AMP PEAK 57(22Q11.21) MUTATED AMP PEAK 57(22Q11.21) WILD-TYPE 
                          10.65                           16.75 
[1] "0.0 - 18.0 (10.7)"  "0.0 - 158.8 (16.8)"
[1] "hr="     "1200000"
D53V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 57(22Q11.21) MUTATED         4        1         0        0         2
  AMP PEAK 57(22Q11.21) WILD-TYPE     276       50       109        2        43
                                 vv
clus                              STAGE IVC
  AMP PEAK 57(22Q11.21) MUTATED           0
  AMP PEAK 57(22Q11.21) WILD-TYPE         6
D53V3, multiclass
           clus
vv          AMP PEAK 57(22Q11.21) MUTATED AMP PEAK 57(22Q11.21) WILD-TYPE
  STAGE I                               4                             276
  STAGE II                              1                              50
  STAGE III                             0                             109
  STAGE IV                              0                               2
  STAGE IVA                             2                              43
  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(22Q11.21) MUTATED     3   3   1   0
  AMP PEAK 57(22Q11.21) WILD-TYPE 137 163 164  21
D53V4, multiclass
    clus
vv   AMP PEAK 57(22Q11.21) MUTATED AMP PEAK 57(22Q11.21) WILD-TYPE
  T1                             3                             137
  T2                             3                             163
  T3                             1                             164
  T4                             0                              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"
D53V5, binary
                                 cls
clus                                0   1
  AMP PEAK 57(22Q11.21) MUTATED     4   3
  AMP PEAK 57(22Q11.21) WILD-TYPE 219 219
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 57(22Q11.21) MUTATED      4    3
  AMP PEAK 57(22Q11.21) WILD-TYPE  219  219
   clus
vv  AMP PEAK 57(22Q11.21) MUTATED AMP PEAK 57(22Q11.21) WILD-TYPE
  0                             4                             219
  1                             3                             219
[1] 2 2
[1] FALSE
                                 vv
clus                               M0  M1  MX
  AMP PEAK 57(22Q11.21) MUTATED     2   0   5
  AMP PEAK 57(22Q11.21) WILD-TYPE 271   9 207
D53V6, multiclass
    clus
vv   AMP PEAK 57(22Q11.21) MUTATED AMP PEAK 57(22Q11.21) WILD-TYPE
  M0                             2                             271
  M1                             0                               9
  MX                             5                             207
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                                 cls
clus                                0   1
  AMP PEAK 57(22Q11.21) MUTATED     7   0
  AMP PEAK 57(22Q11.21) WILD-TYPE 357 131
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 57(22Q11.21) MUTATED      7    0
  AMP PEAK 57(22Q11.21) WILD-TYPE  357  131
        clus
vv       AMP PEAK 57(22Q11.21) MUTATED AMP PEAK 57(22Q11.21) WILD-TYPE
  FEMALE                             7                             357
  MALE                               0                             131
[1] 2 2
[1] FALSE
                                 vv
clus                              OTHER  SPECIFY
  AMP PEAK 57(22Q11.21) MUTATED                0
  AMP PEAK 57(22Q11.21) WILD-TYPE              9
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 57(22Q11.21) MUTATED                                               4
  AMP PEAK 57(22Q11.21) WILD-TYPE                                           349
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 57(22Q11.21) MUTATED                                                                        3
  AMP PEAK 57(22Q11.21) WILD-TYPE                                                                     95
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 57(22Q11.21) MUTATED                                                                     0
  AMP PEAK 57(22Q11.21) WILD-TYPE                                                                  35
D53V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 57(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 57(22Q11.21) WILD-TYPE
  OTHER  SPECIFY                                                                                       9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      349
  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"
D53V9, binary
                                 cls
clus                                0   1
  AMP PEAK 57(22Q11.21) MUTATED     0   7
  AMP PEAK 57(22Q11.21) WILD-TYPE  14 474
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 57(22Q11.21) MUTATED      0    7
  AMP PEAK 57(22Q11.21) WILD-TYPE   14  474
     clus
vv    AMP PEAK 57(22Q11.21) MUTATED AMP PEAK 57(22Q11.21) WILD-TYPE
  NO                              0                              14
  YES                             7                             474
[1] 2 2
[1] FALSE
D53V10, binary
                                 cls
clus                                0   1
  AMP PEAK 57(22Q11.21) MUTATED     6   0
  AMP PEAK 57(22Q11.21) WILD-TYPE 411  17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 57(22Q11.21) MUTATED      6    0
  AMP PEAK 57(22Q11.21) WILD-TYPE  411   17
     clus
vv    AMP PEAK 57(22Q11.21) MUTATED AMP PEAK 57(22Q11.21) WILD-TYPE
  NO                              6                             411
  YES                             0                              17
[1] 2 2
[1] FALSE
                                 vv
clus                              MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 57(22Q11.21) MUTATED              1                       0    5
  AMP PEAK 57(22Q11.21) WILD-TYPE          129                      16  323
                                 vv
clus                              VERY ADVANCED (T4B)
  AMP PEAK 57(22Q11.21) MUTATED                     0
  AMP PEAK 57(22Q11.21) WILD-TYPE                   1
D53V11, multiclass
                         clus
vv                        AMP PEAK 57(22Q11.21) MUTATED
  MINIMAL (T3)                                        1
  MODERATE/ADVANCED (T4A)                             0
  NONE                                                5
  VERY ADVANCED (T4B)                                 0
                         clus
vv                        AMP PEAK 57(22Q11.21) WILD-TYPE
  MINIMAL (T3)                                        129
  MODERATE/ADVANCED (T4A)                              16
  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 57(22Q11.21) MUTATED     2   2   0   2
  AMP PEAK 57(22Q11.21) WILD-TYPE 376  49   4  28
D53V12, multiclass
    clus
vv   AMP PEAK 57(22Q11.21) MUTATED AMP PEAK 57(22Q11.21) WILD-TYPE
  R0                             2                             376
  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"
D53V13, continuous
D53V14, binary
                                 cls
clus                                0   1
  AMP PEAK 57(22Q11.21) MUTATED     3   4
  AMP PEAK 57(22Q11.21) WILD-TYPE 221 257
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 57(22Q11.21) MUTATED      3    4
  AMP PEAK 57(22Q11.21) WILD-TYPE  221  257
            clus
vv           AMP PEAK 57(22Q11.21) MUTATED AMP PEAK 57(22Q11.21) WILD-TYPE
  MULTIFOCAL                             3                             221
  UNIFOCAL                               4                             257
[1] 2 2
[1] FALSE
D53V15, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 57(22Q11.21) MUTATED                                  0     0
  AMP PEAK 57(22Q11.21) WILD-TYPE                                1    49
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 57(22Q11.21) MUTATED                           1     3
  AMP PEAK 57(22Q11.21) WILD-TYPE                        25   318
D53V16, multiclass
                                  clus
vv                                 AMP PEAK 57(22Q11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                    1
  WHITE                                                        3
                                  clus
vv                                 AMP PEAK 57(22Q11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         49
  BLACK OR AFRICAN AMERICAN                                     25
  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"
D53V17, binary
                                 cls
clus                                0   1
  AMP PEAK 57(22Q11.21) MUTATED     1   4
  AMP PEAK 57(22Q11.21) WILD-TYPE  37 346
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 57(22Q11.21) MUTATED      1    4
  AMP PEAK 57(22Q11.21) WILD-TYPE   37  346
                        clus
vv                       AMP PEAK 57(22Q11.21) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                             4
                        clus
vv                       AMP PEAK 57(22Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                  37
  NOT HISPANIC OR LATINO                             346
[1] 2 2
[1] FALSE

Clustering(54) Variable = AMP PEAK 58(XP22.12) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 58(XP22.12) MUTATED     9   1
  AMP PEAK 58(XP22.12) WILD-TYPE 468  13
  AMP PEAK 58(XP22.12) MUTATED AMP PEAK 58(XP22.12) WILD-TYPE 
                            10                            481 
  AMP PEAK 58(XP22.12) MUTATED AMP PEAK 58(XP22.12) WILD-TYPE 
                             1                             13 
$`AMP PEAK 58(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        54.21        57.01        10.65 
TCGA-EM-A3AI TCGA-ET-A40S TCGA-FY-A3NM TCGA-QD-A8IV 
       17.46         5.03         0.99         5.19 

$`AMP PEAK 58(XP22.12) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       24.79        18.21        16.34        14.73         8.25        18.87 
TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ 
        4.01        11.57        16.73         7.56        15.12        17.69 
TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       23.34        20.71        20.58         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
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        15.48        23.31        18.64         5.75 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
        6.48         0.03         3.45         6.35         7.82         6.18 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
        5.06         8.98         4.93         5.98         0.53         0.10 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
        0.20         0.23        11.38        10.68         0.10         0.39 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.10        20.22        15.42        36.46         5.98        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-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
        4.27         3.22         2.76        17.26        14.07       137.88 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
        3.39         8.71        25.35        13.41        11.90        14.60 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        7.99        11.01       100.01        18.51        13.12         7.99 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96         7.20         1.45         8.88         1.02         5.95 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS 
       10.09         7.99         5.33         8.48        10.45         1.51 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY 
        9.60        12.56         8.28         7.69         5.52         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.42         8.12         9.34         6.77         9.21         9.44 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
        9.90         8.61        10.09         7.07        10.36        12.43 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        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        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04         1.15        22.29 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA 
       32.48       116.91        98.24        41.29        95.38        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN 
       82.82        77.36        78.97        31.50        50.33        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        52.50        45.53        48.16         7.07        44.65 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       45.80        19.30        45.96        37.94        31.04        19.59 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        33.60        28.73        41.13        37.78        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       13.32        11.87         8.71        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I 
       12.36        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        11.74        11.15 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        16.44        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        2.99        12.30        15.19        10.49        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       13.84        19.73        17.59        12.07        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        18.97        15.68        14.14        19.63 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        16.44        16.77        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        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        11.15         7.33        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       13.91         7.82        11.51        16.41        15.62        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        70.65        16.90         9.01         4.83         8.61 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
        8.38         9.80         5.03        37.87        12.72         0.95 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       47.47        48.20        29.69        32.35        14.79        12.33 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       14.79        27.09        18.38        29.49        54.05        22.09 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       12.26        16.08        29.19        19.76         2.66        58.22 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
       13.74        71.01        80.02        65.36        84.89        98.56 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
       61.02        58.72        57.11        55.10        59.15        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
        5.85         4.18         2.43         5.56        24.72        38.30 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       42.25         2.37         4.50        80.81        69.24        59.87 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       43.50         0.30        17.98        25.32       132.36        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        3.22         7.17         4.80         2.14         4.01         1.94 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        59.70        31.59        44.25        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      102.90        66.77        81.34        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        46.06         4.08 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        0.89        22.03         0.92        48.10        91.17         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        1.15        17.82         1.64         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
        4.67        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 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
        1.15         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        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90         9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74 
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         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z 
       10.98 

  AMP PEAK 58(XP22.12) MUTATED AMP PEAK 58(XP22.12) WILD-TYPE 
                          0.99                           0.03 
  AMP PEAK 58(XP22.12) MUTATED AMP PEAK 58(XP22.12) WILD-TYPE 
                         57.01                         158.83 
  AMP PEAK 58(XP22.12) MUTATED AMP PEAK 58(XP22.12) WILD-TYPE 
                        12.215                         16.640 
[1] "1.0 - 57.0 (12.2)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "5.5"
D54V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 58(XP22.12) MUTATED         2        4         2        1         1
  AMP PEAK 58(XP22.12) WILD-TYPE     278       47       107        1        44
                                vv
clus                             STAGE IVC
  AMP PEAK 58(XP22.12) MUTATED           0
  AMP PEAK 58(XP22.12) WILD-TYPE         6
D54V3, multiclass
           clus
vv          AMP PEAK 58(XP22.12) MUTATED AMP PEAK 58(XP22.12) WILD-TYPE
  STAGE I                              2                            278
  STAGE II                             4                             47
  STAGE III                            2                            107
  STAGE IV                             1                              1
  STAGE IVA                            1                             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 58(XP22.12) MUTATED     1   5   3   1
  AMP PEAK 58(XP22.12) WILD-TYPE 139 161 162  20
D54V4, multiclass
    clus
vv   AMP PEAK 58(XP22.12) MUTATED AMP PEAK 58(XP22.12) WILD-TYPE
  T1                            1                            139
  T2                            5                            161
  T3                            3                            162
  T4                            1                             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"
D54V5, binary
                                cls
clus                               0   1
  AMP PEAK 58(XP22.12) MUTATED     7   2
  AMP PEAK 58(XP22.12) WILD-TYPE 216 220
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 58(XP22.12) MUTATED      7    2
  AMP PEAK 58(XP22.12) WILD-TYPE  216  220
   clus
vv  AMP PEAK 58(XP22.12) MUTATED AMP PEAK 58(XP22.12) WILD-TYPE
  0                            7                            216
  1                            2                            220
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 58(XP22.12) MUTATED     1   0   9
  AMP PEAK 58(XP22.12) WILD-TYPE 272   9 203
D54V6, multiclass
    clus
vv   AMP PEAK 58(XP22.12) MUTATED AMP PEAK 58(XP22.12) WILD-TYPE
  M0                            1                            272
  M1                            0                              9
  MX                            9                            203
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                                cls
clus                               0   1
  AMP PEAK 58(XP22.12) MUTATED     8   2
  AMP PEAK 58(XP22.12) WILD-TYPE 356 129
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 58(XP22.12) MUTATED      8    2
  AMP PEAK 58(XP22.12) WILD-TYPE  356  129
        clus
vv       AMP PEAK 58(XP22.12) MUTATED AMP PEAK 58(XP22.12) WILD-TYPE
  FEMALE                            8                            356
  MALE                              2                            129
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 58(XP22.12) MUTATED                0
  AMP PEAK 58(XP22.12) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 58(XP22.12) MUTATED                                               6
  AMP PEAK 58(XP22.12) WILD-TYPE                                           347
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 58(XP22.12) MUTATED                                                                        4
  AMP PEAK 58(XP22.12) WILD-TYPE                                                                     94
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 58(XP22.12) MUTATED                                                                     0
  AMP PEAK 58(XP22.12) WILD-TYPE                                                                  35
D54V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 58(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 58(XP22.12) WILD-TYPE
  OTHER  SPECIFY                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     347
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             94
  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"
D54V9, binary
                                cls
clus                               0   1
  AMP PEAK 58(XP22.12) MUTATED     0  10
  AMP PEAK 58(XP22.12) WILD-TYPE  14 471
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 58(XP22.12) MUTATED      0   10
  AMP PEAK 58(XP22.12) WILD-TYPE   14  471
     clus
vv    AMP PEAK 58(XP22.12) MUTATED AMP PEAK 58(XP22.12) WILD-TYPE
  NO                             0                             14
  YES                           10                            471
[1] 2 2
[1] FALSE
D54V10, binary
                                cls
clus                               0   1
  AMP PEAK 58(XP22.12) MUTATED     8   1
  AMP PEAK 58(XP22.12) WILD-TYPE 409  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 58(XP22.12) MUTATED      8    1
  AMP PEAK 58(XP22.12) WILD-TYPE  409   16
     clus
vv    AMP PEAK 58(XP22.12) MUTATED AMP PEAK 58(XP22.12) WILD-TYPE
  NO                             8                            409
  YES                            1                             16
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 58(XP22.12) MUTATED              2                       0    7
  AMP PEAK 58(XP22.12) WILD-TYPE          128                      16  321
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 58(XP22.12) MUTATED                     1
  AMP PEAK 58(XP22.12) WILD-TYPE                   0
D54V11, multiclass
                         clus
vv                        AMP PEAK 58(XP22.12) MUTATED
  MINIMAL (T3)                                       2
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               7
  VERY ADVANCED (T4B)                                1
                         clus
vv                        AMP PEAK 58(XP22.12) WILD-TYPE
  MINIMAL (T3)                                       128
  MODERATE/ADVANCED (T4A)                             16
  NONE                                               321
  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(XP22.12) MUTATED     5   2   0   3
  AMP PEAK 58(XP22.12) WILD-TYPE 373  49   4  27
D54V12, multiclass
    clus
vv   AMP PEAK 58(XP22.12) MUTATED AMP PEAK 58(XP22.12) WILD-TYPE
  R0                            5                            373
  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"
D54V13, continuous
D54V14, binary
                                cls
clus                               0   1
  AMP PEAK 58(XP22.12) MUTATED     6   4
  AMP PEAK 58(XP22.12) WILD-TYPE 218 257
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 58(XP22.12) MUTATED      6    4
  AMP PEAK 58(XP22.12) WILD-TYPE  218  257
            clus
vv           AMP PEAK 58(XP22.12) MUTATED AMP PEAK 58(XP22.12) WILD-TYPE
  MULTIFOCAL                            6                            218
  UNIFOCAL                              4                            257
[1] 2 2
[1] FALSE
D54V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 58(XP22.12) MUTATED                                  0     0
  AMP PEAK 58(XP22.12) WILD-TYPE                                1    49
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 58(XP22.12) MUTATED                           1     4
  AMP PEAK 58(XP22.12) WILD-TYPE                        25   317
D54V16, multiclass
                                  clus
vv                                 AMP PEAK 58(XP22.12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                       4
                                  clus
vv                                 AMP PEAK 58(XP22.12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        49
  BLACK OR AFRICAN AMERICAN                                    25
  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"
D54V17, binary
                                cls
clus                               0   1
  AMP PEAK 58(XP22.12) MUTATED     0   6
  AMP PEAK 58(XP22.12) WILD-TYPE  38 344
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 58(XP22.12) MUTATED      0    6
  AMP PEAK 58(XP22.12) WILD-TYPE   38  344
                        clus
vv                       AMP PEAK 58(XP22.12) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            6
                        clus
vv                       AMP PEAK 58(XP22.12) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            344
[1] 2 2
[1] FALSE

Clustering(55) Variable = AMP PEAK 59(XP11.4) MUTATION ANALYSIS
D55V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 59(XP11.4) MUTATED     8   1
  AMP PEAK 59(XP11.4) WILD-TYPE 469  13
  AMP PEAK 59(XP11.4) MUTATED AMP PEAK 59(XP11.4) WILD-TYPE 
                            9                           482 
  AMP PEAK 59(XP11.4) MUTATED AMP PEAK 59(XP11.4) WILD-TYPE 
                            1                            13 
$`AMP PEAK 59(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        54.21        57.01        10.65 
TCGA-EM-A3AI TCGA-ET-A40S TCGA-FY-A3NM 
       17.46         5.03         0.99 

$`AMP PEAK 59(XP11.4) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
        1.22        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        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
        4.27         3.22         2.76        17.26        14.07       137.88 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
        3.39         8.71        25.35        13.41        11.90        14.60 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        7.99        11.01       100.01        18.51        13.12         7.99 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96         7.20         1.45         8.88         1.02         5.95 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS 
       10.09         7.99         5.33         8.48        10.45         1.51 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY 
        9.60        12.56         8.28         7.69         5.52         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.42         8.12         9.34         6.77         9.21         9.44 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
        9.90         8.61        10.09         7.07        10.36        12.43 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        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        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04         1.15        22.29 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA 
       32.48       116.91        98.24        41.29        95.38        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN 
       82.82        77.36        78.97        31.50        50.33        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        52.50        45.53        48.16         7.07        44.65 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       45.80        19.30        45.96        37.94        31.04        19.59 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        33.60        28.73        41.13        37.78        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       13.32        11.87         8.71        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I 
       12.36        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        11.74        11.15 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        16.44        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        2.99        12.30        15.19        10.49        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       13.84        19.73        17.59        12.07        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        18.97        15.68        14.14        19.63 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        16.44        16.77        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        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        11.15         7.33        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       13.91         7.82        11.51        16.41        15.62        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        70.65        16.90         9.01         4.83         8.61 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
        8.38         9.80         5.03        37.87        12.72         0.95 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       47.47        48.20        29.69        32.35        14.79        12.33 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       14.79        27.09        18.38        29.49        54.05        22.09 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       12.26        16.08        29.19        19.76         2.66        58.22 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
       13.74        71.01        80.02        65.36        84.89        98.56 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
       61.02        58.72        57.11        55.10        59.15        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
        5.85         4.18         2.43         5.56        24.72        38.30 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       42.25         2.37         4.50        80.81        69.24        59.87 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       43.50         0.30        17.98        25.32       132.36        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        3.22         7.17         4.80         2.14         4.01         1.94 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        59.70        31.59        44.25        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      102.90        66.77        81.34        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        46.06         4.08 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        0.89        22.03         0.92        48.10        91.17         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        1.15        17.82         1.64         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
        4.67        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 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
        1.15         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        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90         9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74 
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         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  AMP PEAK 59(XP11.4) MUTATED AMP PEAK 59(XP11.4) WILD-TYPE 
                         0.99                          0.03 
  AMP PEAK 59(XP11.4) MUTATED AMP PEAK 59(XP11.4) WILD-TYPE 
                        57.01                        158.83 
  AMP PEAK 59(XP11.4) MUTATED AMP PEAK 59(XP11.4) WILD-TYPE 
                        17.46                         16.57 
[1] "1.0 - 57.0 (17.5)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "5.3"
D55V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 59(XP11.4) MUTATED         2        3         2        1         1
  AMP PEAK 59(XP11.4) WILD-TYPE     278       48       107        1        44
                               vv
clus                            STAGE IVC
  AMP PEAK 59(XP11.4) MUTATED           0
  AMP PEAK 59(XP11.4) WILD-TYPE         6
D55V3, multiclass
           clus
vv          AMP PEAK 59(XP11.4) MUTATED AMP PEAK 59(XP11.4) WILD-TYPE
  STAGE I                             2                           278
  STAGE II                            3                            48
  STAGE III                           2                           107
  STAGE IV                            1                             1
  STAGE IVA                           1                            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 59(XP11.4) MUTATED     1   4   3   1
  AMP PEAK 59(XP11.4) WILD-TYPE 139 162 162  20
D55V4, multiclass
    clus
vv   AMP PEAK 59(XP11.4) MUTATED AMP PEAK 59(XP11.4) WILD-TYPE
  T1                           1                           139
  T2                           4                           162
  T3                           3                           162
  T4                           1                            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"
D55V5, binary
                               cls
clus                              0   1
  AMP PEAK 59(XP11.4) MUTATED     6   2
  AMP PEAK 59(XP11.4) WILD-TYPE 217 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 59(XP11.4) MUTATED      6    2
  AMP PEAK 59(XP11.4) WILD-TYPE  217  220
   clus
vv  AMP PEAK 59(XP11.4) MUTATED AMP PEAK 59(XP11.4) WILD-TYPE
  0                           6                           217
  1                           2                           220
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK 59(XP11.4) MUTATED     2   0   7
  AMP PEAK 59(XP11.4) WILD-TYPE 271   9 205
D55V6, multiclass
    clus
vv   AMP PEAK 59(XP11.4) MUTATED AMP PEAK 59(XP11.4) WILD-TYPE
  M0                           2                           271
  M1                           0                             9
  MX                           7                           205
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                               cls
clus                              0   1
  AMP PEAK 59(XP11.4) MUTATED     7   2
  AMP PEAK 59(XP11.4) WILD-TYPE 357 129
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 59(XP11.4) MUTATED      7    2
  AMP PEAK 59(XP11.4) WILD-TYPE  357  129
        clus
vv       AMP PEAK 59(XP11.4) MUTATED AMP PEAK 59(XP11.4) WILD-TYPE
  FEMALE                           7                           357
  MALE                             2                           129
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 59(XP11.4) MUTATED                0
  AMP PEAK 59(XP11.4) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 59(XP11.4) MUTATED                                               5
  AMP PEAK 59(XP11.4) WILD-TYPE                                           348
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 59(XP11.4) MUTATED                                                                        4
  AMP PEAK 59(XP11.4) WILD-TYPE                                                                     94
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 59(XP11.4) MUTATED                                                                     0
  AMP PEAK 59(XP11.4) WILD-TYPE                                                                  35
D55V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 59(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 59(XP11.4) WILD-TYPE
  OTHER  SPECIFY                                                                                     9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    348
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            94
  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"
D55V9, binary
                               cls
clus                              0   1
  AMP PEAK 59(XP11.4) MUTATED     0   9
  AMP PEAK 59(XP11.4) WILD-TYPE  14 472
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 59(XP11.4) MUTATED      0    9
  AMP PEAK 59(XP11.4) WILD-TYPE   14  472
     clus
vv    AMP PEAK 59(XP11.4) MUTATED AMP PEAK 59(XP11.4) WILD-TYPE
  NO                            0                            14
  YES                           9                           472
[1] 2 2
[1] FALSE
D55V10, binary
                               cls
clus                              0   1
  AMP PEAK 59(XP11.4) MUTATED     8   1
  AMP PEAK 59(XP11.4) WILD-TYPE 409  16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 59(XP11.4) MUTATED      8    1
  AMP PEAK 59(XP11.4) WILD-TYPE  409   16
     clus
vv    AMP PEAK 59(XP11.4) MUTATED AMP PEAK 59(XP11.4) WILD-TYPE
  NO                            8                           409
  YES                           1                            16
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 59(XP11.4) MUTATED              1                       0    7
  AMP PEAK 59(XP11.4) WILD-TYPE          129                      16  321
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 59(XP11.4) MUTATED                     1
  AMP PEAK 59(XP11.4) WILD-TYPE                   0
D55V11, multiclass
                         clus
vv                        AMP PEAK 59(XP11.4) MUTATED
  MINIMAL (T3)                                      1
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              7
  VERY ADVANCED (T4B)                               1
                         clus
vv                        AMP PEAK 59(XP11.4) WILD-TYPE
  MINIMAL (T3)                                      129
  MODERATE/ADVANCED (T4A)                            16
  NONE                                              321
  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(XP11.4) MUTATED     5   2   0   2
  AMP PEAK 59(XP11.4) WILD-TYPE 373  49   4  28
D55V12, multiclass
    clus
vv   AMP PEAK 59(XP11.4) MUTATED AMP PEAK 59(XP11.4) WILD-TYPE
  R0                           5                           373
  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"
D55V13, continuous
D55V14, binary
                               cls
clus                              0   1
  AMP PEAK 59(XP11.4) MUTATED     5   4
  AMP PEAK 59(XP11.4) WILD-TYPE 219 257
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 59(XP11.4) MUTATED      5    4
  AMP PEAK 59(XP11.4) WILD-TYPE  219  257
            clus
vv           AMP PEAK 59(XP11.4) MUTATED AMP PEAK 59(XP11.4) WILD-TYPE
  MULTIFOCAL                           5                           219
  UNIFOCAL                             4                           257
[1] 2 2
[1] FALSE
D55V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 59(XP11.4) MUTATED                                  0     0
  AMP PEAK 59(XP11.4) WILD-TYPE                                1    49
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 59(XP11.4) MUTATED                           0     5
  AMP PEAK 59(XP11.4) WILD-TYPE                        26   316
D55V16, multiclass
                                  clus
vv                                 AMP PEAK 59(XP11.4) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      5
                                  clus
vv                                 AMP PEAK 59(XP11.4) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       49
  BLACK OR AFRICAN AMERICAN                                   26
  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"
D55V17, binary
                               cls
clus                              0   1
  AMP PEAK 59(XP11.4) MUTATED     0   5
  AMP PEAK 59(XP11.4) WILD-TYPE  38 345
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 59(XP11.4) MUTATED      0    5
  AMP PEAK 59(XP11.4) WILD-TYPE   38  345
                        clus
vv                       AMP PEAK 59(XP11.4) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           5
                        clus
vv                       AMP PEAK 59(XP11.4) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           345
[1] 2 2
[1] FALSE

Clustering(56) Variable = AMP PEAK 60(XP11.22) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 60(XP11.22) MUTATED     7   1
  AMP PEAK 60(XP11.22) WILD-TYPE 470  13
  AMP PEAK 60(XP11.22) MUTATED AMP PEAK 60(XP11.22) WILD-TYPE 
                             8                            483 
  AMP PEAK 60(XP11.22) MUTATED AMP PEAK 60(XP11.22) WILD-TYPE 
                             1                             13 
$`AMP PEAK 60(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        54.21        57.01        10.65        17.46 
TCGA-ET-A3BS TCGA-FY-A3NM 
        5.56         0.99 

$`AMP PEAK 60(XP11.22) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
        1.22        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        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
        1.45        74.30        45.40        33.47       108.36        39.32 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        30.18       102.84        65.39       124.04        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       37.25       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        38.66        52.73       139.00       131.15       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        12.16       147.42       130.72 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       116.91        98.24        41.29        95.38 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE 
       20.91        12.36        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        11.74 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.15        14.24        16.44        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
        6.05         2.99        12.30        15.19        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        13.84        19.73        17.59        12.07        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        18.97        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       19.63        13.38         8.35        16.44        16.77        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        16.80        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        11.15         7.33        12.53 
TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
        9.24        13.91         7.82        11.51        16.41        15.62 
TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       13.51        12.79        70.65        16.90         9.01         4.83 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
        8.61         8.38         9.80         5.03        37.87        12.72 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
        0.95        47.47        48.20        29.69        32.35        14.79 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       12.33        14.79        27.09        18.38        29.49        54.05 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       22.09        12.26        16.08        29.19        19.76         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       58.22        13.74        71.01        80.02        65.36        84.89 
TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       98.56        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BT TCGA-ET-A3BU 
       28.24         5.85         4.18         2.43        24.72        38.30 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       42.25         2.37         4.50        80.81        69.24        59.87 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       43.50         0.30        17.98        25.32       132.36        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
        3.22         7.17         4.80         5.03         2.14         4.01 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
        1.94        73.74        59.70        31.59        44.25        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       102.90        66.77        81.34        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        46.06 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.08         0.89        22.03         0.92        48.10        91.17 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25         1.15        17.82         1.64         1.51         0.76 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
        0.03         4.67        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         6.87         4.14         6.58         4.54         0.89 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35         1.15         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 
       10.26        16.90         9.80         9.63         2.96         8.65 
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        86.70         6.02        12.43 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
        6.74        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         0.72        16.64        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        8.71        10.98         5.19 

  AMP PEAK 60(XP11.22) MUTATED AMP PEAK 60(XP11.22) WILD-TYPE 
                          0.99                           0.03 
  AMP PEAK 60(XP11.22) MUTATED AMP PEAK 60(XP11.22) WILD-TYPE 
                         57.01                         158.83 
  AMP PEAK 60(XP11.22) MUTATED AMP PEAK 60(XP11.22) WILD-TYPE 
                        14.055                         16.570 
[1] "1.0 - 57.0 (14.1)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "5.6"
D56V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 60(XP11.22) MUTATED         3        2         2        1         0
  AMP PEAK 60(XP11.22) WILD-TYPE     277       49       107        1        45
                                vv
clus                             STAGE IVC
  AMP PEAK 60(XP11.22) MUTATED           0
  AMP PEAK 60(XP11.22) WILD-TYPE         6
D56V3, multiclass
           clus
vv          AMP PEAK 60(XP11.22) MUTATED AMP PEAK 60(XP11.22) WILD-TYPE
  STAGE I                              3                            277
  STAGE II                             2                             49
  STAGE III                            2                            107
  STAGE IV                             1                              1
  STAGE IVA                            0                             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(XP11.22) MUTATED     1   3   3   1
  AMP PEAK 60(XP11.22) WILD-TYPE 139 163 162  20
D56V4, multiclass
    clus
vv   AMP PEAK 60(XP11.22) MUTATED AMP PEAK 60(XP11.22) WILD-TYPE
  T1                            1                            139
  T2                            3                            163
  T3                            3                            162
  T4                            1                             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"
D56V5, binary
                                cls
clus                               0   1
  AMP PEAK 60(XP11.22) MUTATED     5   2
  AMP PEAK 60(XP11.22) WILD-TYPE 218 220
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 60(XP11.22) MUTATED      5    2
  AMP PEAK 60(XP11.22) WILD-TYPE  218  220
   clus
vv  AMP PEAK 60(XP11.22) MUTATED AMP PEAK 60(XP11.22) WILD-TYPE
  0                            5                            218
  1                            2                            220
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 60(XP11.22) MUTATED     1   0   7
  AMP PEAK 60(XP11.22) WILD-TYPE 272   9 205
D56V6, multiclass
    clus
vv   AMP PEAK 60(XP11.22) MUTATED AMP PEAK 60(XP11.22) WILD-TYPE
  M0                            1                            272
  M1                            0                              9
  MX                            7                            205
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                                cls
clus                               0   1
  AMP PEAK 60(XP11.22) MUTATED     7   1
  AMP PEAK 60(XP11.22) WILD-TYPE 357 130
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 60(XP11.22) MUTATED      7    1
  AMP PEAK 60(XP11.22) WILD-TYPE  357  130
        clus
vv       AMP PEAK 60(XP11.22) MUTATED AMP PEAK 60(XP11.22) WILD-TYPE
  FEMALE                            7                            357
  MALE                              1                            130
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 60(XP11.22) MUTATED                0
  AMP PEAK 60(XP11.22) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 60(XP11.22) MUTATED                                               4
  AMP PEAK 60(XP11.22) WILD-TYPE                                           349
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 60(XP11.22) MUTATED                                                                        4
  AMP PEAK 60(XP11.22) WILD-TYPE                                                                     94
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 60(XP11.22) MUTATED                                                                     0
  AMP PEAK 60(XP11.22) WILD-TYPE                                                                  35
D56V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 60(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 60(XP11.22) WILD-TYPE
  OTHER  SPECIFY                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     349
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             94
  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"
D56V9, binary
                                cls
clus                               0   1
  AMP PEAK 60(XP11.22) MUTATED     0   8
  AMP PEAK 60(XP11.22) WILD-TYPE  14 473
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 60(XP11.22) MUTATED      0    8
  AMP PEAK 60(XP11.22) WILD-TYPE   14  473
     clus
vv    AMP PEAK 60(XP11.22) MUTATED AMP PEAK 60(XP11.22) WILD-TYPE
  NO                             0                             14
  YES                            8                            473
[1] 2 2
[1] FALSE
D56V10, binary
                                cls
clus                               0   1
  AMP PEAK 60(XP11.22) MUTATED     7   1
  AMP PEAK 60(XP11.22) WILD-TYPE 410  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 60(XP11.22) MUTATED      7    1
  AMP PEAK 60(XP11.22) WILD-TYPE  410   16
     clus
vv    AMP PEAK 60(XP11.22) MUTATED AMP PEAK 60(XP11.22) WILD-TYPE
  NO                             7                            410
  YES                            1                             16
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 60(XP11.22) MUTATED              2                       0    5
  AMP PEAK 60(XP11.22) WILD-TYPE          128                      16  323
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 60(XP11.22) MUTATED                     1
  AMP PEAK 60(XP11.22) WILD-TYPE                   0
D56V11, multiclass
                         clus
vv                        AMP PEAK 60(XP11.22) MUTATED
  MINIMAL (T3)                                       2
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               5
  VERY ADVANCED (T4B)                                1
                         clus
vv                        AMP PEAK 60(XP11.22) WILD-TYPE
  MINIMAL (T3)                                       128
  MODERATE/ADVANCED (T4A)                             16
  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 60(XP11.22) MUTATED     5   2   0   1
  AMP PEAK 60(XP11.22) WILD-TYPE 373  49   4  29
D56V12, multiclass
    clus
vv   AMP PEAK 60(XP11.22) MUTATED AMP PEAK 60(XP11.22) WILD-TYPE
  R0                            5                            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"
D56V13, continuous
D56V14, binary
                                cls
clus                               0   1
  AMP PEAK 60(XP11.22) MUTATED     5   3
  AMP PEAK 60(XP11.22) WILD-TYPE 219 258
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 60(XP11.22) MUTATED      5    3
  AMP PEAK 60(XP11.22) WILD-TYPE  219  258
            clus
vv           AMP PEAK 60(XP11.22) MUTATED AMP PEAK 60(XP11.22) WILD-TYPE
  MULTIFOCAL                            5                            219
  UNIFOCAL                              3                            258
[1] 2 2
[1] FALSE
D56V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 60(XP11.22) MUTATED                                  0     1
  AMP PEAK 60(XP11.22) WILD-TYPE                                1    48
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 60(XP11.22) MUTATED                           0     3
  AMP PEAK 60(XP11.22) WILD-TYPE                        26   318
D56V16, multiclass
                                  clus
vv                                 AMP PEAK 60(XP11.22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       3
                                  clus
vv                                 AMP PEAK 60(XP11.22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        48
  BLACK OR AFRICAN AMERICAN                                    26
  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"
D56V17, binary
                                cls
clus                               0   1
  AMP PEAK 60(XP11.22) MUTATED     0   4
  AMP PEAK 60(XP11.22) WILD-TYPE  38 346
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 60(XP11.22) MUTATED      0    4
  AMP PEAK 60(XP11.22) WILD-TYPE   38  346
                        clus
vv                       AMP PEAK 60(XP11.22) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            4
                        clus
vv                       AMP PEAK 60(XP11.22) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            346
[1] 2 2
[1] FALSE

Clustering(57) Variable = AMP PEAK 61(XP11.22) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 61(XP11.22) MUTATED     6   1
  AMP PEAK 61(XP11.22) WILD-TYPE 471  13
  AMP PEAK 61(XP11.22) MUTATED AMP PEAK 61(XP11.22) WILD-TYPE 
                             7                            484 
  AMP PEAK 61(XP11.22) MUTATED AMP PEAK 61(XP11.22) WILD-TYPE 
                             1                             13 
$`AMP PEAK 61(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        54.21        57.01        10.65        17.46 
TCGA-FY-A3NM 
        0.99 

$`AMP PEAK 61(XP11.22) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
        1.22        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        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
        1.45        74.30        45.40        33.47       108.36        39.32 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        30.18       102.84        65.39       124.04        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       37.25       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        38.66        52.73       139.00       131.15       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        12.16       147.42       130.72 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       116.91        98.24        41.29        95.38 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE 
       20.91        12.36        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        11.74 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.15        14.24        16.44        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
        6.05         2.99        12.30        15.19        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        13.84        19.73        17.59        12.07        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        18.97        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       19.63        13.38         8.35        16.44        16.77        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        16.80        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        11.15         7.33        12.53 
TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
        9.24        13.91         7.82        11.51        16.41        15.62 
TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       13.51        12.79        70.65        16.90         9.01         4.83 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
        8.61         8.38         9.80         5.03        37.87        12.72 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
        0.95        47.47        48.20        29.69        32.35        14.79 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       12.33        14.79        27.09        18.38        29.49        54.05 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       22.09        12.26        16.08        29.19        19.76         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       58.22        13.74        71.01        80.02        65.36        84.89 
TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       98.56        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24         5.85         4.18         2.43         5.56        24.72 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       38.30        42.25         2.37         4.50        80.81        69.24 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       59.87        43.50         0.30        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        4.01         1.94        73.74        59.70        31.59        44.25 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       102.90        66.77        81.34        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 
       46.06         4.08         0.89        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON 
       91.17         1.25         1.15        17.82         1.64         1.51 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        0.76         0.03         4.67        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         6.87         4.14         6.58         4.54 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
        0.89         1.35         1.15         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        10.26        16.90         9.80         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        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        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       12.43         6.74        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         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

  AMP PEAK 61(XP11.22) MUTATED AMP PEAK 61(XP11.22) WILD-TYPE 
                          0.99                           0.03 
  AMP PEAK 61(XP11.22) MUTATED AMP PEAK 61(XP11.22) WILD-TYPE 
                         57.01                         158.83 
  AMP PEAK 61(XP11.22) MUTATED AMP PEAK 61(XP11.22) WILD-TYPE 
                         17.46                          16.57 
[1] "1.0 - 57.0 (17.5)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "5.6"
D57V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 61(XP11.22) MUTATED         3        2         2        1         0
  AMP PEAK 61(XP11.22) WILD-TYPE     277       49       107        1        45
                                vv
clus                             STAGE IVC
  AMP PEAK 61(XP11.22) MUTATED           0
  AMP PEAK 61(XP11.22) WILD-TYPE         6
D57V3, multiclass
           clus
vv          AMP PEAK 61(XP11.22) MUTATED AMP PEAK 61(XP11.22) WILD-TYPE
  STAGE I                              3                            277
  STAGE II                             2                             49
  STAGE III                            2                            107
  STAGE IV                             1                              1
  STAGE IVA                            0                             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(XP11.22) MUTATED     2   3   2   1
  AMP PEAK 61(XP11.22) WILD-TYPE 138 163 163  20
D57V4, multiclass
    clus
vv   AMP PEAK 61(XP11.22) MUTATED AMP PEAK 61(XP11.22) WILD-TYPE
  T1                            2                            138
  T2                            3                            163
  T3                            2                            163
  T4                            1                             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"
D57V5, binary
                                cls
clus                               0   1
  AMP PEAK 61(XP11.22) MUTATED     5   1
  AMP PEAK 61(XP11.22) WILD-TYPE 218 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 61(XP11.22) MUTATED      5    1
  AMP PEAK 61(XP11.22) WILD-TYPE  218  221
   clus
vv  AMP PEAK 61(XP11.22) MUTATED AMP PEAK 61(XP11.22) WILD-TYPE
  0                            5                            218
  1                            1                            221
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 61(XP11.22) MUTATED     1   0   7
  AMP PEAK 61(XP11.22) WILD-TYPE 272   9 205
D57V6, multiclass
    clus
vv   AMP PEAK 61(XP11.22) MUTATED AMP PEAK 61(XP11.22) WILD-TYPE
  M0                            1                            272
  M1                            0                              9
  MX                            7                            205
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                                cls
clus                               0   1
  AMP PEAK 61(XP11.22) MUTATED     7   1
  AMP PEAK 61(XP11.22) WILD-TYPE 357 130
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 61(XP11.22) MUTATED      7    1
  AMP PEAK 61(XP11.22) WILD-TYPE  357  130
        clus
vv       AMP PEAK 61(XP11.22) MUTATED AMP PEAK 61(XP11.22) WILD-TYPE
  FEMALE                            7                            357
  MALE                              1                            130
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 61(XP11.22) MUTATED                0
  AMP PEAK 61(XP11.22) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 61(XP11.22) MUTATED                                               4
  AMP PEAK 61(XP11.22) WILD-TYPE                                           349
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 61(XP11.22) MUTATED                                                                        4
  AMP PEAK 61(XP11.22) WILD-TYPE                                                                     94
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 61(XP11.22) MUTATED                                                                     0
  AMP PEAK 61(XP11.22) WILD-TYPE                                                                  35
D57V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 61(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 61(XP11.22) WILD-TYPE
  OTHER  SPECIFY                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     349
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             94
  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"
D57V9, binary
                                cls
clus                               0   1
  AMP PEAK 61(XP11.22) MUTATED     0   8
  AMP PEAK 61(XP11.22) WILD-TYPE  14 473
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 61(XP11.22) MUTATED      0    8
  AMP PEAK 61(XP11.22) WILD-TYPE   14  473
     clus
vv    AMP PEAK 61(XP11.22) MUTATED AMP PEAK 61(XP11.22) WILD-TYPE
  NO                             0                             14
  YES                            8                            473
[1] 2 2
[1] FALSE
D57V10, binary
                                cls
clus                               0   1
  AMP PEAK 61(XP11.22) MUTATED     8   0
  AMP PEAK 61(XP11.22) WILD-TYPE 409  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 61(XP11.22) MUTATED      8    0
  AMP PEAK 61(XP11.22) WILD-TYPE  409   17
     clus
vv    AMP PEAK 61(XP11.22) MUTATED AMP PEAK 61(XP11.22) WILD-TYPE
  NO                             8                            409
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 61(XP11.22) MUTATED              1                       0    6
  AMP PEAK 61(XP11.22) WILD-TYPE          129                      16  322
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 61(XP11.22) MUTATED                     1
  AMP PEAK 61(XP11.22) WILD-TYPE                   0
D57V11, multiclass
                         clus
vv                        AMP PEAK 61(XP11.22) MUTATED
  MINIMAL (T3)                                       1
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               6
  VERY ADVANCED (T4B)                                1
                         clus
vv                        AMP PEAK 61(XP11.22) WILD-TYPE
  MINIMAL (T3)                                       129
  MODERATE/ADVANCED (T4A)                             16
  NONE                                               322
  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(XP11.22) MUTATED     4   3   0   1
  AMP PEAK 61(XP11.22) WILD-TYPE 374  48   4  29
D57V12, multiclass
    clus
vv   AMP PEAK 61(XP11.22) MUTATED AMP PEAK 61(XP11.22) WILD-TYPE
  R0                            4                            374
  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 61(XP11.22) MUTATED     5   3
  AMP PEAK 61(XP11.22) WILD-TYPE 219 258
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 61(XP11.22) MUTATED      5    3
  AMP PEAK 61(XP11.22) WILD-TYPE  219  258
            clus
vv           AMP PEAK 61(XP11.22) MUTATED AMP PEAK 61(XP11.22) WILD-TYPE
  MULTIFOCAL                            5                            219
  UNIFOCAL                              3                            258
[1] 2 2
[1] FALSE
D57V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 61(XP11.22) MUTATED                                  0     0
  AMP PEAK 61(XP11.22) WILD-TYPE                                1    49
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 61(XP11.22) MUTATED                           0     4
  AMP PEAK 61(XP11.22) WILD-TYPE                        26   317
D57V16, multiclass
                                  clus
vv                                 AMP PEAK 61(XP11.22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       4
                                  clus
vv                                 AMP PEAK 61(XP11.22) 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"
D57V17, binary
                                cls
clus                               0   1
  AMP PEAK 61(XP11.22) MUTATED     0   4
  AMP PEAK 61(XP11.22) WILD-TYPE  38 346
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 61(XP11.22) MUTATED      0    4
  AMP PEAK 61(XP11.22) WILD-TYPE   38  346
                        clus
vv                       AMP PEAK 61(XP11.22) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            4
                        clus
vv                       AMP PEAK 61(XP11.22) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            346
[1] 2 2
[1] FALSE

Clustering(58) Variable = AMP PEAK 62(XP11.21) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 62(XP11.21) MUTATED     8   1
  AMP PEAK 62(XP11.21) WILD-TYPE 469  13
  AMP PEAK 62(XP11.21) MUTATED AMP PEAK 62(XP11.21) WILD-TYPE 
                             9                            482 
  AMP PEAK 62(XP11.21) MUTATED AMP PEAK 62(XP11.21) WILD-TYPE 
                             1                             13 
$`AMP PEAK 62(XP11.21) MUTATED`
TCGA-BJ-A2N9 TCGA-EL-A3GU TCGA-EL-A3T9 TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N 
       20.48       124.04         5.72        54.21        57.01        10.65 
TCGA-EM-A3AI TCGA-ET-A2N3 TCGA-FY-A3NM 
       17.46        19.76         0.99 

$`AMP PEAK 62(XP11.21) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
        1.22        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        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
        1.45        74.30        45.40        33.47       108.36        39.32 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GV TCGA-EL-A3GW 
        1.41        30.18       102.84        65.39        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA 
       32.48       116.91        98.24        41.29        95.38        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN 
       82.82        77.36        78.97        31.50        50.33        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        52.50        45.53        48.16         7.07        44.65 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       45.80        19.30        45.96        37.94        31.04        19.59 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        33.60        28.73        41.13        37.78        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       13.32        11.87         8.71        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I 
       12.36        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        11.74        11.15 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        16.44        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        2.99        12.30        15.19        10.49        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       13.84        19.73        17.59        12.07        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        18.97        15.68        14.14        19.63 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        16.44        16.77        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        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        11.15         7.33        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       13.91         7.82        11.51        16.41        15.62        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        70.65        16.90         9.01         4.83         8.61 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
        8.38         9.80         5.03        37.87        12.72         0.95 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       47.47        48.20        29.69        32.35        14.79        12.33 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       14.79        27.09        18.38        29.49        54.05        22.09 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       12.26        16.08        29.19         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
       71.01        80.02        65.36        84.89        98.56        61.02 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       58.72        57.11        55.10        59.15        28.24         5.85 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
        4.18         2.43         5.56        24.72        38.30        42.25 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
        2.37         4.50        80.81        69.24        59.87        43.50 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
        0.30        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        59.70        31.59        44.25        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      102.90        66.77        81.34        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        46.06         4.08 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        0.89        22.03         0.92        48.10        91.17         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        1.15        17.82         1.64         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
        4.67        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 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
        1.15         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        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90         9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74 
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         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  AMP PEAK 62(XP11.21) MUTATED AMP PEAK 62(XP11.21) WILD-TYPE 
                          0.99                           0.03 
  AMP PEAK 62(XP11.21) MUTATED AMP PEAK 62(XP11.21) WILD-TYPE 
                        124.04                         158.83 
  AMP PEAK 62(XP11.21) MUTATED AMP PEAK 62(XP11.21) WILD-TYPE 
                        19.760                         16.505 
[1] "1.0 - 124.0 (19.8)" "0.0 - 158.8 (16.5)"
[1] "hr=" "2.8"
D58V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 62(XP11.21) MUTATED         3        2         3        1         0
  AMP PEAK 62(XP11.21) WILD-TYPE     277       49       106        1        45
                                vv
clus                             STAGE IVC
  AMP PEAK 62(XP11.21) MUTATED           0
  AMP PEAK 62(XP11.21) WILD-TYPE         6
D58V3, multiclass
           clus
vv          AMP PEAK 62(XP11.21) MUTATED AMP PEAK 62(XP11.21) WILD-TYPE
  STAGE I                              3                            277
  STAGE II                             2                             49
  STAGE III                            3                            106
  STAGE IV                             1                              1
  STAGE IVA                            0                             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 62(XP11.21) MUTATED     1   4   3   1
  AMP PEAK 62(XP11.21) WILD-TYPE 139 162 162  20
D58V4, multiclass
    clus
vv   AMP PEAK 62(XP11.21) MUTATED AMP PEAK 62(XP11.21) WILD-TYPE
  T1                            1                            139
  T2                            4                            162
  T3                            3                            162
  T4                            1                             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"
D58V5, binary
                                cls
clus                               0   1
  AMP PEAK 62(XP11.21) MUTATED     5   2
  AMP PEAK 62(XP11.21) WILD-TYPE 218 220
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 62(XP11.21) MUTATED      5    2
  AMP PEAK 62(XP11.21) WILD-TYPE  218  220
   clus
vv  AMP PEAK 62(XP11.21) MUTATED AMP PEAK 62(XP11.21) WILD-TYPE
  0                            5                            218
  1                            2                            220
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK 62(XP11.21) MUTATED     2   0   7
  AMP PEAK 62(XP11.21) WILD-TYPE 271   9 205
D58V6, multiclass
    clus
vv   AMP PEAK 62(XP11.21) MUTATED AMP PEAK 62(XP11.21) WILD-TYPE
  M0                            2                            271
  M1                            0                              9
  MX                            7                            205
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                                cls
clus                               0   1
  AMP PEAK 62(XP11.21) MUTATED     9   0
  AMP PEAK 62(XP11.21) WILD-TYPE 355 131
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 62(XP11.21) MUTATED      9    0
  AMP PEAK 62(XP11.21) WILD-TYPE  355  131
        clus
vv       AMP PEAK 62(XP11.21) MUTATED AMP PEAK 62(XP11.21) WILD-TYPE
  FEMALE                            9                            355
  MALE                              0                            131
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  AMP PEAK 62(XP11.21) MUTATED                0
  AMP PEAK 62(XP11.21) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 62(XP11.21) MUTATED                                               4
  AMP PEAK 62(XP11.21) WILD-TYPE                                           349
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 62(XP11.21) MUTATED                                                                        5
  AMP PEAK 62(XP11.21) WILD-TYPE                                                                     93
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 62(XP11.21) MUTATED                                                                     0
  AMP PEAK 62(XP11.21) WILD-TYPE                                                                  35
D58V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 62(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 62(XP11.21) WILD-TYPE
  OTHER  SPECIFY                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     349
  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"
D58V9, binary
                                cls
clus                               0   1
  AMP PEAK 62(XP11.21) MUTATED     0   9
  AMP PEAK 62(XP11.21) WILD-TYPE  14 472
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 62(XP11.21) MUTATED      0    9
  AMP PEAK 62(XP11.21) WILD-TYPE   14  472
     clus
vv    AMP PEAK 62(XP11.21) MUTATED AMP PEAK 62(XP11.21) WILD-TYPE
  NO                             0                             14
  YES                            9                            472
[1] 2 2
[1] FALSE
D58V10, binary
                                cls
clus                               0   1
  AMP PEAK 62(XP11.21) MUTATED     9   0
  AMP PEAK 62(XP11.21) WILD-TYPE 408  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 62(XP11.21) MUTATED      9    0
  AMP PEAK 62(XP11.21) WILD-TYPE  408   17
     clus
vv    AMP PEAK 62(XP11.21) MUTATED AMP PEAK 62(XP11.21) WILD-TYPE
  NO                             9                            408
  YES                            0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 62(XP11.21) MUTATED              2                       0    6
  AMP PEAK 62(XP11.21) WILD-TYPE          128                      16  322
                                vv
clus                             VERY ADVANCED (T4B)
  AMP PEAK 62(XP11.21) MUTATED                     1
  AMP PEAK 62(XP11.21) WILD-TYPE                   0
D58V11, multiclass
                         clus
vv                        AMP PEAK 62(XP11.21) MUTATED
  MINIMAL (T3)                                       2
  MODERATE/ADVANCED (T4A)                            0
  NONE                                               6
  VERY ADVANCED (T4B)                                1
                         clus
vv                        AMP PEAK 62(XP11.21) WILD-TYPE
  MINIMAL (T3)                                       128
  MODERATE/ADVANCED (T4A)                             16
  NONE                                               322
  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 62(XP11.21) MUTATED     5   2   0   2
  AMP PEAK 62(XP11.21) WILD-TYPE 373  49   4  28
D58V12, multiclass
    clus
vv   AMP PEAK 62(XP11.21) MUTATED AMP PEAK 62(XP11.21) WILD-TYPE
  R0                            5                            373
  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"
D58V13, continuous
D58V14, binary
                                cls
clus                               0   1
  AMP PEAK 62(XP11.21) MUTATED     4   5
  AMP PEAK 62(XP11.21) WILD-TYPE 220 256
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 62(XP11.21) MUTATED      4    5
  AMP PEAK 62(XP11.21) WILD-TYPE  220  256
            clus
vv           AMP PEAK 62(XP11.21) MUTATED AMP PEAK 62(XP11.21) WILD-TYPE
  MULTIFOCAL                            4                            220
  UNIFOCAL                              5                            256
[1] 2 2
[1] FALSE
D58V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 62(XP11.21) MUTATED                                  0     0
  AMP PEAK 62(XP11.21) WILD-TYPE                                1    49
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 62(XP11.21) MUTATED                           0     5
  AMP PEAK 62(XP11.21) WILD-TYPE                        26   316
D58V16, multiclass
                                  clus
vv                                 AMP PEAK 62(XP11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       5
                                  clus
vv                                 AMP PEAK 62(XP11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        49
  BLACK OR AFRICAN AMERICAN                                    26
  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"
D58V17, binary
                                cls
clus                               0   1
  AMP PEAK 62(XP11.21) MUTATED     1   4
  AMP PEAK 62(XP11.21) WILD-TYPE  37 346
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 62(XP11.21) MUTATED      1    4
  AMP PEAK 62(XP11.21) WILD-TYPE   37  346
                        clus
vv                       AMP PEAK 62(XP11.21) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                            4
                        clus
vv                       AMP PEAK 62(XP11.21) WILD-TYPE
  HISPANIC OR LATINO                                 37
  NOT HISPANIC OR LATINO                            346
[1] 2 2
[1] FALSE

Clustering(59) Variable = AMP PEAK 63(XQ21.2) MUTATION ANALYSIS
D59V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 63(XQ21.2) MUTATED     7   1
  AMP PEAK 63(XQ21.2) WILD-TYPE 470  13
  AMP PEAK 63(XQ21.2) MUTATED AMP PEAK 63(XQ21.2) WILD-TYPE 
                            8                           483 
  AMP PEAK 63(XQ21.2) MUTATED AMP PEAK 63(XQ21.2) WILD-TYPE 
                            1                            13 
$`AMP PEAK 63(XQ21.2) MUTATED`
TCGA-BJ-A2N9 TCGA-EL-A3T9 TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A3AI 
       20.48         5.72        54.21        57.01        10.65        17.46 
TCGA-EM-A3FK TCGA-FY-A3NM 
       23.77         0.99 

$`AMP PEAK 63(XQ21.2) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
        1.22        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        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
        1.45        74.30        45.40        33.47       108.36        39.32 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        30.18       102.84        65.39       124.04        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       37.25       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        38.66        52.73       139.00       131.15       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        12.16       147.42       130.72 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       116.91        98.24        41.29        95.38 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE 
       20.91        12.36        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        11.74 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.15        14.24        16.44        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
        6.05         2.99        12.30        15.19        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        13.84        19.73        17.59        12.07        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        18.97        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       19.63        13.38         8.35        16.44        16.77        27.95 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        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        11.15         7.33        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       13.91         7.82        11.51        16.41        15.62        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        70.65        16.90         9.01         4.83         8.61 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
        8.38         9.80         5.03        37.87        12.72         0.95 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       47.47        48.20        29.69        32.35        14.79        12.33 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       14.79        27.09        18.38        29.49        54.05        22.09 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       12.26        16.08        29.19        19.76         2.66        58.22 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
       13.74        71.01        80.02        65.36        84.89        98.56 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
       61.02        58.72        57.11        55.10        59.15        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
        5.85         4.18         2.43         5.56        24.72        38.30 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       42.25         2.37         4.50        80.81        69.24        59.87 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       43.50         0.30        17.98        25.32       132.36        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
        3.22         7.17         4.80         5.03         2.14         4.01 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
        1.94        73.74        59.70        31.59        44.25        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       102.90        66.77        81.34        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        46.06 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.08         0.89        22.03         0.92        48.10        91.17 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25         1.15        17.82         1.64         1.51         0.76 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
        0.03         4.67        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         6.87         4.14         6.58         4.54         0.89 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35         1.15         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 
       10.26        16.90         9.80         9.63         2.96         8.65 
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        86.70         6.02        12.43 
TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC TCGA-KS-A4ID 
        6.74        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         0.72        16.64        32.45 
TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
        8.71        10.98         5.19 

  AMP PEAK 63(XQ21.2) MUTATED AMP PEAK 63(XQ21.2) WILD-TYPE 
                         0.99                          0.03 
  AMP PEAK 63(XQ21.2) MUTATED AMP PEAK 63(XQ21.2) WILD-TYPE 
                        57.01                        158.83 
  AMP PEAK 63(XQ21.2) MUTATED AMP PEAK 63(XQ21.2) WILD-TYPE 
                        18.97                         16.57 
[1] "1.0 - 57.0 (19.0)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "5.3"
D59V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 63(XQ21.2) MUTATED         3        2         2        1         0
  AMP PEAK 63(XQ21.2) WILD-TYPE     277       49       107        1        45
                               vv
clus                            STAGE IVC
  AMP PEAK 63(XQ21.2) MUTATED           0
  AMP PEAK 63(XQ21.2) WILD-TYPE         6
D59V3, multiclass
           clus
vv          AMP PEAK 63(XQ21.2) MUTATED AMP PEAK 63(XQ21.2) WILD-TYPE
  STAGE I                             3                           277
  STAGE II                            2                            49
  STAGE III                           2                           107
  STAGE IV                            1                             1
  STAGE IVA                           0                            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 63(XQ21.2) MUTATED     2   3   2   1
  AMP PEAK 63(XQ21.2) WILD-TYPE 138 163 163  20
D59V4, multiclass
    clus
vv   AMP PEAK 63(XQ21.2) MUTATED AMP PEAK 63(XQ21.2) WILD-TYPE
  T1                           2                           138
  T2                           3                           163
  T3                           2                           163
  T4                           1                            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"
D59V5, binary
                               cls
clus                              0   1
  AMP PEAK 63(XQ21.2) MUTATED     5   2
  AMP PEAK 63(XQ21.2) WILD-TYPE 218 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 63(XQ21.2) MUTATED      5    2
  AMP PEAK 63(XQ21.2) WILD-TYPE  218  220
   clus
vv  AMP PEAK 63(XQ21.2) MUTATED AMP PEAK 63(XQ21.2) WILD-TYPE
  0                           5                           218
  1                           2                           220
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK 63(XQ21.2) MUTATED     1   0   7
  AMP PEAK 63(XQ21.2) WILD-TYPE 272   9 205
D59V6, multiclass
    clus
vv   AMP PEAK 63(XQ21.2) MUTATED AMP PEAK 63(XQ21.2) WILD-TYPE
  M0                           1                           272
  M1                           0                             9
  MX                           7                           205
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                               cls
clus                              0   1
  AMP PEAK 63(XQ21.2) MUTATED     8   0
  AMP PEAK 63(XQ21.2) WILD-TYPE 356 131
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 63(XQ21.2) MUTATED      8    0
  AMP PEAK 63(XQ21.2) WILD-TYPE  356  131
        clus
vv       AMP PEAK 63(XQ21.2) MUTATED AMP PEAK 63(XQ21.2) WILD-TYPE
  FEMALE                           8                           356
  MALE                             0                           131
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 63(XQ21.2) MUTATED                0
  AMP PEAK 63(XQ21.2) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 63(XQ21.2) MUTATED                                               4
  AMP PEAK 63(XQ21.2) WILD-TYPE                                           349
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 63(XQ21.2) MUTATED                                                                        4
  AMP PEAK 63(XQ21.2) WILD-TYPE                                                                     94
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 63(XQ21.2) MUTATED                                                                     0
  AMP PEAK 63(XQ21.2) WILD-TYPE                                                                  35
D59V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 63(XQ21.2) 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 63(XQ21.2) WILD-TYPE
  OTHER  SPECIFY                                                                                     9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    349
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            94
  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"
D59V9, binary
                               cls
clus                              0   1
  AMP PEAK 63(XQ21.2) MUTATED     0   8
  AMP PEAK 63(XQ21.2) WILD-TYPE  14 473
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 63(XQ21.2) MUTATED      0    8
  AMP PEAK 63(XQ21.2) WILD-TYPE   14  473
     clus
vv    AMP PEAK 63(XQ21.2) MUTATED AMP PEAK 63(XQ21.2) WILD-TYPE
  NO                            0                            14
  YES                           8                           473
[1] 2 2
[1] FALSE
D59V10, binary
                               cls
clus                              0   1
  AMP PEAK 63(XQ21.2) MUTATED     8   0
  AMP PEAK 63(XQ21.2) WILD-TYPE 409  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 63(XQ21.2) MUTATED      8    0
  AMP PEAK 63(XQ21.2) WILD-TYPE  409   17
     clus
vv    AMP PEAK 63(XQ21.2) MUTATED AMP PEAK 63(XQ21.2) WILD-TYPE
  NO                            8                           409
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 63(XQ21.2) MUTATED              1                       0    6
  AMP PEAK 63(XQ21.2) WILD-TYPE          129                      16  322
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 63(XQ21.2) MUTATED                     1
  AMP PEAK 63(XQ21.2) WILD-TYPE                   0
D59V11, multiclass
                         clus
vv                        AMP PEAK 63(XQ21.2) MUTATED
  MINIMAL (T3)                                      1
  MODERATE/ADVANCED (T4A)                           0
  NONE                                              6
  VERY ADVANCED (T4B)                               1
                         clus
vv                        AMP PEAK 63(XQ21.2) WILD-TYPE
  MINIMAL (T3)                                      129
  MODERATE/ADVANCED (T4A)                            16
  NONE                                              322
  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 63(XQ21.2) MUTATED     5   2   0   1
  AMP PEAK 63(XQ21.2) WILD-TYPE 373  49   4  29
D59V12, multiclass
    clus
vv   AMP PEAK 63(XQ21.2) MUTATED AMP PEAK 63(XQ21.2) WILD-TYPE
  R0                           5                           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"
D59V13, continuous
D59V14, binary
                               cls
clus                              0   1
  AMP PEAK 63(XQ21.2) MUTATED     5   3
  AMP PEAK 63(XQ21.2) WILD-TYPE 219 258
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 63(XQ21.2) MUTATED      5    3
  AMP PEAK 63(XQ21.2) WILD-TYPE  219  258
            clus
vv           AMP PEAK 63(XQ21.2) MUTATED AMP PEAK 63(XQ21.2) WILD-TYPE
  MULTIFOCAL                           5                           219
  UNIFOCAL                             3                           258
[1] 2 2
[1] FALSE
D59V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 63(XQ21.2) MUTATED                                  0     0
  AMP PEAK 63(XQ21.2) WILD-TYPE                                1    49
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 63(XQ21.2) MUTATED                           0     3
  AMP PEAK 63(XQ21.2) WILD-TYPE                        26   318
D59V16, multiclass
                                  clus
vv                                 AMP PEAK 63(XQ21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      3
                                  clus
vv                                 AMP PEAK 63(XQ21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       49
  BLACK OR AFRICAN AMERICAN                                   26
  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"
D59V17, binary
                               cls
clus                              0   1
  AMP PEAK 63(XQ21.2) MUTATED     0   3
  AMP PEAK 63(XQ21.2) WILD-TYPE  38 347
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 63(XQ21.2) MUTATED      0    3
  AMP PEAK 63(XQ21.2) WILD-TYPE   38  347
                        clus
vv                       AMP PEAK 63(XQ21.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           3
                        clus
vv                       AMP PEAK 63(XQ21.2) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           347
[1] 2 2
[1] FALSE

Clustering(60) Variable = AMP PEAK 64(XQ22.3) MUTATION ANALYSIS
D60V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 64(XQ22.3) MUTATED    14   1
  AMP PEAK 64(XQ22.3) WILD-TYPE 463  13
  AMP PEAK 64(XQ22.3) MUTATED AMP PEAK 64(XQ22.3) WILD-TYPE 
                           15                           476 
  AMP PEAK 64(XQ22.3) MUTATED AMP PEAK 64(XQ22.3) WILD-TYPE 
                            1                            13 
$`AMP PEAK 64(XQ22.3) MUTATED`
TCGA-BJ-A2N9 TCGA-DJ-A4UT TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-EL-A3T9 TCGA-EL-A4K1 
       20.48        14.14         3.12        15.81         5.72        19.59 
TCGA-EL-A4KH TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A3AI TCGA-EM-A3FK 
       11.87        54.21        57.01        10.65        17.46        23.77 
TCGA-EM-A4FQ TCGA-FY-A3NM TCGA-KS-A4I5 
        9.80         0.99         6.74 

$`AMP PEAK 64(XQ22.3) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
        1.22        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        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       10.98        14.70        17.82        24.33        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 
       30.31        14.04         1.15        22.29        19.59        13.61 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 
       14.27        13.81        14.07        14.27         3.02        14.43 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
       14.70        14.10        14.96         7.69        20.68        13.78 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
       13.58        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 
       80.91         4.18        58.82         1.45        74.30        45.40 
TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR 
       33.47       108.36        39.32         1.41        30.18       102.84 
TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY 
       65.39       124.04        50.37        37.25       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        38.66        52.73 
TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ 
      139.00       131.15       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 
       12.16       147.42       130.72       129.57        32.48       116.91 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       98.24        41.29        95.38        66.90        82.82        77.36 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       78.97        31.50        50.33        53.06        47.38        52.50 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       45.53        48.16         7.07        44.65        45.80        19.30 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       45.96        37.94        31.04        30.51        33.60        28.73 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KI TCGA-EM-A1CS 
       41.13        37.78        29.95        13.32         8.71        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        12.36        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 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT 
       23.51         6.05         2.99        12.30        15.19        10.49 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        13.84        19.73        17.59        12.07 
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        18.97        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR 
       14.14        19.63        13.38         8.35        16.44        16.77 
TCGA-EM-A3FJ TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       27.95        16.80        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        11.15         7.33        12.53 
TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
        9.24        13.91         7.82        11.51        16.41        15.62 
TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       13.51        12.79        70.65        16.90         9.01         4.83 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
        8.61         8.38         5.03        37.87        12.72         0.95 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       47.47        48.20        29.69        32.35        14.79        12.33 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       14.79        27.09        18.38        29.49        54.05        22.09 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       12.26        16.08        29.19        19.76         2.66        58.22 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
       13.74        71.01        80.02        65.36        84.89        98.56 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
       61.02        58.72        57.11        55.10        59.15        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
        5.85         4.18         2.43         5.56        24.72        38.30 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       42.25         2.37         4.50        80.81        69.24        59.87 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       43.50         0.30        17.98        25.32       132.36        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
        3.22         7.17         4.80         5.03         2.14         4.01 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
        1.94        73.74        59.70        31.59        44.25        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       102.90        66.77        81.34        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        46.06 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.08         0.89        22.03         0.92        48.10        91.17 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25         1.15        17.82         1.64         1.51         0.76 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
        0.03         4.67        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         6.87         4.14         6.58         4.54         0.89 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35         1.15         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 
       10.26        16.90         9.80         9.63         2.96         8.65 
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        86.70         6.02        12.43 
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         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  AMP PEAK 64(XQ22.3) MUTATED AMP PEAK 64(XQ22.3) WILD-TYPE 
                         0.99                          0.03 
  AMP PEAK 64(XQ22.3) MUTATED AMP PEAK 64(XQ22.3) WILD-TYPE 
                        57.01                        158.83 
  AMP PEAK 64(XQ22.3) MUTATED AMP PEAK 64(XQ22.3) WILD-TYPE 
                       14.140                        16.685 
[1] "1.0 - 57.0 (14.1)"  "0.0 - 158.8 (16.7)"
[1] "hr=" "4.6"
D60V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 64(XQ22.3) MUTATED         8        2         3        1         1
  AMP PEAK 64(XQ22.3) WILD-TYPE     272       49       106        1        44
                               vv
clus                            STAGE IVC
  AMP PEAK 64(XQ22.3) MUTATED           0
  AMP PEAK 64(XQ22.3) WILD-TYPE         6
D60V3, multiclass
           clus
vv          AMP PEAK 64(XQ22.3) MUTATED AMP PEAK 64(XQ22.3) WILD-TYPE
  STAGE I                             8                           272
  STAGE II                            2                            49
  STAGE III                           3                           106
  STAGE IV                            1                             1
  STAGE IVA                           1                            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 64(XQ22.3) MUTATED     5   6   3   1
  AMP PEAK 64(XQ22.3) WILD-TYPE 135 160 162  20
D60V4, multiclass
    clus
vv   AMP PEAK 64(XQ22.3) MUTATED AMP PEAK 64(XQ22.3) WILD-TYPE
  T1                           5                           135
  T2                           6                           160
  T3                           3                           162
  T4                           1                            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"
D60V5, binary
                               cls
clus                              0   1
  AMP PEAK 64(XQ22.3) MUTATED     9   5
  AMP PEAK 64(XQ22.3) WILD-TYPE 214 217
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 64(XQ22.3) MUTATED      9    5
  AMP PEAK 64(XQ22.3) WILD-TYPE  214  217
   clus
vv  AMP PEAK 64(XQ22.3) MUTATED AMP PEAK 64(XQ22.3) WILD-TYPE
  0                           9                           214
  1                           5                           217
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK 64(XQ22.3) MUTATED     7   0   8
  AMP PEAK 64(XQ22.3) WILD-TYPE 266   9 204
D60V6, multiclass
    clus
vv   AMP PEAK 64(XQ22.3) MUTATED AMP PEAK 64(XQ22.3) WILD-TYPE
  M0                           7                           266
  M1                           0                             9
  MX                           8                           204
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, binary
                               cls
clus                              0   1
  AMP PEAK 64(XQ22.3) MUTATED    15   0
  AMP PEAK 64(XQ22.3) WILD-TYPE 349 131
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 64(XQ22.3) MUTATED     15    0
  AMP PEAK 64(XQ22.3) WILD-TYPE  349  131
        clus
vv       AMP PEAK 64(XQ22.3) MUTATED AMP PEAK 64(XQ22.3) WILD-TYPE
  FEMALE                          15                           349
  MALE                             0                           131
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  AMP PEAK 64(XQ22.3) MUTATED                0
  AMP PEAK 64(XQ22.3) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 64(XQ22.3) MUTATED                                               9
  AMP PEAK 64(XQ22.3) WILD-TYPE                                           344
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 64(XQ22.3) MUTATED                                                                        5
  AMP PEAK 64(XQ22.3) WILD-TYPE                                                                     93
                               vv
clus                            THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 64(XQ22.3) MUTATED                                                                     1
  AMP PEAK 64(XQ22.3) WILD-TYPE                                                                  34
D60V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 64(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 64(XQ22.3) WILD-TYPE
  OTHER  SPECIFY                                                                                     9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    344
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            93
  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"
D60V9, binary
                               cls
clus                              0   1
  AMP PEAK 64(XQ22.3) MUTATED     0  15
  AMP PEAK 64(XQ22.3) WILD-TYPE  14 466
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 64(XQ22.3) MUTATED      0   15
  AMP PEAK 64(XQ22.3) WILD-TYPE   14  466
     clus
vv    AMP PEAK 64(XQ22.3) MUTATED AMP PEAK 64(XQ22.3) WILD-TYPE
  NO                            0                            14
  YES                          15                           466
[1] 2 2
[1] FALSE
D60V10, binary
                               cls
clus                              0   1
  AMP PEAK 64(XQ22.3) MUTATED    15   0
  AMP PEAK 64(XQ22.3) WILD-TYPE 402  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 64(XQ22.3) MUTATED     15    0
  AMP PEAK 64(XQ22.3) WILD-TYPE  402   17
     clus
vv    AMP PEAK 64(XQ22.3) MUTATED AMP PEAK 64(XQ22.3) WILD-TYPE
  NO                           15                           402
  YES                           0                            17
[1] 2 2
[1] FALSE
                               vv
clus                            MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 64(XQ22.3) MUTATED              1                       0   13
  AMP PEAK 64(XQ22.3) WILD-TYPE          129                      16  315
                               vv
clus                            VERY ADVANCED (T4B)
  AMP PEAK 64(XQ22.3) MUTATED                     1
  AMP PEAK 64(XQ22.3) WILD-TYPE                   0
D60V11, multiclass
                         clus
vv                        AMP PEAK 64(XQ22.3) MUTATED
  MINIMAL (T3)                                      1
  MODERATE/ADVANCED (T4A)                           0
  NONE                                             13
  VERY ADVANCED (T4B)                               1
                         clus
vv                        AMP PEAK 64(XQ22.3) WILD-TYPE
  MINIMAL (T3)                                      129
  MODERATE/ADVANCED (T4A)                            16
  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 64(XQ22.3) MUTATED    12   2   0   1
  AMP PEAK 64(XQ22.3) WILD-TYPE 366  49   4  29
D60V12, multiclass
    clus
vv   AMP PEAK 64(XQ22.3) MUTATED AMP PEAK 64(XQ22.3) WILD-TYPE
  R0                          12                           366
  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 64(XQ22.3) MUTATED     9   6
  AMP PEAK 64(XQ22.3) WILD-TYPE 215 255
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 64(XQ22.3) MUTATED      9    6
  AMP PEAK 64(XQ22.3) WILD-TYPE  215  255
            clus
vv           AMP PEAK 64(XQ22.3) MUTATED AMP PEAK 64(XQ22.3) WILD-TYPE
  MULTIFOCAL                           9                           215
  UNIFOCAL                             6                           255
[1] 2 2
[1] FALSE
D60V15, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 64(XQ22.3) MUTATED                                  0     0
  AMP PEAK 64(XQ22.3) WILD-TYPE                                1    49
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 64(XQ22.3) MUTATED                           0     8
  AMP PEAK 64(XQ22.3) WILD-TYPE                        26   313
D60V16, multiclass
                                  clus
vv                                 AMP PEAK 64(XQ22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      8
                                  clus
vv                                 AMP PEAK 64(XQ22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       49
  BLACK OR AFRICAN AMERICAN                                   26
  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"
D60V17, binary
                               cls
clus                              0   1
  AMP PEAK 64(XQ22.3) MUTATED     0   8
  AMP PEAK 64(XQ22.3) WILD-TYPE  38 342
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 64(XQ22.3) MUTATED      0    8
  AMP PEAK 64(XQ22.3) WILD-TYPE   38  342
                        clus
vv                       AMP PEAK 64(XQ22.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           8
                        clus
vv                       AMP PEAK 64(XQ22.3) WILD-TYPE
  HISPANIC OR LATINO                                38
  NOT HISPANIC OR LATINO                           342
[1] 2 2
[1] FALSE

Clustering(61) Variable = AMP PEAK 65(XQ23) MUTATION ANALYSIS
D61V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 65(XQ23) MUTATED     8   1
  AMP PEAK 65(XQ23) WILD-TYPE 469  13
  AMP PEAK 65(XQ23) MUTATED AMP PEAK 65(XQ23) WILD-TYPE 
                          9                         482 
  AMP PEAK 65(XQ23) MUTATED AMP PEAK 65(XQ23) WILD-TYPE 
                          1                          13 
$`AMP PEAK 65(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        54.21        57.01        10.65 
TCGA-EM-A3AI TCGA-EM-A3FK TCGA-FY-A3NM 
       17.46        23.77         0.99 

$`AMP PEAK 65(XQ23) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
        1.22        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        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
        1.45        74.30        45.40        33.47       108.36        39.32 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        30.18       102.84        65.39       124.04        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       37.25       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        38.66        52.73       139.00       131.15       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        12.16       147.42       130.72 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       116.91        98.24        41.29        95.38 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I 
       12.36        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        11.74        11.15 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        16.44        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        2.99        12.30        15.19        10.49        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       13.84        19.73        17.59        12.07        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        18.97        15.68        14.14        19.63 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FL 
       13.38         8.35        16.44        16.77        27.95        16.80 
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        11.15         7.33        12.53         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        16.41        15.62        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        9.80         5.03        37.87        12.72         0.95        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
       71.01        80.02        65.36        84.89        98.56        61.02 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       58.72        57.11        55.10        59.15        28.24         5.85 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
        4.18         2.43         5.56        24.72        38.30        42.25 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
        2.37         4.50        80.81        69.24        59.87        43.50 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
        0.30        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        59.70        31.59        44.25        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      102.90        66.77        81.34        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        46.06         4.08 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        0.89        22.03         0.92        48.10        91.17         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        1.15        17.82         1.64         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
        4.67        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 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
        1.15         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        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90         9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74 
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         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  AMP PEAK 65(XQ23) MUTATED AMP PEAK 65(XQ23) WILD-TYPE 
                       0.99                        0.03 
  AMP PEAK 65(XQ23) MUTATED AMP PEAK 65(XQ23) WILD-TYPE 
                      57.01                      158.83 
  AMP PEAK 65(XQ23) MUTATED AMP PEAK 65(XQ23) WILD-TYPE 
                     20.480                      16.505 
[1] "1.0 - 57.0 (20.5)"  "0.0 - 158.8 (16.5)"
[1] "hr=" "5.1"
D61V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 65(XQ23) MUTATED         4        2         2        1         0
  AMP PEAK 65(XQ23) WILD-TYPE     276       49       107        1        45
                             vv
clus                          STAGE IVC
  AMP PEAK 65(XQ23) MUTATED           0
  AMP PEAK 65(XQ23) WILD-TYPE         6
D61V3, multiclass
           clus
vv          AMP PEAK 65(XQ23) MUTATED AMP PEAK 65(XQ23) WILD-TYPE
  STAGE I                           4                         276
  STAGE II                          2                          49
  STAGE III                         2                         107
  STAGE IV                          1                           1
  STAGE IVA                         0                          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(XQ23) MUTATED     2   3   3   1
  AMP PEAK 65(XQ23) WILD-TYPE 138 163 162  20
D61V4, multiclass
    clus
vv   AMP PEAK 65(XQ23) MUTATED AMP PEAK 65(XQ23) WILD-TYPE
  T1                         2                         138
  T2                         3                         163
  T3                         3                         162
  T4                         1                          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"
D61V5, binary
                             cls
clus                            0   1
  AMP PEAK 65(XQ23) MUTATED     5   3
  AMP PEAK 65(XQ23) WILD-TYPE 218 219
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 65(XQ23) MUTATED      5    3
  AMP PEAK 65(XQ23) WILD-TYPE  218  219
   clus
vv  AMP PEAK 65(XQ23) MUTATED AMP PEAK 65(XQ23) WILD-TYPE
  0                         5                         218
  1                         3                         219
[1] 2 2
[1] FALSE
                             vv
clus                           M0  M1  MX
  AMP PEAK 65(XQ23) MUTATED     2   0   7
  AMP PEAK 65(XQ23) WILD-TYPE 271   9 205
D61V6, multiclass
    clus
vv   AMP PEAK 65(XQ23) MUTATED AMP PEAK 65(XQ23) WILD-TYPE
  M0                         2                         271
  M1                         0                           9
  MX                         7                         205
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                             cls
clus                            0   1
  AMP PEAK 65(XQ23) MUTATED     8   1
  AMP PEAK 65(XQ23) WILD-TYPE 356 130
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 65(XQ23) MUTATED      8    1
  AMP PEAK 65(XQ23) WILD-TYPE  356  130
        clus
vv       AMP PEAK 65(XQ23) MUTATED AMP PEAK 65(XQ23) WILD-TYPE
  FEMALE                         8                         356
  MALE                           1                         130
[1] 2 2
[1] FALSE
                             vv
clus                          OTHER  SPECIFY
  AMP PEAK 65(XQ23) MUTATED                0
  AMP PEAK 65(XQ23) WILD-TYPE              9
                             vv
clus                          THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 65(XQ23) MUTATED                                               5
  AMP PEAK 65(XQ23) WILD-TYPE                                           348
                             vv
clus                          THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 65(XQ23) MUTATED                                                                        4
  AMP PEAK 65(XQ23) WILD-TYPE                                                                     94
                             vv
clus                          THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 65(XQ23) MUTATED                                                                     0
  AMP PEAK 65(XQ23) WILD-TYPE                                                                  35
D61V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 65(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 65(XQ23) WILD-TYPE
  OTHER  SPECIFY                                                                                   9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  348
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          94
  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"
D61V9, binary
                             cls
clus                            0   1
  AMP PEAK 65(XQ23) MUTATED     0   9
  AMP PEAK 65(XQ23) WILD-TYPE  14 472
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 65(XQ23) MUTATED      0    9
  AMP PEAK 65(XQ23) WILD-TYPE   14  472
     clus
vv    AMP PEAK 65(XQ23) MUTATED AMP PEAK 65(XQ23) WILD-TYPE
  NO                          0                          14
  YES                         9                         472
[1] 2 2
[1] FALSE
D61V10, binary
                             cls
clus                            0   1
  AMP PEAK 65(XQ23) MUTATED     8   0
  AMP PEAK 65(XQ23) WILD-TYPE 409  17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 65(XQ23) MUTATED      8    0
  AMP PEAK 65(XQ23) WILD-TYPE  409   17
     clus
vv    AMP PEAK 65(XQ23) MUTATED AMP PEAK 65(XQ23) WILD-TYPE
  NO                          8                         409
  YES                         0                          17
[1] 2 2
[1] FALSE
                             vv
clus                          MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 65(XQ23) MUTATED              1                       0    7
  AMP PEAK 65(XQ23) WILD-TYPE          129                      16  321
                             vv
clus                          VERY ADVANCED (T4B)
  AMP PEAK 65(XQ23) MUTATED                     1
  AMP PEAK 65(XQ23) WILD-TYPE                   0
D61V11, multiclass
                         clus
vv                        AMP PEAK 65(XQ23) MUTATED AMP PEAK 65(XQ23) WILD-TYPE
  MINIMAL (T3)                                    1                         129
  MODERATE/ADVANCED (T4A)                         0                          16
  NONE                                            7                         321
  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(XQ23) MUTATED     5   2   0   1
  AMP PEAK 65(XQ23) WILD-TYPE 373  49   4  29
D61V12, multiclass
    clus
vv   AMP PEAK 65(XQ23) MUTATED AMP PEAK 65(XQ23) WILD-TYPE
  R0                         5                         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"
D61V13, continuous
D61V14, binary
                             cls
clus                            0   1
  AMP PEAK 65(XQ23) MUTATED     6   3
  AMP PEAK 65(XQ23) WILD-TYPE 218 258
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 65(XQ23) MUTATED      6    3
  AMP PEAK 65(XQ23) WILD-TYPE  218  258
            clus
vv           AMP PEAK 65(XQ23) MUTATED AMP PEAK 65(XQ23) WILD-TYPE
  MULTIFOCAL                         6                         218
  UNIFOCAL                           3                         258
[1] 2 2
[1] FALSE
D61V15, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 65(XQ23) MUTATED                                  0     0
  AMP PEAK 65(XQ23) WILD-TYPE                                1    49
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 65(XQ23) MUTATED                           0     3
  AMP PEAK 65(XQ23) WILD-TYPE                        26   318
D61V16, multiclass
                                  clus
vv                                 AMP PEAK 65(XQ23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                0
  WHITE                                                    3
                                  clus
vv                                 AMP PEAK 65(XQ23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     49
  BLACK OR AFRICAN AMERICAN                                 26
  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"
D61V17, binary
                             cls
clus                            0   1
  AMP PEAK 65(XQ23) MUTATED     0   3
  AMP PEAK 65(XQ23) WILD-TYPE  38 347
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 65(XQ23) MUTATED      0    3
  AMP PEAK 65(XQ23) WILD-TYPE   38  347
                        clus
vv                       AMP PEAK 65(XQ23) MUTATED AMP PEAK 65(XQ23) WILD-TYPE
  HISPANIC OR LATINO                             0                          38
  NOT HISPANIC OR LATINO                         3                         347
[1] 2 2
[1] FALSE

Clustering(62) Variable = AMP PEAK 66(XQ24) MUTATION ANALYSIS
D62V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 66(XQ24) MUTATED     8   1
  AMP PEAK 66(XQ24) WILD-TYPE 469  13
  AMP PEAK 66(XQ24) MUTATED AMP PEAK 66(XQ24) WILD-TYPE 
                          9                         482 
  AMP PEAK 66(XQ24) MUTATED AMP PEAK 66(XQ24) WILD-TYPE 
                          1                          13 
$`AMP PEAK 66(XQ24) MUTATED`
TCGA-BJ-A2N9 TCGA-EL-A3T9 TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A3AI 
       20.48         5.72        54.21        57.01        10.65        17.46 
TCGA-EM-A3FK TCGA-ET-A25G TCGA-FY-A3NM 
       23.77        47.47         0.99 

$`AMP PEAK 66(XQ24) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
        1.22        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        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
        1.45        74.30        45.40        33.47       108.36        39.32 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        30.18       102.84        65.39       124.04        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       37.25       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        38.66        52.73       139.00       131.15       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        12.16       147.42       130.72 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       116.91        98.24        41.29        95.38 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE 
       20.91        12.36        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        11.74 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.15        14.24        16.44        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
        6.05         2.99        12.30        15.19        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        13.84        19.73        17.59        12.07        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        18.97        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       19.63        13.38         8.35        16.44        16.77        27.95 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        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        11.15         7.33        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       13.91         7.82        11.51        16.41        15.62        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        70.65        16.90         9.01         4.83         8.61 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
        8.38         9.80         5.03        37.87        12.72         0.95 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
       71.01        80.02        65.36        84.89        98.56        61.02 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       58.72        57.11        55.10        59.15        28.24         5.85 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
        4.18         2.43         5.56        24.72        38.30        42.25 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
        2.37         4.50        80.81        69.24        59.87        43.50 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
        0.30        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        59.70        31.59        44.25        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      102.90        66.77        81.34        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        46.06         4.08 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        0.89        22.03         0.92        48.10        91.17         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        1.15        17.82         1.64         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
        4.67        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 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
        1.15         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        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90         9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74 
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         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  AMP PEAK 66(XQ24) MUTATED AMP PEAK 66(XQ24) WILD-TYPE 
                       0.99                        0.03 
  AMP PEAK 66(XQ24) MUTATED AMP PEAK 66(XQ24) WILD-TYPE 
                      57.01                      158.83 
  AMP PEAK 66(XQ24) MUTATED AMP PEAK 66(XQ24) WILD-TYPE 
                     20.480                      16.505 
[1] "1.0 - 57.0 (20.5)"  "0.0 - 158.8 (16.5)"
[1] "hr=" "4.2"
D62V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 66(XQ24) MUTATED         3        2         3        1         0
  AMP PEAK 66(XQ24) WILD-TYPE     277       49       106        1        45
                             vv
clus                          STAGE IVC
  AMP PEAK 66(XQ24) MUTATED           0
  AMP PEAK 66(XQ24) WILD-TYPE         6
D62V3, multiclass
           clus
vv          AMP PEAK 66(XQ24) MUTATED AMP PEAK 66(XQ24) WILD-TYPE
  STAGE I                           3                         277
  STAGE II                          2                          49
  STAGE III                         3                         106
  STAGE IV                          1                           1
  STAGE IVA                         0                          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 66(XQ24) MUTATED     2   3   3   1
  AMP PEAK 66(XQ24) WILD-TYPE 138 163 162  20
D62V4, multiclass
    clus
vv   AMP PEAK 66(XQ24) MUTATED AMP PEAK 66(XQ24) WILD-TYPE
  T1                         2                         138
  T2                         3                         163
  T3                         3                         162
  T4                         1                          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"
D62V5, binary
                             cls
clus                            0   1
  AMP PEAK 66(XQ24) MUTATED     6   2
  AMP PEAK 66(XQ24) WILD-TYPE 217 220
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 66(XQ24) MUTATED      6    2
  AMP PEAK 66(XQ24) WILD-TYPE  217  220
   clus
vv  AMP PEAK 66(XQ24) MUTATED AMP PEAK 66(XQ24) WILD-TYPE
  0                         6                         217
  1                         2                         220
[1] 2 2
[1] FALSE
                             vv
clus                           M0  M1  MX
  AMP PEAK 66(XQ24) MUTATED     1   0   8
  AMP PEAK 66(XQ24) WILD-TYPE 272   9 204
D62V6, multiclass
    clus
vv   AMP PEAK 66(XQ24) MUTATED AMP PEAK 66(XQ24) WILD-TYPE
  M0                         1                         272
  M1                         0                           9
  MX                         8                         204
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                             cls
clus                            0   1
  AMP PEAK 66(XQ24) MUTATED     9   0
  AMP PEAK 66(XQ24) WILD-TYPE 355 131
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 66(XQ24) MUTATED      9    0
  AMP PEAK 66(XQ24) WILD-TYPE  355  131
        clus
vv       AMP PEAK 66(XQ24) MUTATED AMP PEAK 66(XQ24) WILD-TYPE
  FEMALE                         9                         355
  MALE                           0                         131
[1] 2 2
[1] FALSE
                             vv
clus                          OTHER  SPECIFY
  AMP PEAK 66(XQ24) MUTATED                0
  AMP PEAK 66(XQ24) WILD-TYPE              9
                             vv
clus                          THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 66(XQ24) MUTATED                                               4
  AMP PEAK 66(XQ24) WILD-TYPE                                           349
                             vv
clus                          THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 66(XQ24) MUTATED                                                                        4
  AMP PEAK 66(XQ24) WILD-TYPE                                                                     94
                             vv
clus                          THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 66(XQ24) MUTATED                                                                     1
  AMP PEAK 66(XQ24) WILD-TYPE                                                                  34
D62V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 66(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 66(XQ24) WILD-TYPE
  OTHER  SPECIFY                                                                                   9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  349
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          94
  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"
D62V9, binary
                             cls
clus                            0   1
  AMP PEAK 66(XQ24) MUTATED     0   9
  AMP PEAK 66(XQ24) WILD-TYPE  14 472
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 66(XQ24) MUTATED      0    9
  AMP PEAK 66(XQ24) WILD-TYPE   14  472
     clus
vv    AMP PEAK 66(XQ24) MUTATED AMP PEAK 66(XQ24) WILD-TYPE
  NO                          0                          14
  YES                         9                         472
[1] 2 2
[1] FALSE
D62V10, binary
                             cls
clus                            0   1
  AMP PEAK 66(XQ24) MUTATED     9   0
  AMP PEAK 66(XQ24) WILD-TYPE 408  17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 66(XQ24) MUTATED      9    0
  AMP PEAK 66(XQ24) WILD-TYPE  408   17
     clus
vv    AMP PEAK 66(XQ24) MUTATED AMP PEAK 66(XQ24) WILD-TYPE
  NO                          9                         408
  YES                         0                          17
[1] 2 2
[1] FALSE
                             vv
clus                          MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 66(XQ24) MUTATED              2                       0    6
  AMP PEAK 66(XQ24) WILD-TYPE          128                      16  322
                             vv
clus                          VERY ADVANCED (T4B)
  AMP PEAK 66(XQ24) MUTATED                     1
  AMP PEAK 66(XQ24) WILD-TYPE                   0
D62V11, multiclass
                         clus
vv                        AMP PEAK 66(XQ24) MUTATED AMP PEAK 66(XQ24) WILD-TYPE
  MINIMAL (T3)                                    2                         128
  MODERATE/ADVANCED (T4A)                         0                          16
  NONE                                            6                         322
  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 66(XQ24) MUTATED     6   2   0   1
  AMP PEAK 66(XQ24) WILD-TYPE 372  49   4  29
D62V12, multiclass
    clus
vv   AMP PEAK 66(XQ24) MUTATED AMP PEAK 66(XQ24) WILD-TYPE
  R0                         6                         372
  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 66(XQ24) MUTATED     5   4
  AMP PEAK 66(XQ24) WILD-TYPE 219 257
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 66(XQ24) MUTATED      5    4
  AMP PEAK 66(XQ24) WILD-TYPE  219  257
            clus
vv           AMP PEAK 66(XQ24) MUTATED AMP PEAK 66(XQ24) WILD-TYPE
  MULTIFOCAL                         5                         219
  UNIFOCAL                           4                         257
[1] 2 2
[1] FALSE
D62V15, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 66(XQ24) MUTATED                                  0     0
  AMP PEAK 66(XQ24) WILD-TYPE                                1    49
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 66(XQ24) MUTATED                           0     4
  AMP PEAK 66(XQ24) WILD-TYPE                        26   317
D62V16, multiclass
                                  clus
vv                                 AMP PEAK 66(XQ24) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                0
  WHITE                                                    4
                                  clus
vv                                 AMP PEAK 66(XQ24) 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"
D62V17, binary
                             cls
clus                            0   1
  AMP PEAK 66(XQ24) MUTATED     0   4
  AMP PEAK 66(XQ24) WILD-TYPE  38 346
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 66(XQ24) MUTATED      0    4
  AMP PEAK 66(XQ24) WILD-TYPE   38  346
                        clus
vv                       AMP PEAK 66(XQ24) MUTATED AMP PEAK 66(XQ24) WILD-TYPE
  HISPANIC OR LATINO                             0                          38
  NOT HISPANIC OR LATINO                         4                         346
[1] 2 2
[1] FALSE

Clustering(63) Variable = AMP PEAK 67(XQ24) MUTATION ANALYSIS
D63V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 67(XQ24) MUTATED     8   1
  AMP PEAK 67(XQ24) WILD-TYPE 469  13
  AMP PEAK 67(XQ24) MUTATED AMP PEAK 67(XQ24) WILD-TYPE 
                          9                         482 
  AMP PEAK 67(XQ24) MUTATED AMP PEAK 67(XQ24) WILD-TYPE 
                          1                          13 
$`AMP PEAK 67(XQ24) MUTATED`
TCGA-BJ-A2N9 TCGA-DJ-A2Q6 TCGA-EL-A3T9 TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N 
       20.48         8.61         5.72        54.21        57.01        10.65 
TCGA-EM-A3AI TCGA-EM-A3FK TCGA-FY-A3NM 
       17.46        23.77         0.99 

$`AMP PEAK 67(XQ24) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
        1.22        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        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
        9.44         9.90        10.09         7.07        10.36        12.43 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        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        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04         1.15        22.29 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA 
       32.48       116.91        98.24        41.29        95.38        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN 
       82.82        77.36        78.97        31.50        50.33        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        52.50        45.53        48.16         7.07        44.65 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       45.80        19.30        45.96        37.94        31.04        19.59 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        33.60        28.73        41.13        37.78        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       13.32        11.87         8.71        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A22I 
       12.36        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        11.74        11.15 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        16.44        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        2.99        12.30        15.19        10.49        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       13.84        19.73        17.59        12.07        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        18.97        15.68        14.14        19.63 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FL 
       13.38         8.35        16.44        16.77        27.95        16.80 
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        11.15         7.33        12.53         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        16.41        15.62        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        9.80         5.03        37.87        12.72         0.95        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
       71.01        80.02        65.36        84.89        98.56        61.02 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       58.72        57.11        55.10        59.15        28.24         5.85 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
        4.18         2.43         5.56        24.72        38.30        42.25 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
        2.37         4.50        80.81        69.24        59.87        43.50 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
        0.30        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        59.70        31.59        44.25        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      102.90        66.77        81.34        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        46.06         4.08 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        0.89        22.03         0.92        48.10        91.17         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        1.15        17.82         1.64         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
        4.67        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 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
        1.15         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        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90         9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74 
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         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  AMP PEAK 67(XQ24) MUTATED AMP PEAK 67(XQ24) WILD-TYPE 
                       0.99                        0.03 
  AMP PEAK 67(XQ24) MUTATED AMP PEAK 67(XQ24) WILD-TYPE 
                      57.01                      158.83 
  AMP PEAK 67(XQ24) MUTATED AMP PEAK 67(XQ24) WILD-TYPE 
                      17.46                       16.57 
[1] "1.0 - 57.0 (17.5)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "5.2"
D63V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 67(XQ24) MUTATED         4        2         2        1         0
  AMP PEAK 67(XQ24) WILD-TYPE     276       49       107        1        45
                             vv
clus                          STAGE IVC
  AMP PEAK 67(XQ24) MUTATED           0
  AMP PEAK 67(XQ24) WILD-TYPE         6
D63V3, multiclass
           clus
vv          AMP PEAK 67(XQ24) MUTATED AMP PEAK 67(XQ24) WILD-TYPE
  STAGE I                           4                         276
  STAGE II                          2                          49
  STAGE III                         2                         107
  STAGE IV                          1                           1
  STAGE IVA                         0                          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 67(XQ24) MUTATED     3   3   2   1
  AMP PEAK 67(XQ24) WILD-TYPE 137 163 163  20
D63V4, multiclass
    clus
vv   AMP PEAK 67(XQ24) MUTATED AMP PEAK 67(XQ24) WILD-TYPE
  T1                         3                         137
  T2                         3                         163
  T3                         2                         163
  T4                         1                          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"
D63V5, binary
                             cls
clus                            0   1
  AMP PEAK 67(XQ24) MUTATED     5   3
  AMP PEAK 67(XQ24) WILD-TYPE 218 219
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 67(XQ24) MUTATED      5    3
  AMP PEAK 67(XQ24) WILD-TYPE  218  219
   clus
vv  AMP PEAK 67(XQ24) MUTATED AMP PEAK 67(XQ24) WILD-TYPE
  0                         5                         218
  1                         3                         219
[1] 2 2
[1] FALSE
                             vv
clus                           M0  M1  MX
  AMP PEAK 67(XQ24) MUTATED     2   0   7
  AMP PEAK 67(XQ24) WILD-TYPE 271   9 205
D63V6, multiclass
    clus
vv   AMP PEAK 67(XQ24) MUTATED AMP PEAK 67(XQ24) WILD-TYPE
  M0                         2                         271
  M1                         0                           9
  MX                         7                         205
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, binary
                             cls
clus                            0   1
  AMP PEAK 67(XQ24) MUTATED     9   0
  AMP PEAK 67(XQ24) WILD-TYPE 355 131
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 67(XQ24) MUTATED      9    0
  AMP PEAK 67(XQ24) WILD-TYPE  355  131
        clus
vv       AMP PEAK 67(XQ24) MUTATED AMP PEAK 67(XQ24) WILD-TYPE
  FEMALE                         9                         355
  MALE                           0                         131
[1] 2 2
[1] FALSE
                             vv
clus                          OTHER  SPECIFY
  AMP PEAK 67(XQ24) MUTATED                0
  AMP PEAK 67(XQ24) WILD-TYPE              9
                             vv
clus                          THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 67(XQ24) MUTATED                                               5
  AMP PEAK 67(XQ24) WILD-TYPE                                           348
                             vv
clus                          THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 67(XQ24) MUTATED                                                                        4
  AMP PEAK 67(XQ24) WILD-TYPE                                                                     94
                             vv
clus                          THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 67(XQ24) MUTATED                                                                     0
  AMP PEAK 67(XQ24) WILD-TYPE                                                                  35
D63V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 67(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 67(XQ24) WILD-TYPE
  OTHER  SPECIFY                                                                                   9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  348
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          94
  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"
D63V9, binary
                             cls
clus                            0   1
  AMP PEAK 67(XQ24) MUTATED     0   9
  AMP PEAK 67(XQ24) WILD-TYPE  14 472
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 67(XQ24) MUTATED      0    9
  AMP PEAK 67(XQ24) WILD-TYPE   14  472
     clus
vv    AMP PEAK 67(XQ24) MUTATED AMP PEAK 67(XQ24) WILD-TYPE
  NO                          0                          14
  YES                         9                         472
[1] 2 2
[1] FALSE
D63V10, binary
                             cls
clus                            0   1
  AMP PEAK 67(XQ24) MUTATED     9   0
  AMP PEAK 67(XQ24) WILD-TYPE 408  17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 67(XQ24) MUTATED      9    0
  AMP PEAK 67(XQ24) WILD-TYPE  408   17
     clus
vv    AMP PEAK 67(XQ24) MUTATED AMP PEAK 67(XQ24) WILD-TYPE
  NO                          9                         408
  YES                         0                          17
[1] 2 2
[1] FALSE
                             vv
clus                          MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 67(XQ24) MUTATED              2                       0    6
  AMP PEAK 67(XQ24) WILD-TYPE          128                      16  322
                             vv
clus                          VERY ADVANCED (T4B)
  AMP PEAK 67(XQ24) MUTATED                     1
  AMP PEAK 67(XQ24) WILD-TYPE                   0
D63V11, multiclass
                         clus
vv                        AMP PEAK 67(XQ24) MUTATED AMP PEAK 67(XQ24) WILD-TYPE
  MINIMAL (T3)                                    2                         128
  MODERATE/ADVANCED (T4A)                         0                          16
  NONE                                            6                         322
  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 67(XQ24) MUTATED     6   2   0   1
  AMP PEAK 67(XQ24) WILD-TYPE 372  49   4  29
D63V12, multiclass
    clus
vv   AMP PEAK 67(XQ24) MUTATED AMP PEAK 67(XQ24) WILD-TYPE
  R0                         6                         372
  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"
D63V13, continuous
D63V14, binary
                             cls
clus                            0   1
  AMP PEAK 67(XQ24) MUTATED     6   3
  AMP PEAK 67(XQ24) WILD-TYPE 218 258
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 67(XQ24) MUTATED      6    3
  AMP PEAK 67(XQ24) WILD-TYPE  218  258
            clus
vv           AMP PEAK 67(XQ24) MUTATED AMP PEAK 67(XQ24) WILD-TYPE
  MULTIFOCAL                         6                         218
  UNIFOCAL                           3                         258
[1] 2 2
[1] FALSE
D63V15, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 67(XQ24) MUTATED                                  0     0
  AMP PEAK 67(XQ24) WILD-TYPE                                1    49
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 67(XQ24) MUTATED                           0     4
  AMP PEAK 67(XQ24) WILD-TYPE                        26   317
D63V16, multiclass
                                  clus
vv                                 AMP PEAK 67(XQ24) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                0
  WHITE                                                    4
                                  clus
vv                                 AMP PEAK 67(XQ24) 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"
D63V17, binary
                             cls
clus                            0   1
  AMP PEAK 67(XQ24) MUTATED     0   4
  AMP PEAK 67(XQ24) WILD-TYPE  38 346
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 67(XQ24) MUTATED      0    4
  AMP PEAK 67(XQ24) WILD-TYPE   38  346
                        clus
vv                       AMP PEAK 67(XQ24) MUTATED AMP PEAK 67(XQ24) WILD-TYPE
  HISPANIC OR LATINO                             0                          38
  NOT HISPANIC OR LATINO                         4                         346
[1] 2 2
[1] FALSE

Clustering(64) Variable = AMP PEAK 68(XQ28) MUTATION ANALYSIS
D64V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 68(XQ28) MUTATED     9   1
  AMP PEAK 68(XQ28) WILD-TYPE 468  13
  AMP PEAK 68(XQ28) MUTATED AMP PEAK 68(XQ28) WILD-TYPE 
                         10                         481 
  AMP PEAK 68(XQ28) MUTATED AMP PEAK 68(XQ28) WILD-TYPE 
                          1                          13 
$`AMP PEAK 68(XQ28) MUTATED`
TCGA-BJ-A2N9 TCGA-EL-A3T9 TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22N TCGA-EM-A3AI 
       20.48         5.72        54.21        57.01        10.65        17.46 
TCGA-EM-A3AQ TCGA-EM-A3FK TCGA-FE-A22Z TCGA-FY-A3NM 
       16.44        23.77        73.74         0.99 

$`AMP PEAK 68(XQ28) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
        1.22        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        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
        1.45        74.30        45.40        33.47       108.36        39.32 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        30.18       102.84        65.39       124.04        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       37.25       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        38.66        52.73       139.00       131.15       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        12.16       147.42       130.72 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       116.91        98.24        41.29        95.38 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YE 
       20.91        12.36        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        11.74 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.15        14.24        16.44        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
        6.05         2.99        12.30        15.19        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        13.84        19.73        17.59        12.07        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        18.97        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FL 
       19.63        13.38         8.35        16.77        27.95        16.80 
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        11.15         7.33        12.53         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        16.41        15.62        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        9.80         5.03        37.87        12.72         0.95        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
       71.01        80.02        65.36        84.89        98.56        61.02 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       58.72        57.11        55.10        59.15        28.24         5.85 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
        4.18         2.43         5.56        24.72        38.30        42.25 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
        2.37         4.50        80.81        69.24        59.87        43.50 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
        0.30        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       59.70        31.59        44.25        24.69        68.22       102.90 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77        81.34        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        46.06         4.08         0.89 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10        91.17         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       17.82         1.64         1.51         0.76         0.03         4.67 
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         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74        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         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  AMP PEAK 68(XQ28) MUTATED AMP PEAK 68(XQ28) WILD-TYPE 
                       0.99                        0.03 
  AMP PEAK 68(XQ28) MUTATED AMP PEAK 68(XQ28) WILD-TYPE 
                      73.74                      158.83 
  AMP PEAK 68(XQ28) MUTATED AMP PEAK 68(XQ28) WILD-TYPE 
                      18.97                       16.57 
[1] "1.0 - 73.7 (19.0)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "3.2"
D64V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 68(XQ28) MUTATED         4        2         2        1         1
  AMP PEAK 68(XQ28) WILD-TYPE     276       49       107        1        44
                             vv
clus                          STAGE IVC
  AMP PEAK 68(XQ28) MUTATED           0
  AMP PEAK 68(XQ28) WILD-TYPE         6
D64V3, multiclass
           clus
vv          AMP PEAK 68(XQ28) MUTATED AMP PEAK 68(XQ28) WILD-TYPE
  STAGE I                           4                         276
  STAGE II                          2                          49
  STAGE III                         2                         107
  STAGE IV                          1                           1
  STAGE IVA                         1                          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 68(XQ28) MUTATED     3   3   2   2
  AMP PEAK 68(XQ28) WILD-TYPE 137 163 163  19
D64V4, multiclass
    clus
vv   AMP PEAK 68(XQ28) MUTATED AMP PEAK 68(XQ28) WILD-TYPE
  T1                         3                         137
  T2                         3                         163
  T3                         2                         163
  T4                         2                          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"
D64V5, binary
                             cls
clus                            0   1
  AMP PEAK 68(XQ28) MUTATED     6   3
  AMP PEAK 68(XQ28) WILD-TYPE 217 219
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 68(XQ28) MUTATED      6    3
  AMP PEAK 68(XQ28) WILD-TYPE  217  219
   clus
vv  AMP PEAK 68(XQ28) MUTATED AMP PEAK 68(XQ28) WILD-TYPE
  0                         6                         217
  1                         3                         219
[1] 2 2
[1] FALSE
                             vv
clus                           M0  M1  MX
  AMP PEAK 68(XQ28) MUTATED     1   0   9
  AMP PEAK 68(XQ28) WILD-TYPE 272   9 203
D64V6, multiclass
    clus
vv   AMP PEAK 68(XQ28) MUTATED AMP PEAK 68(XQ28) WILD-TYPE
  M0                         1                         272
  M1                         0                           9
  MX                         9                         203
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V7, binary
                             cls
clus                            0   1
  AMP PEAK 68(XQ28) MUTATED    10   0
  AMP PEAK 68(XQ28) WILD-TYPE 354 131
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 68(XQ28) MUTATED     10    0
  AMP PEAK 68(XQ28) WILD-TYPE  354  131
        clus
vv       AMP PEAK 68(XQ28) MUTATED AMP PEAK 68(XQ28) WILD-TYPE
  FEMALE                        10                         354
  MALE                           0                         131
[1] 2 2
[1] FALSE
                             vv
clus                          OTHER  SPECIFY
  AMP PEAK 68(XQ28) MUTATED                0
  AMP PEAK 68(XQ28) WILD-TYPE              9
                             vv
clus                          THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  AMP PEAK 68(XQ28) MUTATED                                               5
  AMP PEAK 68(XQ28) WILD-TYPE                                           348
                             vv
clus                          THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  AMP PEAK 68(XQ28) MUTATED                                                                        5
  AMP PEAK 68(XQ28) WILD-TYPE                                                                     93
                             vv
clus                          THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  AMP PEAK 68(XQ28) MUTATED                                                                     0
  AMP PEAK 68(XQ28) WILD-TYPE                                                                  35
D64V8, multiclass
                                                                        clus
vv                                                                       AMP PEAK 68(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 68(XQ28) WILD-TYPE
  OTHER  SPECIFY                                                                                   9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  348
  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"
D64V9, binary
                             cls
clus                            0   1
  AMP PEAK 68(XQ28) MUTATED     1   9
  AMP PEAK 68(XQ28) WILD-TYPE  13 472
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 68(XQ28) MUTATED      1    9
  AMP PEAK 68(XQ28) WILD-TYPE   13  472
     clus
vv    AMP PEAK 68(XQ28) MUTATED AMP PEAK 68(XQ28) WILD-TYPE
  NO                          1                          13
  YES                         9                         472
[1] 2 2
[1] FALSE
D64V10, binary
                             cls
clus                            0   1
  AMP PEAK 68(XQ28) MUTATED    10   0
  AMP PEAK 68(XQ28) WILD-TYPE 407  17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 68(XQ28) MUTATED     10    0
  AMP PEAK 68(XQ28) WILD-TYPE  407   17
     clus
vv    AMP PEAK 68(XQ28) MUTATED AMP PEAK 68(XQ28) WILD-TYPE
  NO                         10                         407
  YES                         0                          17
[1] 2 2
[1] FALSE
                             vv
clus                          MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  AMP PEAK 68(XQ28) MUTATED              1                       1    7
  AMP PEAK 68(XQ28) WILD-TYPE          129                      15  321
                             vv
clus                          VERY ADVANCED (T4B)
  AMP PEAK 68(XQ28) MUTATED                     1
  AMP PEAK 68(XQ28) WILD-TYPE                   0
D64V11, multiclass
                         clus
vv                        AMP PEAK 68(XQ28) MUTATED AMP PEAK 68(XQ28) WILD-TYPE
  MINIMAL (T3)                                    1                         129
  MODERATE/ADVANCED (T4A)                         1                          15
  NONE                                            7                         321
  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 68(XQ28) MUTATED     7   2   0   1
  AMP PEAK 68(XQ28) WILD-TYPE 371  49   4  29
D64V12, multiclass
    clus
vv   AMP PEAK 68(XQ28) MUTATED AMP PEAK 68(XQ28) WILD-TYPE
  R0                         7                         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"
D64V13, continuous
D64V14, binary
                             cls
clus                            0   1
  AMP PEAK 68(XQ28) MUTATED     6   4
  AMP PEAK 68(XQ28) WILD-TYPE 218 257
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 68(XQ28) MUTATED      6    4
  AMP PEAK 68(XQ28) WILD-TYPE  218  257
            clus
vv           AMP PEAK 68(XQ28) MUTATED AMP PEAK 68(XQ28) WILD-TYPE
  MULTIFOCAL                         6                         218
  UNIFOCAL                           4                         257
[1] 2 2
[1] FALSE
D64V15, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 68(XQ28) MUTATED                                  0     0
  AMP PEAK 68(XQ28) WILD-TYPE                                1    49
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 68(XQ28) MUTATED                           0     4
  AMP PEAK 68(XQ28) WILD-TYPE                        26   317
D64V16, multiclass
                                  clus
vv                                 AMP PEAK 68(XQ28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                0
  WHITE                                                    4
                                  clus
vv                                 AMP PEAK 68(XQ28) 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"
D64V17, binary
                             cls
clus                            0   1
  AMP PEAK 68(XQ28) MUTATED     0   4
  AMP PEAK 68(XQ28) WILD-TYPE  38 346
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 68(XQ28) MUTATED      0    4
  AMP PEAK 68(XQ28) WILD-TYPE   38  346
                        clus
vv                       AMP PEAK 68(XQ28) MUTATED AMP PEAK 68(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             0                          38
  NOT HISPANIC OR LATINO                         4                         346
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK  1(1Q24.2) MUTATION ANALYSIS
D65V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  1(1Q24.2) MUTATED     3   0
  DEL PEAK  1(1Q24.2) WILD-TYPE 474  14
  DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE 
                            3                           488 
  DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE 
                            0                            14 
$`DEL PEAK  1(1Q24.2) MUTATED`
TCGA-EM-A1YE TCGA-ET-A39N TCGA-FY-A3I5 
       54.08        98.56         1.64 

$`DEL PEAK  1(1Q24.2) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        5.52         8.78         8.42         8.12         9.34         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
        9.21         9.44         9.90         8.61        10.09         7.07 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       10.36        12.43        10.85        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        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 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.07        14.27         3.02        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        13.78        13.58        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        80.91         4.18 
TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 
       58.82         1.45        74.30        45.40        33.47       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
       39.32         1.41        30.18       102.84        65.39       124.04 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        37.25       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        38.66        52.73       139.00       131.15 
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        12.16       147.42 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      130.72       129.57        32.48       116.91        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
       95.38         5.72        66.90        82.82        77.36        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       31.50        50.33        53.06        47.38        52.50        45.53 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       48.16         7.07        44.65        45.80        19.30        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        19.59        30.51        33.60        28.73 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        37.78        29.95        13.32        11.87         8.71 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        12.36        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.46        54.21        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        11.74        11.15        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       16.44        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
       12.30        15.19        10.49        13.15        22.16        13.84 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        17.59        12.07        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        17.46        18.97        15.68        14.14        19.63 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        16.44        16.77        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        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        11.15         7.33        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       13.91         7.82        11.51        16.41        15.62        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        70.65        16.90         9.01         4.83         8.61 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
        8.38         9.80         5.03        37.87        12.72         0.95 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       47.47        48.20        29.69        32.35        14.79        12.33 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       14.79        27.09        18.38        29.49        54.05        22.09 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       12.26        16.08        29.19        19.76         2.66        58.22 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O 
       13.74        71.01        80.02        65.36        84.89        61.02 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       58.72        57.11        55.10        59.15        28.24         5.85 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
        4.18         2.43         5.56        24.72        38.30        42.25 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
        2.37         4.50        80.81        69.24        59.87        43.50 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
        0.30        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        59.70        31.59        44.25        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      102.90        66.77        81.34        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        46.06         4.08 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        0.89        22.03         0.92        48.10        91.17         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        1.15        17.82         0.99         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
        4.67        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 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
        1.15         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        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90         9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74 
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         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE 
                         1.64                          0.03 
  DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE 
                        98.56                        158.83 
  DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE 
                        54.08                         16.57 
[1] "1.6 - 98.6 (54.1)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "9200000"
D65V2, 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     279       50       108        2        45
                               vv
clus                            STAGE IVC
  DEL PEAK  1(1Q24.2) MUTATED           0
  DEL PEAK  1(1Q24.2) WILD-TYPE         6
D65V3, multiclass
           clus
vv          DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE
  STAGE I                             1                           279
  STAGE II                            1                            50
  STAGE III                           1                           108
  STAGE IV                            0                             2
  STAGE IVA                           0                            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  1(1Q24.2) MUTATED     0   1   2   0
  DEL PEAK  1(1Q24.2) WILD-TYPE 140 165 163  21
D65V4, multiclass
    clus
vv   DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE
  T1                           0                           140
  T2                           1                           165
  T3                           2                           163
  T4                           0                            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"
D65V5, binary
                               cls
clus                              0   1
  DEL PEAK  1(1Q24.2) MUTATED     2   0
  DEL PEAK  1(1Q24.2) WILD-TYPE 221 222
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(1Q24.2) MUTATED      2    0
  DEL PEAK  1(1Q24.2) WILD-TYPE  221  222
   clus
vv  DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE
  0                           2                           221
  1                           0                           222
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  DEL PEAK  1(1Q24.2) MUTATED     0   0   3
  DEL PEAK  1(1Q24.2) WILD-TYPE 273   9 209
D65V6, multiclass
    clus
vv   DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE
  M0                           0                           273
  M1                           0                             9
  MX                           3                           209
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                               cls
clus                              0   1
  DEL PEAK  1(1Q24.2) MUTATED     3   0
  DEL PEAK  1(1Q24.2) WILD-TYPE 361 131
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(1Q24.2) MUTATED      3    0
  DEL PEAK  1(1Q24.2) WILD-TYPE  361  131
        clus
vv       DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE
  FEMALE                           3                           361
  MALE                             0                           131
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  DEL PEAK  1(1Q24.2) MUTATED                0
  DEL PEAK  1(1Q24.2) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK  1(1Q24.2) MUTATED                                               1
  DEL PEAK  1(1Q24.2) WILD-TYPE                                           352
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK  1(1Q24.2) MUTATED                                                                        2
  DEL PEAK  1(1Q24.2) WILD-TYPE                                                                     96
                               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                                                                  35
D65V8, 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                                                                                     9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    352
  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"
D65V9, binary
                               cls
clus                              0   1
  DEL PEAK  1(1Q24.2) MUTATED     0   3
  DEL PEAK  1(1Q24.2) WILD-TYPE  14 478
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(1Q24.2) MUTATED      0    3
  DEL PEAK  1(1Q24.2) WILD-TYPE   14  478
     clus
vv    DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE
  NO                            0                            14
  YES                           3                           478
[1] 2 2
[1] FALSE
D65V10, binary
                               cls
clus                              0   1
  DEL PEAK  1(1Q24.2) MUTATED     2   0
  DEL PEAK  1(1Q24.2) WILD-TYPE 415  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(1Q24.2) MUTATED      2    0
  DEL PEAK  1(1Q24.2) WILD-TYPE  415   17
     clus
vv    DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE
  NO                            2                           415
  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          130                      16  325
                               vv
clus                            VERY ADVANCED (T4B)
  DEL PEAK  1(1Q24.2) MUTATED                     0
  DEL PEAK  1(1Q24.2) WILD-TYPE                   1
D65V11, 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)                                      130
  MODERATE/ADVANCED (T4A)                            16
  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  1(1Q24.2) MUTATED     3   0   0   0
  DEL PEAK  1(1Q24.2) WILD-TYPE 375  51   4  30
D65V12, multiclass
    clus
vv   DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE
  R0                           3                           375
  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"
D65V13, 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                           389 
                   TCGA-BJ-A0Z0                    TCGA-BJ-A0Z3 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A0Z9                    TCGA-BJ-A0ZA 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A0ZB                    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-A28R 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A28T                    TCGA-BJ-A28W 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A28X                    TCGA-BJ-A28Z 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A290                    TCGA-BJ-A291 
"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-A3EZ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A3PR                    TCGA-BJ-A3PU 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A45C                    TCGA-BJ-A45D 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A45E                    TCGA-BJ-A45G 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A45I                    TCGA-BJ-A45J 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A45K                    TCGA-BJ-A4O8 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A4O9                    TCGA-CE-A13K 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-CE-A3MD                    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-A13P                    TCGA-DJ-A13R 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A13T                    TCGA-DJ-A13U 
"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-A3VJ                    TCGA-DJ-A3VL 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A4UL                    TCGA-DJ-A4UQ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A4UR                    TCGA-DJ-A4UW 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A4V2                    TCGA-DJ-A4V5 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DO-A1K0                    TCGA-DO-A2HM 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E3-A3DY                    TCGA-E3-A3DZ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E3-A3E0                    TCGA-E3-A3E1 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E3-A3E2                    TCGA-E3-A3E3 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E3-A3E5                    TCGA-E8-A242 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E8-A2EA                    TCGA-E8-A2JQ 
"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-A3ZN                    TCGA-EL-A3ZO 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3ZP                    TCGA-EL-A3ZS 
"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-A4KD                    TCGA-EL-A4KG 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A4KI                    TCGA-EM-A1CS 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A1CT                    TCGA-EM-A1CU 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A1CV                    TCGA-EM-A1CW 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A1YA                    TCGA-EM-A1YB 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A1YC                    TCGA-EM-A1YD 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A22I                    TCGA-EM-A22J 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A22K                    TCGA-EM-A22L 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A22M                    TCGA-EM-A22N 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A22O                    TCGA-EM-A22P 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A22Q                    TCGA-EM-A2CK 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A2CN                    TCGA-EM-A2CP 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A2CQ                    TCGA-EM-A2CS 
"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-A2OW 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A2OX                    TCGA-EM-A2OY 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A2OZ                    TCGA-EM-A2P0 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A2P1                    TCGA-EM-A2P2 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A2P3                    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-A3FL                    TCGA-EM-A3FM 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A3FN                    TCGA-EM-A3FO 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A3FP                    TCGA-EM-A3FQ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A3FR                    TCGA-EM-A3O3 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A3O7                    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-A3SY                    TCGA-EM-A3SZ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A4FF                    TCGA-EM-A4FH 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A4FK                    TCGA-EM-A4FM 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A4FN                    TCGA-EM-A4FO 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A4FQ                    TCGA-EM-A4FR 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EM-A4FU                    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" 
D65V14, binary
                               cls
clus                              0   1
  DEL PEAK  1(1Q24.2) MUTATED     1   2
  DEL PEAK  1(1Q24.2) WILD-TYPE 223 259
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(1Q24.2) MUTATED      1    2
  DEL PEAK  1(1Q24.2) WILD-TYPE  223  259
            clus
vv           DEL PEAK  1(1Q24.2) MUTATED DEL PEAK  1(1Q24.2) WILD-TYPE
  MULTIFOCAL                           1                           223
  UNIFOCAL                             2                           259
[1] 2 2
[1] FALSE
D65V15, 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    49
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1Q24.2) MUTATED                           0     2
  DEL PEAK  1(1Q24.2) WILD-TYPE                        26   319
D65V16, 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                           395 
                   TCGA-BJ-A0YZ                    TCGA-BJ-A0Z2 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A0Z3                    TCGA-BJ-A0Z5 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A0Z9                    TCGA-BJ-A0ZA 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A0ZB                    TCGA-BJ-A0ZC 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A0ZE                    TCGA-BJ-A0ZG 
"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-A192                    TCGA-BJ-A28R 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A28S                    TCGA-BJ-A28T 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A28V                    TCGA-BJ-A28W 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A28X                    TCGA-BJ-A28Z 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A290                    TCGA-BJ-A291 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A2N7                    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-A2P4                    TCGA-BJ-A3EZ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A3F0                    TCGA-BJ-A3PR 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A3PT                    TCGA-BJ-A3PU 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A45C                    TCGA-BJ-A45D 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A45E                    TCGA-BJ-A45F 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A45G                    TCGA-BJ-A45H 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A45I                    TCGA-BJ-A45J 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A45K                    TCGA-BJ-A4O8 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-BJ-A4O9                    TCGA-CE-A13K 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-CE-A27D                    TCGA-CE-A3MD 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-CE-A3ME                    TCGA-CE-A481 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-CE-A482                    TCGA-CE-A483 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-CE-A484                    TCGA-CE-A485 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DE-A0XZ                    TCGA-DE-A0Y2 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DE-A0Y3                    TCGA-DE-A2OL 
"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-A4M9                    TCGA-DE-A4MA 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DE-A4MB                    TCGA-DE-A4MC 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DE-A4MD                    TCGA-DE-A69J 
"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-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-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-A2Q9                    TCGA-DJ-A2QA 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A2QB                    TCGA-DJ-A3UK 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3UM                    TCGA-DJ-A3UN 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3UO                    TCGA-DJ-A3UQ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3UR                    TCGA-DJ-A3US 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3UT                    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-A3UY                    TCGA-DJ-A3UZ 
"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-A3VD 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3VE                    TCGA-DJ-A3VF 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3VG                    TCGA-DJ-A3VJ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A3VL                    TCGA-DJ-A3VM 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-DJ-A4UL                    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-A2JQ                    TCGA-E8-A3X7 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E8-A413                    TCGA-E8-A414 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E8-A415                    TCGA-E8-A416 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E8-A417                    TCGA-E8-A418 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E8-A419                    TCGA-E8-A432 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E8-A433                    TCGA-E8-A434 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-E8-A436                    TCGA-E8-A437 
"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-E8-A44M                    TCGA-EL-A3CL 
"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-A3CP 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3CR                    TCGA-EL-A3CS 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3CT                    TCGA-EL-A3CU 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3CV                    TCGA-EL-A3CW 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3CX                    TCGA-EL-A3CY 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3CZ                    TCGA-EL-A3D0 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3D1                    TCGA-EL-A3D4 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3D5                    TCGA-EL-A3D6 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3GO                    TCGA-EL-A3GP 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3GQ                    TCGA-EL-A3GR 
"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-A3GW 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3GX                    TCGA-EL-A3GY 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3GZ                    TCGA-EL-A3H1 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3H2                    TCGA-EL-A3H3 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3H4                    TCGA-EL-A3H5 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3H7                    TCGA-EL-A3H8 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3MW                    TCGA-EL-A3MX 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3MY                    TCGA-EL-A3MZ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3N2                    TCGA-EL-A3N3 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3T0                    TCGA-EL-A3T1 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3T2                    TCGA-EL-A3T3 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3T6                    TCGA-EL-A3T7 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3T8                    TCGA-EL-A3T9 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3TA                    TCGA-EL-A3TB 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3ZG                    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-A3ZN                    TCGA-EL-A3ZO 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3ZP                    TCGA-EL-A3ZQ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3ZR                    TCGA-EL-A3ZS 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A3ZT                    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-A4K9 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A4KD                    TCGA-EL-A4KG 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-EL-A4KH                    TCGA-EL-A4KI 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A25G                    TCGA-ET-A25I 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A25J                    TCGA-ET-A25K 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A25L                    TCGA-ET-A25M 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A25N                    TCGA-ET-A25O 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A25P                    TCGA-ET-A25R 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A2MX                    TCGA-ET-A2MY 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A2MZ                    TCGA-ET-A2N0 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A2N1                    TCGA-ET-A2N3 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A2N4                    TCGA-ET-A2N5 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A39I                    TCGA-ET-A39J 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A39K                    TCGA-ET-A39M 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A39O                    TCGA-ET-A39P 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A39R                    TCGA-ET-A39S 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A39T                    TCGA-ET-A3BN 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A3BO                    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-A3DO 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A3DP                    TCGA-ET-A3DQ 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A3DR                    TCGA-ET-A3DS 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A3DT                    TCGA-ET-A3DU 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A3DV                    TCGA-ET-A3DW 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A40P                    TCGA-ET-A40Q 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A40R                    TCGA-ET-A40S 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A40T                    TCGA-ET-A4KN 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-ET-A4KQ                    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-A3PA 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FE-A3PB                    TCGA-FE-A3PC 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FE-A3PD                    TCGA-FK-A3S3 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FK-A3SB                    TCGA-FK-A3SD 
"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-A3BL 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FY-A3I4                    TCGA-FY-A3NM 
"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-A3R8 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FY-A3R9                    TCGA-FY-A3RA 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FY-A3W9                    TCGA-FY-A3WA 
"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-A4B0 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FY-A4B3                    TCGA-FY-A4B4 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-FY-A76V                    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-A4ET                    TCGA-L6-A4EU 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-MK-A4N6                    TCGA-MK-A4N7 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-MK-A4N9                    TCGA-MK-A84Z 
"DEL PEAK  1(1Q24.2) WILD-TYPE" "DEL PEAK  1(1Q24.2) WILD-TYPE" 
                   TCGA-QD-A8IV 
"DEL PEAK  1(1Q24.2) WILD-TYPE" 
D65V17, binary
                               cls
clus                              0   1
  DEL PEAK  1(1Q24.2) MUTATED     0   2
  DEL PEAK  1(1Q24.2) WILD-TYPE  38 348
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(1Q24.2) MUTATED      0    2
  DEL PEAK  1(1Q24.2) WILD-TYPE   38  348
                        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                           348
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK  2(1Q42.13) MUTATION ANALYSIS
D66V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  2(1Q42.13) MUTATED     5   0
  DEL PEAK  2(1Q42.13) WILD-TYPE 472  14
  DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE 
                             5                            486 
  DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE 
                             0                             14 
$`DEL PEAK  2(1Q42.13) MUTATED`
TCGA-EL-A3CV TCGA-EL-A3CX TCGA-EM-A1YE TCGA-ET-A39N TCGA-FY-A3I5 
       37.94        80.91        54.08        98.56         1.64 

$`DEL PEAK  2(1Q42.13) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        5.52         8.78         8.42         8.12         9.34         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
        9.21         9.44         9.90         8.61        10.09         7.07 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       10.36        12.43        10.85        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        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 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.07        14.27         3.02        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        13.78        13.58        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        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        12.36        18.05        19.79        19.46        54.21 
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        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       10.49        13.15        22.16        13.84        19.73        17.59 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       12.07        17.59        17.46        17.29        14.60        17.46 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       18.97        15.68        14.14        19.63        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       16.44        16.77        27.95        23.77        16.80        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 
       11.15         7.33        12.53         9.24        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        16.41        15.62        13.51        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       80.02        65.36        84.89        61.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        59.15        28.24         5.85         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        24.69        68.22       102.90        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       81.34        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        46.06         4.08         0.89        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10        91.17         1.25         1.15        17.82 
TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
        0.99         1.51         0.76         0.03         4.67        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         6.87         4.14 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58         4.54         0.89         1.35         1.15         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        10.26        16.90         9.80 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
        9.63         2.96         8.65        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 
       86.70         6.02        12.43         6.74        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 
        0.72        16.64        32.45         8.71        10.98         5.19 

  DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE 
                          1.64                           0.03 
  DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE 
                         98.56                         158.83 
  DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE 
                        54.080                         16.505 
[1] "1.6 - 98.6 (54.1)"  "0.0 - 158.8 (16.5)"
[1] "hr="     "2.5e+07"
D66V2, 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     277       50       108        2        45
                                vv
clus                             STAGE IVC
  DEL PEAK  2(1Q42.13) MUTATED           0
  DEL PEAK  2(1Q42.13) WILD-TYPE         6
D66V3, multiclass
           clus
vv          DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE
  STAGE I                              3                            277
  STAGE II                             1                             50
  STAGE III                            1                            108
  STAGE IV                             0                              2
  STAGE IVA                            0                             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  2(1Q42.13) MUTATED     0   2   3   0
  DEL PEAK  2(1Q42.13) WILD-TYPE 140 164 162  21
D66V4, multiclass
    clus
vv   DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE
  T1                            0                            140
  T2                            2                            164
  T3                            3                            162
  T4                            0                             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"
D66V5, binary
                                cls
clus                               0   1
  DEL PEAK  2(1Q42.13) MUTATED     3   1
  DEL PEAK  2(1Q42.13) WILD-TYPE 220 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1Q42.13) MUTATED      3    1
  DEL PEAK  2(1Q42.13) WILD-TYPE  220  221
   clus
vv  DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE
  0                            3                            220
  1                            1                            221
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK  2(1Q42.13) MUTATED     2   0   3
  DEL PEAK  2(1Q42.13) WILD-TYPE 271   9 209
D66V6, multiclass
    clus
vv   DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE
  M0                            2                            271
  M1                            0                              9
  MX                            3                            209
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                                cls
clus                               0   1
  DEL PEAK  2(1Q42.13) MUTATED     4   1
  DEL PEAK  2(1Q42.13) WILD-TYPE 360 130
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1Q42.13) MUTATED      4    1
  DEL PEAK  2(1Q42.13) WILD-TYPE  360  130
        clus
vv       DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE
  FEMALE                            4                            360
  MALE                              1                            130
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK  2(1Q42.13) MUTATED                0
  DEL PEAK  2(1Q42.13) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK  2(1Q42.13) MUTATED                                               3
  DEL PEAK  2(1Q42.13) WILD-TYPE                                           350
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK  2(1Q42.13) MUTATED                                                                        2
  DEL PEAK  2(1Q42.13) WILD-TYPE                                                                     96
                                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                                                                  35
D66V8, 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                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     350
  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"
D66V9, binary
                                cls
clus                               0   1
  DEL PEAK  2(1Q42.13) MUTATED     0   5
  DEL PEAK  2(1Q42.13) WILD-TYPE  14 476
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1Q42.13) MUTATED      0    5
  DEL PEAK  2(1Q42.13) WILD-TYPE   14  476
     clus
vv    DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE
  NO                             0                             14
  YES                            5                            476
[1] 2 2
[1] FALSE
D66V10, binary
                                cls
clus                               0   1
  DEL PEAK  2(1Q42.13) MUTATED     4   0
  DEL PEAK  2(1Q42.13) WILD-TYPE 413  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1Q42.13) MUTATED      4    0
  DEL PEAK  2(1Q42.13) WILD-TYPE  413   17
     clus
vv    DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE
  NO                             4                            413
  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          129                      16  324
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK  2(1Q42.13) MUTATED                     0
  DEL PEAK  2(1Q42.13) WILD-TYPE                   1
D66V11, 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)                                       129
  MODERATE/ADVANCED (T4A)                             16
  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  2(1Q42.13) MUTATED     4   1   0   0
  DEL PEAK  2(1Q42.13) WILD-TYPE 374  50   4  30
D66V12, multiclass
    clus
vv   DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE
  R0                            4                            374
  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"
D66V13, continuous
D66V14, binary
                                cls
clus                               0   1
  DEL PEAK  2(1Q42.13) MUTATED     2   3
  DEL PEAK  2(1Q42.13) WILD-TYPE 222 258
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1Q42.13) MUTATED      2    3
  DEL PEAK  2(1Q42.13) WILD-TYPE  222  258
            clus
vv           DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE
  MULTIFOCAL                            2                            222
  UNIFOCAL                              3                            258
[1] 2 2
[1] FALSE
D66V15, 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    49
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1Q42.13) MUTATED                           0     4
  DEL PEAK  2(1Q42.13) WILD-TYPE                        26   317
D66V16, 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                                                        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"
D66V17, binary
                                cls
clus                               0   1
  DEL PEAK  2(1Q42.13) MUTATED     2   2
  DEL PEAK  2(1Q42.13) WILD-TYPE  36 348
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1Q42.13) MUTATED      2    2
  DEL PEAK  2(1Q42.13) WILD-TYPE   36  348
                        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                            348
[1] 2 2
[1] FALSE

Clustering(67) Variable = DEL PEAK  3(2P23.1) MUTATION ANALYSIS
D67V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2P23.1) MUTATED    12   0
  DEL PEAK  3(2P23.1) WILD-TYPE 465  14
  DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE 
                           12                           479 
  DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE 
                            0                            14 
$`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         8.12        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 
       17.59         9.24        13.51         5.03         0.30         1.64 

$`DEL PEAK  3(2P23.1) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
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        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.78         8.42         9.34         6.77         9.21         9.44 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
        9.90         8.61        10.09         7.07        10.36        12.43 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        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        24.23        17.69        43.00 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       11.34        21.37        12.76        25.02        20.22        30.61 
TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       14.56        19.20         9.83        21.27        20.48        11.93 
TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ 
       22.92        21.01        18.97         7.76         8.32        17.36 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       17.23        27.62        18.21        10.78        10.98        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        30.31        14.04         1.15        22.29        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       14.43        14.70        14.10        14.96         7.69        20.68 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       13.78        13.58        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        80.91         4.18        58.82         1.45        74.30 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       45.40        33.47       108.36        39.32         1.41        30.18 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
      102.84        65.39       124.04        50.37        37.25       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        38.66 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       52.73       139.00       131.15       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        12.16       147.42       130.72       129.57        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      116.91        98.24        41.29        95.38         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN 
       82.82        77.36        78.97        31.50        50.33        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        52.50        45.53        48.16         7.07        44.65 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       45.80        19.30        45.96        37.94        31.04        19.59 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        33.60        28.73        41.13        37.78        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       13.32        11.87         8.71        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
       12.36        18.05        19.79        19.46        54.21        57.01 
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        11.74 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.15        14.24        16.44        17.88        13.18        23.51 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        2.99        12.30        15.19        10.49        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       13.84        19.73        12.07        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        17.46        18.97        15.68        14.14        19.63 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        16.44        16.77        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        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        11.15         7.33        12.53        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
        7.82        11.51        16.41        15.62        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       37.87        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       29.49        54.05        22.09        12.26        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       65.36        84.89        98.56        61.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        59.15        28.24         5.85         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU 
       80.81        69.24        59.87        43.50        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       102.90        66.77        81.34 
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        46.06         4.08         0.89        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM 
       48.10        91.17         1.25         1.15        17.82         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
        1.51         0.76         0.03         4.67        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         6.87         4.14         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
        4.54         0.89         1.35         1.15         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        10.26        16.90         9.80         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        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        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        12.43         6.74        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         0.72 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       16.64        32.45         8.71        10.98         5.19 

  DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE 
                         0.30                          0.03 
  DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE 
                        54.08                        158.83 
  DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE 
                        9.945                        16.730 
[1] "0.3 - 54.1 (9.9)"   "0.0 - 158.8 (16.7)"
[1] "hr="     "9100000"
D67V2, 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     274       46       108        2        45
                               vv
clus                            STAGE IVC
  DEL PEAK  3(2P23.1) MUTATED           0
  DEL PEAK  3(2P23.1) WILD-TYPE         6
D67V3, multiclass
           clus
vv          DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE
  STAGE I                             6                           274
  STAGE II                            5                            46
  STAGE III                           1                           108
  STAGE IV                            0                             2
  STAGE IVA                           0                            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  3(2P23.1) MUTATED     4   5   3   0
  DEL PEAK  3(2P23.1) WILD-TYPE 136 161 162  21
D67V4, multiclass
    clus
vv   DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE
  T1                           4                           136
  T2                           5                           161
  T3                           3                           162
  T4                           0                            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"
D67V5, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P23.1) MUTATED     9   1
  DEL PEAK  3(2P23.1) WILD-TYPE 214 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P23.1) MUTATED      9    1
  DEL PEAK  3(2P23.1) WILD-TYPE  214  221
   clus
vv  DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE
  0                           9                           214
  1                           1                           221
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  DEL PEAK  3(2P23.1) MUTATED     2   0  10
  DEL PEAK  3(2P23.1) WILD-TYPE 271   9 202
D67V6, multiclass
    clus
vv   DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE
  M0                           2                           271
  M1                           0                             9
  MX                          10                           202
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P23.1) MUTATED     8   4
  DEL PEAK  3(2P23.1) WILD-TYPE 356 127
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P23.1) MUTATED      8    4
  DEL PEAK  3(2P23.1) WILD-TYPE  356  127
        clus
vv       DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE
  FEMALE                           8                           356
  MALE                             4                           127
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  DEL PEAK  3(2P23.1) MUTATED                1
  DEL PEAK  3(2P23.1) WILD-TYPE              8
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK  3(2P23.1) MUTATED                                               4
  DEL PEAK  3(2P23.1) WILD-TYPE                                           349
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK  3(2P23.1) MUTATED                                                                        7
  DEL PEAK  3(2P23.1) WILD-TYPE                                                                     91
                               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                                                                  35
D67V8, 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                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    349
  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"
D67V9, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P23.1) MUTATED     0  12
  DEL PEAK  3(2P23.1) WILD-TYPE  14 469
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P23.1) MUTATED      0   12
  DEL PEAK  3(2P23.1) WILD-TYPE   14  469
     clus
vv    DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE
  NO                            0                            14
  YES                          12                           469
[1] 2 2
[1] FALSE
D67V10, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P23.1) MUTATED    11   0
  DEL PEAK  3(2P23.1) WILD-TYPE 406  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P23.1) MUTATED     11    0
  DEL PEAK  3(2P23.1) WILD-TYPE  406   17
     clus
vv    DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE
  NO                           11                           406
  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          130                      16  316
                               vv
clus                            VERY ADVANCED (T4B)
  DEL PEAK  3(2P23.1) MUTATED                     0
  DEL PEAK  3(2P23.1) WILD-TYPE                   1
D67V11, 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)                                      130
  MODERATE/ADVANCED (T4A)                            16
  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
  DEL PEAK  3(2P23.1) MUTATED    11   0   0   1
  DEL PEAK  3(2P23.1) WILD-TYPE 367  51   4  29
D67V12, multiclass
    clus
vv   DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE
  R0                          11                           367
  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"
D67V13, continuous
D67V14, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P23.1) MUTATED     6   6
  DEL PEAK  3(2P23.1) WILD-TYPE 218 255
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P23.1) MUTATED      6    6
  DEL PEAK  3(2P23.1) WILD-TYPE  218  255
            clus
vv           DEL PEAK  3(2P23.1) MUTATED DEL PEAK  3(2P23.1) WILD-TYPE
  MULTIFOCAL                           6                           218
  UNIFOCAL                             6                           255
[1] 2 2
[1] FALSE
D67V15, 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    49
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(2P23.1) MUTATED                           0     5
  DEL PEAK  3(2P23.1) WILD-TYPE                        26   316
D67V16, 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                                                       49
  BLACK OR AFRICAN AMERICAN                                   26
  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"
D67V17, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P23.1) MUTATED     0   5
  DEL PEAK  3(2P23.1) WILD-TYPE  38 345
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P23.1) MUTATED      0    5
  DEL PEAK  3(2P23.1) WILD-TYPE   38  345
                        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                           345
[1] 2 2
[1] FALSE

Clustering(68) Variable = DEL PEAK  4(2Q22.1) MUTATION ANALYSIS
D68V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(2Q22.1) MUTATED    10   0
  DEL PEAK  4(2Q22.1) WILD-TYPE 467  14
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           10                           481 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                            0                            14 
$`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         8.12        54.08        10.65         6.05        17.59 
TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A39N TCGA-FY-A3I5 
        9.24        13.51        98.56         1.64 

$`DEL PEAK  4(2Q22.1) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
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        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.78         8.42         9.34         6.77         9.21         9.44 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
        9.90         8.61        10.09         7.07        10.36        12.43 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        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        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04         1.15        22.29 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        12.36        18.05        19.79        19.46        54.21 
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 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         2.99        12.30        15.19        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        13.84        19.73        12.07        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        17.46        18.97        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       19.63        13.38         8.35        16.44        16.77        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        16.80        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        11.15         7.33        12.53 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ 
       13.91         7.82        11.51        16.41        15.62        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        9.80         5.03        37.87        12.72         0.95        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
       71.01        80.02        65.36        84.89        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        2.43         5.56        24.72        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       59.70        31.59        44.25        24.69        68.22       102.90 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77        81.34        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        46.06         4.08         0.89 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10        91.17         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       17.82         0.99         1.51         0.76         0.03         4.67 
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         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74        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         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                         1.64                          0.03 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                        98.56                        158.83 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                        12.08                         16.64 
[1] "1.6 - 98.6 (12.1)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "9200000"
D68V2, 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     276       46       108        2        45
                               vv
clus                            STAGE IVC
  DEL PEAK  4(2Q22.1) MUTATED           0
  DEL PEAK  4(2Q22.1) WILD-TYPE         6
D68V3, multiclass
           clus
vv          DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  STAGE I                             4                           276
  STAGE II                            5                            46
  STAGE III                           1                           108
  STAGE IV                            0                             2
  STAGE IVA                           0                            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  4(2Q22.1) MUTATED     2   5   3   0
  DEL PEAK  4(2Q22.1) WILD-TYPE 138 161 162  21
D68V4, multiclass
    clus
vv   DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  T1                           2                           138
  T2                           5                           161
  T3                           3                           162
  T4                           0                            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"
D68V5, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED     7   0
  DEL PEAK  4(2Q22.1) WILD-TYPE 216 222
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      7    0
  DEL PEAK  4(2Q22.1) WILD-TYPE  216  222
   clus
vv  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  0                           7                           216
  1                           0                           222
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  DEL PEAK  4(2Q22.1) MUTATED     1   0   9
  DEL PEAK  4(2Q22.1) WILD-TYPE 272   9 203
D68V6, multiclass
    clus
vv   DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  M0                           1                           272
  M1                           0                             9
  MX                           9                           203
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED     7   3
  DEL PEAK  4(2Q22.1) WILD-TYPE 357 128
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      7    3
  DEL PEAK  4(2Q22.1) WILD-TYPE  357  128
        clus
vv       DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  FEMALE                           7                           357
  MALE                             3                           128
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  DEL PEAK  4(2Q22.1) MUTATED                0
  DEL PEAK  4(2Q22.1) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK  4(2Q22.1) MUTATED                                               3
  DEL PEAK  4(2Q22.1) WILD-TYPE                                           350
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK  4(2Q22.1) MUTATED                                                                        7
  DEL PEAK  4(2Q22.1) WILD-TYPE                                                                     91
                               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                                                                  35
D68V8, 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                                                                                     9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    350
  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"
D68V9, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED     0  10
  DEL PEAK  4(2Q22.1) WILD-TYPE  14 471
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      0   10
  DEL PEAK  4(2Q22.1) WILD-TYPE   14  471
     clus
vv    DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  NO                            0                            14
  YES                          10                           471
[1] 2 2
[1] FALSE
D68V10, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED     9   0
  DEL PEAK  4(2Q22.1) WILD-TYPE 408  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      9    0
  DEL PEAK  4(2Q22.1) WILD-TYPE  408   17
     clus
vv    DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  NO                            9                           408
  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          130                      16  318
                               vv
clus                            VERY ADVANCED (T4B)
  DEL PEAK  4(2Q22.1) MUTATED                     0
  DEL PEAK  4(2Q22.1) WILD-TYPE                   1
D68V11, 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)                                      130
  MODERATE/ADVANCED (T4A)                            16
  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  4(2Q22.1) MUTATED     9   0   0   1
  DEL PEAK  4(2Q22.1) WILD-TYPE 369  51   4  29
D68V12, multiclass
    clus
vv   DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  R0                           9                           369
  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"
D68V13, continuous
D68V14, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED     5   5
  DEL PEAK  4(2Q22.1) WILD-TYPE 219 256
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      5    5
  DEL PEAK  4(2Q22.1) WILD-TYPE  219  256
            clus
vv           DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  MULTIFOCAL                           5                           219
  UNIFOCAL                             5                           256
[1] 2 2
[1] FALSE
D68V15, 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    49
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q22.1) MUTATED                           0     4
  DEL PEAK  4(2Q22.1) WILD-TYPE                        26   317
D68V16, 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                                                       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"
D68V17, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED     0   4
  DEL PEAK  4(2Q22.1) WILD-TYPE  38 346
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      0    4
  DEL PEAK  4(2Q22.1) WILD-TYPE   38  346
                        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                           346
[1] 2 2
[1] FALSE

Clustering(69) Variable = DEL PEAK  5(2Q37.3) MUTATION ANALYSIS
D69V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(2Q37.3) MUTATED    12   1
  DEL PEAK  5(2Q37.3) WILD-TYPE 465  13
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           13                           478 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                            1                            13 
$`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         8.09         8.12         9.90        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        17.59         9.24        13.51        98.56 
TCGA-FY-A3I5 
        1.64 

$`DEL PEAK  5(2Q37.3) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A28R TCGA-BJ-A28S 
       17.69        23.34        20.71         4.83         4.87        21.04 
TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 
        2.79         5.10        11.31        17.52         1.22        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        15.48        23.31        18.64         5.75 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
        6.48         0.03         3.45         6.35         7.82         6.18 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
        5.06         8.98         4.93         5.98         0.53         0.10 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
        0.20         0.23        11.38        10.68         0.10         0.39 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.10        20.22        15.42        36.46         5.98        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-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
        4.27         3.22         2.76        17.26        14.07       137.88 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
        3.39         8.71        25.35        13.41        11.90        14.60 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        7.99        11.01       100.01        18.51        13.12         7.99 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96         7.20         1.45         8.88         1.02         5.95 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS 
       10.09         7.99         5.33         8.48        10.45         1.51 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY 
        9.60        12.56         8.28         7.69         5.52         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q6 
        8.42         9.34         6.77         9.21         9.44         8.61 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.07        10.36        12.43        10.85        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        12.49        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        24.23        17.69        43.00        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       21.37        12.76        25.02        20.22        30.61        14.56 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20         9.83        21.27        20.48        11.93        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL 
       21.01        18.97         7.76         8.32        17.36        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       27.62        18.21        10.78        10.98        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       17.82         3.12        15.81        24.33        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 
       30.31        14.04         1.15        22.29        19.59        13.61 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 
       14.27        13.81        14.07        14.27         3.02        14.43 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
       14.70        14.10        14.96         7.69        20.68        13.78 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
       13.58        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 
       80.91         4.18        58.82         1.45        74.30        45.40 
TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR 
       33.47       108.36        39.32         1.41        30.18       102.84 
TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY 
       65.39       124.04        50.37        37.25       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        38.66        52.73       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 
      131.15       108.66        57.63        17.52        52.50        12.16 
TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
      147.42       130.72       129.57        32.48       116.91        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       41.29        95.38         5.72        66.90        82.82        77.36 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       78.97        31.50        50.33        53.06        47.38        52.50 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       45.53        48.16         7.07        44.65        45.80        19.30 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        37.94        31.04        19.59        30.51        33.60 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       28.73        41.13        37.78        29.95        13.32        11.87 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
        8.71        26.86        18.18        20.91        12.36        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J 
       19.79        19.46        54.21        57.01        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        11.74        11.15        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CP TCGA-EM-A2CQ 
       16.44        17.88        13.18        23.51         2.99        12.30 
TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        10.49        13.15        22.16        13.84        19.73 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       12.07        17.59        17.46        17.29        14.60        17.46 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       18.97        15.68        14.14        19.63        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       16.44        16.77        27.95        23.77        16.80        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 
       11.15         7.33        12.53        13.91         7.82        11.51 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       16.41        15.62        12.79        70.65        16.90         9.01 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        4.83         8.61         8.38         9.80         5.03        37.87 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       12.72         0.95        47.47        48.20        29.69        32.35 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       14.79        12.33        14.79        27.09        18.38        29.49 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       54.05        22.09        12.26        16.08        29.19        19.76 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        58.22        13.74        71.01        80.02        65.36 
TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24         5.85         4.18         2.43         5.56        24.72 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       38.30        42.25         2.37         4.50        80.81        69.24 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       59.87        43.50         0.30        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        4.01         1.94        73.74        59.70        31.59        44.25 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       102.90        66.77        81.34        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 
       46.06         4.08         0.89        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON 
       91.17         1.25         1.15        17.82         0.99         1.51 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        0.76         0.03         4.67        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         6.87         4.14         6.58         4.54 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
        0.89         1.35         1.15         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        10.26        16.90         9.80         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        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        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       12.43         6.74        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         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                         1.64                          0.03 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                        98.56                        158.83 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                       10.650                        16.685 
[1] "1.6 - 98.6 (10.7)"  "0.0 - 158.8 (16.7)"
[1] "hr=" "3.2"
D69V2, 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     276       45       107        2        44
                               vv
clus                            STAGE IVC
  DEL PEAK  5(2Q37.3) MUTATED           0
  DEL PEAK  5(2Q37.3) WILD-TYPE         6
D69V3, multiclass
           clus
vv          DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  STAGE I                             4                           276
  STAGE II                            6                            45
  STAGE III                           2                           107
  STAGE IV                            0                             2
  STAGE IVA                           1                            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  5(2Q37.3) MUTATED     2   7   4   0
  DEL PEAK  5(2Q37.3) WILD-TYPE 138 159 161  21
D69V4, multiclass
    clus
vv   DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  T1                           2                           138
  T2                           7                           159
  T3                           4                           161
  T4                           0                            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"
D69V5, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.3) MUTATED     8   1
  DEL PEAK  5(2Q37.3) WILD-TYPE 215 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED      8    1
  DEL PEAK  5(2Q37.3) WILD-TYPE  215  221
   clus
vv  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  0                           8                           215
  1                           1                           221
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  DEL PEAK  5(2Q37.3) MUTATED     3   0  10
  DEL PEAK  5(2Q37.3) WILD-TYPE 270   9 202
D69V6, multiclass
    clus
vv   DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  M0                           3                           270
  M1                           0                             9
  MX                          10                           202
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.3) MUTATED     8   5
  DEL PEAK  5(2Q37.3) WILD-TYPE 356 126
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED      8    5
  DEL PEAK  5(2Q37.3) WILD-TYPE  356  126
        clus
vv       DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  FEMALE                           8                           356
  MALE                             5                           126
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  DEL PEAK  5(2Q37.3) MUTATED                0
  DEL PEAK  5(2Q37.3) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK  5(2Q37.3) MUTATED                                               6
  DEL PEAK  5(2Q37.3) WILD-TYPE                                           347
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK  5(2Q37.3) MUTATED                                                                        7
  DEL PEAK  5(2Q37.3) WILD-TYPE                                                                     91
                               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                                                                  35
D69V8, 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                                                                                     9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    347
  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"
D69V9, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.3) MUTATED     0  13
  DEL PEAK  5(2Q37.3) WILD-TYPE  14 468
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED      0   13
  DEL PEAK  5(2Q37.3) WILD-TYPE   14  468
     clus
vv    DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  NO                            0                            14
  YES                          13                           468
[1] 2 2
[1] FALSE
D69V10, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.3) MUTATED    11   1
  DEL PEAK  5(2Q37.3) WILD-TYPE 406  16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED     11    1
  DEL PEAK  5(2Q37.3) WILD-TYPE  406   16
     clus
vv    DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  NO                           11                           406
  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          129                      16  316
                               vv
clus                            VERY ADVANCED (T4B)
  DEL PEAK  5(2Q37.3) MUTATED                     0
  DEL PEAK  5(2Q37.3) WILD-TYPE                   1
D69V11, 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)                                      129
  MODERATE/ADVANCED (T4A)                            16
  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
  DEL PEAK  5(2Q37.3) MUTATED    11   0   0   2
  DEL PEAK  5(2Q37.3) WILD-TYPE 367  51   4  28
D69V12, multiclass
    clus
vv   DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  R0                          11                           367
  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"
D69V13, continuous
D69V14, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.3) MUTATED     5   8
  DEL PEAK  5(2Q37.3) WILD-TYPE 219 253
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED      5    8
  DEL PEAK  5(2Q37.3) WILD-TYPE  219  253
            clus
vv           DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  MULTIFOCAL                           5                           219
  UNIFOCAL                             8                           253
[1] 2 2
[1] FALSE
D69V15, 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    49
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(2Q37.3) MUTATED                           0     7
  DEL PEAK  5(2Q37.3) WILD-TYPE                        26   314
D69V16, 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                                                       49
  BLACK OR AFRICAN AMERICAN                                   26
  WHITE                                                      314
[1] 4 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  5(2Q37.3) MUTATED     0   6
  DEL PEAK  5(2Q37.3) WILD-TYPE  38 344
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED      0    6
  DEL PEAK  5(2Q37.3) WILD-TYPE   38  344
                        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                           344
[1] 2 2
[1] FALSE

Clustering(70) Variable = DEL PEAK  7(4Q34.3) MUTATION ANALYSIS
D70V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(4Q34.3) MUTATED     5   0
  DEL PEAK  7(4Q34.3) WILD-TYPE 472  14
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                            5                           486 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                            0                            14 
$`DEL PEAK  7(4Q34.3) MUTATED`
TCGA-BJ-A190 TCGA-E8-A414 TCGA-EM-A1YE TCGA-ET-A39N TCGA-FE-A22Z 
       20.58        14.27        54.08        98.56        73.74 

$`DEL PEAK  7(4Q34.3) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
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        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       22.29        19.59        13.61        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        12.36        18.05        19.79        19.46        54.21 
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        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       10.49        13.15        22.16        13.84        19.73        17.59 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       12.07        17.59        17.46        17.29        14.60        17.46 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       18.97        15.68        14.14        19.63        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       16.44        16.77        27.95        23.77        16.80        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 
       11.15         7.33        12.53         9.24        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        16.41        15.62        13.51        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       80.02        65.36        84.89        61.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        59.15        28.24         5.85         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A230 TCGA-FE-A231 
        5.03         2.14         4.01         1.94        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       102.90        66.77        81.34 
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        46.06         4.08         0.89        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 
       48.10        91.17         1.25         1.15        17.82         1.64 
TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
        0.99         1.51         0.76         0.03         4.67        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         6.87         4.14 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58         4.54         0.89         1.35         1.15         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        10.26        16.90         9.80 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
        9.63         2.96         8.65        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 
       86.70         6.02        12.43         6.74        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 
        0.72        16.64        32.45         8.71        10.98         5.19 

  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                        14.27                          0.03 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                        98.56                        158.83 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                       54.080                        16.505 
[1] "14.3 - 98.6 (54.1)" "0.0 - 158.8 (16.5)"
[1] "hr="     "2.5e+07"
D70V2, 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     279       49       108        2        44
                               vv
clus                            STAGE IVC
  DEL PEAK  7(4Q34.3) MUTATED           0
  DEL PEAK  7(4Q34.3) WILD-TYPE         6
D70V3, multiclass
           clus
vv          DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  STAGE I                             1                           279
  STAGE II                            2                            49
  STAGE III                           1                           108
  STAGE IV                            0                             2
  STAGE IVA                           1                            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  7(4Q34.3) MUTATED     0   2   2   1
  DEL PEAK  7(4Q34.3) WILD-TYPE 140 164 163  20
D70V4, multiclass
    clus
vv   DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  T1                           0                           140
  T2                           2                           164
  T3                           2                           163
  T4                           1                            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"
D70V5, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q34.3) MUTATED     3   1
  DEL PEAK  7(4Q34.3) WILD-TYPE 220 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED      3    1
  DEL PEAK  7(4Q34.3) WILD-TYPE  220  221
   clus
vv  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  0                           3                           220
  1                           1                           221
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  DEL PEAK  7(4Q34.3) MUTATED     1   0   4
  DEL PEAK  7(4Q34.3) WILD-TYPE 272   9 208
D70V6, multiclass
    clus
vv   DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  M0                           1                           272
  M1                           0                             9
  MX                           4                           208
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q34.3) MUTATED     4   1
  DEL PEAK  7(4Q34.3) WILD-TYPE 360 130
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED      4    1
  DEL PEAK  7(4Q34.3) WILD-TYPE  360  130
        clus
vv       DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  FEMALE                           4                           360
  MALE                             1                           130
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  DEL PEAK  7(4Q34.3) MUTATED                0
  DEL PEAK  7(4Q34.3) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK  7(4Q34.3) MUTATED                                               3
  DEL PEAK  7(4Q34.3) WILD-TYPE                                           350
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK  7(4Q34.3) MUTATED                                                                        2
  DEL PEAK  7(4Q34.3) WILD-TYPE                                                                     96
                               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                                                                  35
D70V8, 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                                                                                     9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    350
  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"
D70V9, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q34.3) MUTATED     1   4
  DEL PEAK  7(4Q34.3) WILD-TYPE  13 477
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED      1    4
  DEL PEAK  7(4Q34.3) WILD-TYPE   13  477
     clus
vv    DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  NO                            1                            13
  YES                           4                           477
[1] 2 2
[1] FALSE
D70V10, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q34.3) MUTATED     5   0
  DEL PEAK  7(4Q34.3) WILD-TYPE 412  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED      5    0
  DEL PEAK  7(4Q34.3) WILD-TYPE  412   17
     clus
vv    DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  NO                            5                           412
  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          130                      15  324
                               vv
clus                            VERY ADVANCED (T4B)
  DEL PEAK  7(4Q34.3) MUTATED                     0
  DEL PEAK  7(4Q34.3) WILD-TYPE                   1
D70V11, 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)                                      130
  MODERATE/ADVANCED (T4A)                            15
  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  7(4Q34.3) MUTATED     5   0   0   0
  DEL PEAK  7(4Q34.3) WILD-TYPE 373  51   4  30
D70V12, multiclass
    clus
vv   DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  R0                           5                           373
  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"
D70V13, continuous
D70V14, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q34.3) MUTATED     1   4
  DEL PEAK  7(4Q34.3) WILD-TYPE 223 257
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED      1    4
  DEL PEAK  7(4Q34.3) WILD-TYPE  223  257
            clus
vv           DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  MULTIFOCAL                           1                           223
  UNIFOCAL                             4                           257
[1] 2 2
[1] FALSE
D70V15, 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    48
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(4Q34.3) MUTATED                           0     3
  DEL PEAK  7(4Q34.3) WILD-TYPE                        26   318
D70V16, 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                                                       48
  BLACK OR AFRICAN AMERICAN                                   26
  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"
D70V17, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q34.3) MUTATED     0   4
  DEL PEAK  7(4Q34.3) WILD-TYPE  38 346
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED      0    4
  DEL PEAK  7(4Q34.3) WILD-TYPE   38  346
                        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                           346
[1] 2 2
[1] FALSE

Clustering(71) Variable = DEL PEAK  8(5P15.2) MUTATION ANALYSIS
D71V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(5P15.2) MUTATED     4   0
  DEL PEAK  8(5P15.2) WILD-TYPE 473  14
  DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE 
                            4                           487 
  DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE 
                            0                            14 
$`DEL PEAK  8(5P15.2) MUTATED`
TCGA-BJ-A4O9 TCGA-DE-A4MB TCGA-DJ-A3V2 TCGA-L6-A4EU 
        5.98        11.57        20.22         0.72 

$`DEL PEAK  8(5P15.2) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-CE-A13K 
        7.82         6.18         5.06         8.98         4.93         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MC TCGA-DE-A4MD 
       15.85        18.54        18.84        30.12        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
        4.27         3.22         2.76        17.26        14.07       137.88 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
        3.39         8.71        25.35        13.41        11.90        14.60 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        7.99        11.01       100.01        18.51        13.12         7.99 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96         7.20         1.45         8.88         1.02         5.95 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS 
       10.09         7.99         5.33         8.48        10.45         1.51 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY 
        9.60        12.56         8.28         7.69         5.52         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.42         8.12         9.34         6.77         9.21         9.44 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
        9.90         8.61        10.09         7.07        10.36        12.43 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        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        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V3 
       43.00        11.34        21.37        12.76        25.02        30.61 
TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       14.56        19.20         9.83        21.27        20.48        11.93 
TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ 
       22.92        21.01        18.97         7.76         8.32        17.36 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       17.23        27.62        18.21        10.78        10.98        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        30.31        14.04         1.15        22.29        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       14.43        14.70        14.10        14.96         7.69        20.68 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       13.78        13.58        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        80.91         4.18        58.82         1.45        74.30 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       45.40        33.47       108.36        39.32         1.41        30.18 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
      102.84        65.39       124.04        50.37        37.25       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        38.66 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       52.73       139.00       131.15       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        12.16       147.42       130.72       129.57        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      116.91        98.24        41.29        95.38         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN 
       82.82        77.36        78.97        31.50        50.33        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        52.50        45.53        48.16         7.07        44.65 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       45.80        19.30        45.96        37.94        31.04        19.59 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        33.60        28.73        41.13        37.78        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       13.32        11.87         8.71        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
       12.36        18.05        19.79        19.46        54.21        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        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       10.49        13.15        22.16        13.84        19.73        17.59 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       12.07        17.59        17.46        17.29        14.60        17.46 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       18.97        15.68        14.14        19.63        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       16.44        16.77        27.95        23.77        16.80        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 
       11.15         7.33        12.53         9.24        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        16.41        15.62        13.51        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
       80.02        65.36        84.89        98.56        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        2.43         5.56        24.72        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       59.70        31.59        44.25        24.69        68.22       102.90 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77        81.34        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        46.06         4.08         0.89 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10        91.17         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       17.82         1.64         0.99         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
        4.67        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 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
        1.15         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        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90         9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74 
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        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE 
                         0.72                          0.03 
  DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE 
                        20.22                        158.83 
  DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE 
                        8.775                        16.640 
[1] "0.7 - 20.2 (8.8)"   "0.0 - 158.8 (16.6)"
[1] "hr="    "450000"
D71V2, 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     279       50       108        2        44
                               vv
clus                            STAGE IVC
  DEL PEAK  8(5P15.2) MUTATED           0
  DEL PEAK  8(5P15.2) WILD-TYPE         6
D71V3, multiclass
           clus
vv          DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE
  STAGE I                             1                           279
  STAGE II                            1                            50
  STAGE III                           1                           108
  STAGE IV                            0                             2
  STAGE IVA                           1                            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  8(5P15.2) MUTATED     0   2   2   0
  DEL PEAK  8(5P15.2) WILD-TYPE 140 164 163  21
D71V4, multiclass
    clus
vv   DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE
  T1                           0                           140
  T2                           2                           164
  T3                           2                           163
  T4                           0                            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"
D71V5, binary
                               cls
clus                              0   1
  DEL PEAK  8(5P15.2) MUTATED     1   3
  DEL PEAK  8(5P15.2) WILD-TYPE 222 219
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5P15.2) MUTATED      1    3
  DEL PEAK  8(5P15.2) WILD-TYPE  222  219
   clus
vv  DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE
  0                           1                           222
  1                           3                           219
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  DEL PEAK  8(5P15.2) MUTATED     4   0   0
  DEL PEAK  8(5P15.2) WILD-TYPE 269   9 212
D71V6, multiclass
    clus
vv   DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE
  M0                           4                           269
  M1                           0                             9
  MX                           0                           212
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(5P15.2) MUTATED     4   0
  DEL PEAK  8(5P15.2) WILD-TYPE 360 131
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5P15.2) MUTATED      4    0
  DEL PEAK  8(5P15.2) WILD-TYPE  360  131
        clus
vv       DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE
  FEMALE                           4                           360
  MALE                             0                           131
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  DEL PEAK  8(5P15.2) MUTATED                1
  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                                           351
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK  8(5P15.2) MUTATED                                                                        0
  DEL PEAK  8(5P15.2) WILD-TYPE                                                                     98
                               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                                                                  34
D71V8, multiclass
                                                                        clus
vv                                                                       DEL PEAK  8(5P15.2) 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)                              1
                                                                        clus
vv                                                                       DEL PEAK  8(5P15.2) WILD-TYPE
  OTHER  SPECIFY                                                                                     8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    351
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            98
  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"
D71V9, binary
                               cls
clus                              0   1
  DEL PEAK  8(5P15.2) MUTATED     0   4
  DEL PEAK  8(5P15.2) WILD-TYPE  14 477
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5P15.2) MUTATED      0    4
  DEL PEAK  8(5P15.2) WILD-TYPE   14  477
     clus
vv    DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE
  NO                            0                            14
  YES                           4                           477
[1] 2 2
[1] FALSE
D71V10, binary
                               cls
clus                              0   1
  DEL PEAK  8(5P15.2) MUTATED     3   0
  DEL PEAK  8(5P15.2) WILD-TYPE 414  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5P15.2) MUTATED      3    0
  DEL PEAK  8(5P15.2) WILD-TYPE  414   17
     clus
vv    DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE
  NO                            3                           414
  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          128                      16  326
                               vv
clus                            VERY ADVANCED (T4B)
  DEL PEAK  8(5P15.2) MUTATED                     0
  DEL PEAK  8(5P15.2) WILD-TYPE                   1
D71V11, 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)                                      128
  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  8(5P15.2) MUTATED     1   2   0   0
  DEL PEAK  8(5P15.2) WILD-TYPE 377  49   4  30
D71V12, multiclass
    clus
vv   DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE
  R0                           1                           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"
D71V13, continuous
D71V14, binary
                               cls
clus                              0   1
  DEL PEAK  8(5P15.2) MUTATED     3   1
  DEL PEAK  8(5P15.2) WILD-TYPE 221 260
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5P15.2) MUTATED      3    1
  DEL PEAK  8(5P15.2) WILD-TYPE  221  260
            clus
vv           DEL PEAK  8(5P15.2) MUTATED DEL PEAK  8(5P15.2) WILD-TYPE
  MULTIFOCAL                           3                           221
  UNIFOCAL                             1                           260
[1] 2 2
[1] FALSE
D71V15, 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    49
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(5P15.2) MUTATED                           1     3
  DEL PEAK  8(5P15.2) WILD-TYPE                        25   318
D71V16, 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                                                       49
  BLACK OR AFRICAN AMERICAN                                   25
  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"
D71V17, binary
                               cls
clus                              0   1
  DEL PEAK  8(5P15.2) MUTATED     1   3
  DEL PEAK  8(5P15.2) WILD-TYPE  37 347
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5P15.2) MUTATED      1    3
  DEL PEAK  8(5P15.2) WILD-TYPE   37  347
                        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                           347
[1] 2 2
[1] FALSE

Clustering(72) Variable = DEL PEAK 11(6Q22.31) MUTATION ANALYSIS
D72V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 11(6Q22.31) MUTATED     4   2
  DEL PEAK 11(6Q22.31) WILD-TYPE 473  12
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                             6                            485 
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                             2                             12 
$`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        98.56        42.25        33.63         1.64 

$`DEL PEAK 11(6Q22.31) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        5.52         8.78         8.42         8.12         9.34         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
        9.21         9.44         9.90         8.61        10.09         7.07 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       10.36        12.43        10.85        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        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 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 
       14.07        14.27         3.02        14.43        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        13.78        13.58        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        80.91         4.18 
TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 
       58.82         1.45        74.30        45.40        33.47       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
       39.32         1.41        30.18       102.84        65.39       124.04 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        37.25       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        38.66        52.73       139.00       131.15       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        12.16       147.42       130.72 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       116.91        98.24        41.29        95.38 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       50.33        53.06        47.38        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       37.78        29.95        13.32        11.87         8.71        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        12.36        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       54.21        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        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        10.49        13.15        22.16        13.84        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       17.59        12.07        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 
       17.46        18.97        15.68        14.14        19.63        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        16.44        16.77        27.95        23.77        16.80 
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        11.15         7.33        12.53         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        16.41        15.62        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        9.80         5.03        37.87        12.72         0.95        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       27.09        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       16.08        29.19        19.76         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
       71.01        80.02        65.36        84.89        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX 
        2.43         5.56        24.72        38.30         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        24.69        68.22       102.90        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB TCGA-FE-A3PC 
       81.34        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        46.06         4.08         0.89        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM 
       48.10        91.17         1.25         1.15        17.82         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
        1.51         0.76         0.03         4.67        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         6.87         4.14         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
        4.54         0.89         1.35         1.15         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        10.26        16.90         9.80         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        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        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        12.43         6.74        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         0.72 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       16.64        32.45         8.71        10.98         5.19 

  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                          1.64                           0.03 
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                         98.56                         158.83 
  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE 
                         37.94                          16.44 
[1] "1.6 - 98.6 (37.9)"  "0.0 - 158.8 (16.4)"
[1] "hr=" "6.4"
D72V2, 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     278       49       106        2        45
                                vv
clus                             STAGE IVC
  DEL PEAK 11(6Q22.31) MUTATED           0
  DEL PEAK 11(6Q22.31) WILD-TYPE         6
D72V3, multiclass
           clus
vv          DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  STAGE I                              2                            278
  STAGE II                             2                             49
  STAGE III                            3                            106
  STAGE IV                             0                              2
  STAGE IVA                            0                             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 11(6Q22.31) MUTATED     1   3   3   0
  DEL PEAK 11(6Q22.31) WILD-TYPE 139 163 162  21
D72V4, multiclass
    clus
vv   DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  T1                            1                            139
  T2                            3                            163
  T3                            3                            162
  T4                            0                             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"
D72V5, binary
                                cls
clus                               0   1
  DEL PEAK 11(6Q22.31) MUTATED     4   1
  DEL PEAK 11(6Q22.31) WILD-TYPE 219 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(6Q22.31) MUTATED      4    1
  DEL PEAK 11(6Q22.31) WILD-TYPE  219  221
   clus
vv  DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  0                            4                            219
  1                            1                            221
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 11(6Q22.31) MUTATED     0   0   7
  DEL PEAK 11(6Q22.31) WILD-TYPE 273   9 205
D72V6, multiclass
    clus
vv   DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  M0                            0                            273
  M1                            0                              9
  MX                            7                            205
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V7, binary
                                cls
clus                               0   1
  DEL PEAK 11(6Q22.31) MUTATED     4   3
  DEL PEAK 11(6Q22.31) WILD-TYPE 360 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(6Q22.31) MUTATED      4    3
  DEL PEAK 11(6Q22.31) WILD-TYPE  360  128
        clus
vv       DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  FEMALE                            4                            360
  MALE                              3                            128
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 11(6Q22.31) MUTATED                0
  DEL PEAK 11(6Q22.31) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 11(6Q22.31) MUTATED                                               5
  DEL PEAK 11(6Q22.31) WILD-TYPE                                           348
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 11(6Q22.31) MUTATED                                                                        2
  DEL PEAK 11(6Q22.31) WILD-TYPE                                                                     96
                                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                                                                  35
D72V8, 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                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     348
  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"
D72V9, binary
                                cls
clus                               0   1
  DEL PEAK 11(6Q22.31) MUTATED     1   6
  DEL PEAK 11(6Q22.31) WILD-TYPE  13 475
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(6Q22.31) MUTATED      1    6
  DEL PEAK 11(6Q22.31) WILD-TYPE   13  475
     clus
vv    DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  NO                             1                             13
  YES                            6                            475
[1] 2 2
[1] FALSE
D72V10, binary
                                cls
clus                               0   1
  DEL PEAK 11(6Q22.31) MUTATED     5   1
  DEL PEAK 11(6Q22.31) WILD-TYPE 412  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(6Q22.31) MUTATED      5    1
  DEL PEAK 11(6Q22.31) WILD-TYPE  412   16
     clus
vv    DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  NO                             5                            412
  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          130                      16  321
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 11(6Q22.31) MUTATED                     0
  DEL PEAK 11(6Q22.31) WILD-TYPE                   1
D72V11, 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)                                       130
  MODERATE/ADVANCED (T4A)                             16
  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 11(6Q22.31) MUTATED     6   1   0   0
  DEL PEAK 11(6Q22.31) WILD-TYPE 372  50   4  30
D72V12, multiclass
    clus
vv   DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  R0                            6                            372
  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"
D72V13, continuous
D72V14, binary
                                cls
clus                               0   1
  DEL PEAK 11(6Q22.31) MUTATED     2   5
  DEL PEAK 11(6Q22.31) WILD-TYPE 222 256
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(6Q22.31) MUTATED      2    5
  DEL PEAK 11(6Q22.31) WILD-TYPE  222  256
            clus
vv           DEL PEAK 11(6Q22.31) MUTATED DEL PEAK 11(6Q22.31) WILD-TYPE
  MULTIFOCAL                            2                            222
  UNIFOCAL                              5                            256
[1] 2 2
[1] FALSE
D72V15, 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    49
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(6Q22.31) MUTATED                           0     6
  DEL PEAK 11(6Q22.31) WILD-TYPE                        26   315
D72V16, 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                                                        49
  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"
D72V17, binary
                                cls
clus                               0   1
  DEL PEAK 11(6Q22.31) MUTATED     0   6
  DEL PEAK 11(6Q22.31) WILD-TYPE  38 344
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(6Q22.31) MUTATED      0    6
  DEL PEAK 11(6Q22.31) WILD-TYPE   38  344
                        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                            344
[1] 2 2
[1] FALSE

Clustering(73) Variable = DEL PEAK 13(7Q34) MUTATION ANALYSIS
D73V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 13(7Q34) MUTATED     4   0
  DEL PEAK 13(7Q34) WILD-TYPE 473  14
  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE 
                          4                         487 
  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE 
                          0                          14 
$`DEL PEAK 13(7Q34) MUTATED`
TCGA-DJ-A2Q8 TCGA-DJ-A3VM TCGA-ET-A2MX TCGA-FY-A40N 
        7.07        27.62        54.05         0.89 

$`DEL PEAK 13(7Q34) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        5.52         8.78         8.42         8.12         9.34         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q9 
        9.21         9.44         9.90         8.61        10.09        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
        8.32        17.36        17.23        18.21        10.78        10.98 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04         1.15        22.29 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        12.36        18.05        19.79        19.46        54.21 
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        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        10.49        13.15        22.16        13.84        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       17.59        12.07        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 
       17.46        18.97        15.68        14.14        19.63        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        16.44        16.77        27.95        23.77        16.80 
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        11.15         7.33        12.53         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ 
        7.82        11.51        16.41        15.62        13.51        12.79 
TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO 
       70.65        16.90         9.01         4.83         8.61         8.38 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        9.80         5.03        37.87        12.72         0.95        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N 
       48.20        29.69        32.35        14.79        12.33        14.79 
TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       27.09        18.38        29.49        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
       80.02        65.36        84.89        98.56        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        2.43         5.56        24.72        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z 
        4.80         5.03         2.14         4.01         1.94        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       59.70        31.59        44.25        24.69        68.22       102.90 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77        81.34        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        46.06         4.08         0.89 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10        91.17         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
       17.82         1.64         0.99         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
        4.67        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 
        6.87         4.14         6.58         4.54         1.35         1.15 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74        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         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE 
                       0.89                        0.03 
  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE 
                      54.05                      158.83 
  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE 
                     17.345                      16.570 
[1] "0.9 - 54.0 (17.3)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "3300000"
D73V2, 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     277       50       109        2        45
                             vv
clus                          STAGE IVC
  DEL PEAK 13(7Q34) MUTATED           0
  DEL PEAK 13(7Q34) WILD-TYPE         6
D73V3, multiclass
           clus
vv          DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  STAGE I                           3                         277
  STAGE II                          1                          50
  STAGE III                         0                         109
  STAGE IV                          0                           2
  STAGE IVA                         0                          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 13(7Q34) MUTATED     2   2   0   0
  DEL PEAK 13(7Q34) WILD-TYPE 138 164 165  21
D73V4, multiclass
    clus
vv   DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  T1                         2                         138
  T2                         2                         164
  T3                         0                         165
  T4                         0                          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"
D73V5, binary
                             cls
clus                            0   1
  DEL PEAK 13(7Q34) MUTATED     3   1
  DEL PEAK 13(7Q34) WILD-TYPE 220 221
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED      3    1
  DEL PEAK 13(7Q34) WILD-TYPE  220  221
   clus
vv  DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  0                         3                         220
  1                         1                         221
[1] 2 2
[1] FALSE
                             vv
clus                           M0  M1  MX
  DEL PEAK 13(7Q34) MUTATED     2   0   2
  DEL PEAK 13(7Q34) WILD-TYPE 271   9 210
D73V6, multiclass
    clus
vv   DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  M0                         2                         271
  M1                         0                           9
  MX                         2                         210
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V7, binary
                             cls
clus                            0   1
  DEL PEAK 13(7Q34) MUTATED     3   1
  DEL PEAK 13(7Q34) WILD-TYPE 361 130
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED      3    1
  DEL PEAK 13(7Q34) WILD-TYPE  361  130
        clus
vv       DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  FEMALE                         3                         361
  MALE                           1                         130
[1] 2 2
[1] FALSE
                             vv
clus                          OTHER  SPECIFY
  DEL PEAK 13(7Q34) MUTATED                0
  DEL PEAK 13(7Q34) WILD-TYPE              9
                             vv
clus                          THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 13(7Q34) MUTATED                                               1
  DEL PEAK 13(7Q34) WILD-TYPE                                           352
                             vv
clus                          THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 13(7Q34) MUTATED                                                                        2
  DEL PEAK 13(7Q34) WILD-TYPE                                                                     96
                             vv
clus                          THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 13(7Q34) MUTATED                                                                     1
  DEL PEAK 13(7Q34) WILD-TYPE                                                                  34
D73V8, 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                                                                                   9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                          96
  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"
D73V9, binary
                             cls
clus                            0   1
  DEL PEAK 13(7Q34) MUTATED     0   4
  DEL PEAK 13(7Q34) WILD-TYPE  14 477
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED      0    4
  DEL PEAK 13(7Q34) WILD-TYPE   14  477
     clus
vv    DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  NO                          0                          14
  YES                         4                         477
[1] 2 2
[1] FALSE
D73V10, binary
                             cls
clus                            0   1
  DEL PEAK 13(7Q34) MUTATED     3   0
  DEL PEAK 13(7Q34) WILD-TYPE 414  17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED      3    0
  DEL PEAK 13(7Q34) WILD-TYPE  414   17
     clus
vv    DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  NO                          3                         414
  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          130                      16  324
                             vv
clus                          VERY ADVANCED (T4B)
  DEL PEAK 13(7Q34) MUTATED                     0
  DEL PEAK 13(7Q34) WILD-TYPE                   1
D73V11, multiclass
                         clus
vv                        DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  MINIMAL (T3)                                    0                         130
  MODERATE/ADVANCED (T4A)                         0                          16
  NONE                                            4                         324
  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 374  51   4  30
D73V12, multiclass
    clus
vv   DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  R0                         4                         374
  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 13(7Q34) MUTATED     1   3
  DEL PEAK 13(7Q34) WILD-TYPE 223 258
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED      1    3
  DEL PEAK 13(7Q34) WILD-TYPE  223  258
            clus
vv           DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  MULTIFOCAL                         1                         223
  UNIFOCAL                           3                         258
[1] 2 2
[1] FALSE
D73V15, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(7Q34) MUTATED                                  0     0
  DEL PEAK 13(7Q34) WILD-TYPE                                1    49
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(7Q34) MUTATED                           0     3
  DEL PEAK 13(7Q34) WILD-TYPE                        26   318
D73V16, 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                                                     49
  BLACK OR AFRICAN AMERICAN                                 26
  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"
D73V17, binary
                             cls
clus                            0   1
  DEL PEAK 13(7Q34) MUTATED     0   4
  DEL PEAK 13(7Q34) WILD-TYPE  38 346
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(7Q34) MUTATED      0    4
  DEL PEAK 13(7Q34) WILD-TYPE   38  346
                        clus
vv                       DEL PEAK 13(7Q34) MUTATED DEL PEAK 13(7Q34) WILD-TYPE
  HISPANIC OR LATINO                             0                          38
  NOT HISPANIC OR LATINO                         4                         346
[1] 2 2
[1] FALSE

Clustering(74) Variable = DEL PEAK 14(8P23.2) MUTATION ANALYSIS
D74V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(8P23.2) MUTATED     4   0
  DEL PEAK 14(8P23.2) WILD-TYPE 473  14
  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE 
                            4                           487 
  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE 
                            0                            14 
$`DEL PEAK 14(8P23.2) MUTATED`
TCGA-BJ-A190 TCGA-DJ-A2Q0 TCGA-EM-A3O9 TCGA-EM-A3SY 
       20.58         8.12         9.24        13.51 

$`DEL PEAK 14(8P23.2) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
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        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.78         8.42         9.34         6.77         9.21         9.44 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
        9.90         8.61        10.09         7.07        10.36        12.43 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        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        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04         1.15        22.29 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        12.36        18.05        19.79        19.46        54.21 
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        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        10.49        13.15        22.16        13.84        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       17.59        12.07        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 
       17.46        18.97        15.68        14.14        19.63        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        16.44        16.77        27.95        23.77        16.80 
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        11.15         7.33        12.53        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       11.51        16.41        15.62        12.79        70.65        16.90 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        9.01         4.83         8.61         8.38         9.80         5.03 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       37.87        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       29.49        54.05        22.09        12.26        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       65.36        84.89        98.56        61.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        59.15        28.24         5.85         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        24.69        68.22       102.90        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       81.34        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        46.06         4.08         0.89        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10        91.17         1.25         1.15        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        1.64         0.99         1.51         0.76         0.03         4.67 
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         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74        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         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE 
                         8.12                          0.03 
  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE 
                        20.58                        158.83 
  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE 
                       11.375                        16.640 
[1] "8.1 - 20.6 (11.4)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "1200000"
D74V2, 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     278       49       109        2        45
                               vv
clus                            STAGE IVC
  DEL PEAK 14(8P23.2) MUTATED           0
  DEL PEAK 14(8P23.2) WILD-TYPE         6
D74V3, multiclass
           clus
vv          DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
  STAGE I                             2                           278
  STAGE II                            2                            49
  STAGE III                           0                           109
  STAGE IV                            0                             2
  STAGE IVA                           0                            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 14(8P23.2) MUTATED     1   2   1   0
  DEL PEAK 14(8P23.2) WILD-TYPE 139 164 164  21
D74V4, multiclass
    clus
vv   DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
  T1                           1                           139
  T2                           2                           164
  T3                           1                           164
  T4                           0                            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"
D74V5, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.2) MUTATED     3   0
  DEL PEAK 14(8P23.2) WILD-TYPE 220 222
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.2) MUTATED      3    0
  DEL PEAK 14(8P23.2) WILD-TYPE  220  222
   clus
vv  DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
  0                           3                           220
  1                           0                           222
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  DEL PEAK 14(8P23.2) MUTATED     1   0   3
  DEL PEAK 14(8P23.2) WILD-TYPE 272   9 209
D74V6, multiclass
    clus
vv   DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
  M0                           1                           272
  M1                           0                             9
  MX                           3                           209
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.2) MUTATED     1   3
  DEL PEAK 14(8P23.2) WILD-TYPE 363 128
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.2) MUTATED      1    3
  DEL PEAK 14(8P23.2) WILD-TYPE  363  128
        clus
vv       DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
  FEMALE                           1                           363
  MALE                             3                           128
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  DEL PEAK 14(8P23.2) MUTATED                0
  DEL PEAK 14(8P23.2) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 14(8P23.2) MUTATED                                               2
  DEL PEAK 14(8P23.2) WILD-TYPE                                           351
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 14(8P23.2) MUTATED                                                                        2
  DEL PEAK 14(8P23.2) WILD-TYPE                                                                     96
                               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                                                                  35
D74V8, 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                                                                                     9
  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"
D74V9, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.2) MUTATED     0   4
  DEL PEAK 14(8P23.2) WILD-TYPE  14 477
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.2) MUTATED      0    4
  DEL PEAK 14(8P23.2) WILD-TYPE   14  477
     clus
vv    DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
  NO                            0                            14
  YES                           4                           477
[1] 2 2
[1] FALSE
D74V10, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.2) MUTATED     4   0
  DEL PEAK 14(8P23.2) WILD-TYPE 413  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.2) MUTATED      4    0
  DEL PEAK 14(8P23.2) WILD-TYPE  413   17
     clus
vv    DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
  NO                            4                           413
  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          130                      16  324
                               vv
clus                            VERY ADVANCED (T4B)
  DEL PEAK 14(8P23.2) MUTATED                     0
  DEL PEAK 14(8P23.2) WILD-TYPE                   1
D74V11, 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)                                      130
  MODERATE/ADVANCED (T4A)                            16
  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 14(8P23.2) MUTATED     4   0   0   0
  DEL PEAK 14(8P23.2) WILD-TYPE 374  51   4  30
D74V12, multiclass
    clus
vv   DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
  R0                           4                           374
  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 14(8P23.2) MUTATED     2   2
  DEL PEAK 14(8P23.2) WILD-TYPE 222 259
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.2) MUTATED      2    2
  DEL PEAK 14(8P23.2) WILD-TYPE  222  259
            clus
vv           DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
  MULTIFOCAL                           2                           222
  UNIFOCAL                             2                           259
[1] 2 2
[1] FALSE
D74V15, 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    49
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(8P23.2) MUTATED                           0     2
  DEL PEAK 14(8P23.2) WILD-TYPE                        26   319
D74V16, 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                           395 
                   TCGA-BJ-A0YZ                    TCGA-BJ-A0Z2 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A0Z3                    TCGA-BJ-A0Z5 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A0Z9                    TCGA-BJ-A0ZA 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A0ZB                    TCGA-BJ-A0ZC 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A0ZE                    TCGA-BJ-A0ZG 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A0ZH                    TCGA-BJ-A0ZJ 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A18Y                    TCGA-BJ-A18Z 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A191                    TCGA-BJ-A192 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A28R                    TCGA-BJ-A28S 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A28T                    TCGA-BJ-A28V 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A28W                    TCGA-BJ-A28X 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A28Z                    TCGA-BJ-A290 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A291                    TCGA-BJ-A2N7 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A2N8                    TCGA-BJ-A2N9 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A2NA                    TCGA-BJ-A2P4 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A3EZ                    TCGA-BJ-A3F0 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A3PR                    TCGA-BJ-A3PT 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A3PU                    TCGA-BJ-A45C 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A45D                    TCGA-BJ-A45E 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A45F                    TCGA-BJ-A45G 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A45H                    TCGA-BJ-A45I 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A45J                    TCGA-BJ-A45K 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-BJ-A4O8                    TCGA-BJ-A4O9 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-CE-A13K                    TCGA-CE-A27D 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-CE-A3MD                    TCGA-CE-A3ME 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-CE-A481                    TCGA-CE-A482 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-CE-A483                    TCGA-CE-A484 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-CE-A485                    TCGA-DE-A0XZ 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DE-A0Y2                    TCGA-DE-A0Y3 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DE-A2OL                    TCGA-DE-A3KN 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DE-A4M8                    TCGA-DE-A4M9 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DE-A4MA                    TCGA-DE-A4MB 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DE-A4MC                    TCGA-DE-A4MD 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DE-A69J                    TCGA-DE-A69K 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DE-A7U5                    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-A2PT                    TCGA-DJ-A2PU 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2PV                    TCGA-DJ-A2PW 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2PX                    TCGA-DJ-A2PY 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2PZ                    TCGA-DJ-A2Q1 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2Q2                    TCGA-DJ-A2Q3 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2Q4                    TCGA-DJ-A2Q5 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2Q6                    TCGA-DJ-A2Q7 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2Q9                    TCGA-DJ-A2QA 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A2QB                    TCGA-DJ-A3UK 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3UM                    TCGA-DJ-A3UN 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3UO                    TCGA-DJ-A3UQ 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3UR                    TCGA-DJ-A3US 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3UT                    TCGA-DJ-A3UU 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3UW                    TCGA-DJ-A3UX 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3UY                    TCGA-DJ-A3UZ 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3V2                    TCGA-DJ-A3V3 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3V4                    TCGA-DJ-A3V5 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3V7                    TCGA-DJ-A3V8 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3V9                    TCGA-DJ-A3VD 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3VE                    TCGA-DJ-A3VF 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3VG                    TCGA-DJ-A3VJ 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A3VL                    TCGA-DJ-A3VM 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-DJ-A4UL                    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-A2JQ                    TCGA-E8-A3X7 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-E8-A413                    TCGA-E8-A414 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-E8-A415                    TCGA-E8-A416 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-E8-A417                    TCGA-E8-A418 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-E8-A419                    TCGA-E8-A432 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-E8-A433                    TCGA-E8-A434 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-E8-A436                    TCGA-E8-A437 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-E8-A438                    TCGA-E8-A44K 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-E8-A44M                    TCGA-EL-A3CL 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3CM                    TCGA-EL-A3CN 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3CO                    TCGA-EL-A3CP 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3CR                    TCGA-EL-A3CS 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3CT                    TCGA-EL-A3CU 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3CV                    TCGA-EL-A3CW 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3CX                    TCGA-EL-A3CY 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3CZ                    TCGA-EL-A3D0 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3D1                    TCGA-EL-A3D4 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3D5                    TCGA-EL-A3D6 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3GO                    TCGA-EL-A3GP 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3GQ                    TCGA-EL-A3GR 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3GS                    TCGA-EL-A3GU 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3GV                    TCGA-EL-A3GW 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3GX                    TCGA-EL-A3GY 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3GZ                    TCGA-EL-A3H1 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3H2                    TCGA-EL-A3H3 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3H4                    TCGA-EL-A3H5 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3H7                    TCGA-EL-A3H8 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3MW                    TCGA-EL-A3MX 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3MY                    TCGA-EL-A3MZ 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3N2                    TCGA-EL-A3N3 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3T0                    TCGA-EL-A3T1 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3T2                    TCGA-EL-A3T3 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3T6                    TCGA-EL-A3T7 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3T8                    TCGA-EL-A3T9 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3TA                    TCGA-EL-A3TB 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3ZG                    TCGA-EL-A3ZH 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3ZK                    TCGA-EL-A3ZL 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3ZN                    TCGA-EL-A3ZO 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3ZP                    TCGA-EL-A3ZQ 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3ZR                    TCGA-EL-A3ZS 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A3ZT                    TCGA-EL-A4JV 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A4JW                    TCGA-EL-A4JX 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A4JZ                    TCGA-EL-A4K0 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A4K1                    TCGA-EL-A4K2 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A4K4                    TCGA-EL-A4K6 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A4K7                    TCGA-EL-A4K9 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A4KD                    TCGA-EL-A4KG 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-EL-A4KH                    TCGA-EL-A4KI 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A25G                    TCGA-ET-A25I 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A25J                    TCGA-ET-A25K 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A25L                    TCGA-ET-A25M 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A25N                    TCGA-ET-A25O 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A25P                    TCGA-ET-A25R 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A2MX                    TCGA-ET-A2MY 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A2MZ                    TCGA-ET-A2N0 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A2N1                    TCGA-ET-A2N3 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A2N4                    TCGA-ET-A2N5 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A39I                    TCGA-ET-A39J 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A39K                    TCGA-ET-A39M 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A39N                    TCGA-ET-A39O 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A39P                    TCGA-ET-A39R 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A39S                    TCGA-ET-A39T 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A3BN                    TCGA-ET-A3BO 
"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-A3DO                    TCGA-ET-A3DP 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A3DQ                    TCGA-ET-A3DR 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A3DS                    TCGA-ET-A3DT 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A3DU                    TCGA-ET-A3DV 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A3DW                    TCGA-ET-A40P 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A40Q                    TCGA-ET-A40R 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A40S                    TCGA-ET-A40T 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-ET-A4KN                    TCGA-ET-A4KQ 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FE-A22Z                    TCGA-FE-A230 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FE-A231                    TCGA-FE-A232 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FE-A233                    TCGA-FE-A234 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FE-A235                    TCGA-FE-A236 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FE-A237                    TCGA-FE-A238 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FE-A239                    TCGA-FE-A23A 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FE-A3PA                    TCGA-FE-A3PB 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FE-A3PC                    TCGA-FE-A3PD 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FK-A3S3                    TCGA-FK-A3SB 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FK-A3SD                    TCGA-FK-A3SE 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FK-A3SG                    TCGA-FK-A3SH 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FK-A4UB                    TCGA-FY-A2QD 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FY-A3BL                    TCGA-FY-A3I4 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FY-A3I5                    TCGA-FY-A3NM 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FY-A3ON                    TCGA-FY-A3R6 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FY-A3R7                    TCGA-FY-A3R8 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FY-A3R9                    TCGA-FY-A3RA 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FY-A3W9                    TCGA-FY-A3WA 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FY-A3YR                    TCGA-FY-A40K 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FY-A40L                    TCGA-FY-A40M 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FY-A40N                    TCGA-FY-A4B0 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FY-A4B3                    TCGA-FY-A4B4 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-FY-A76V                    TCGA-GE-A2C6 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-H2-A26U                    TCGA-H2-A2K9 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-H2-A3RH                    TCGA-H2-A3RI 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-H2-A421                    TCGA-H2-A422 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-IM-A3EB                    TCGA-IM-A3ED 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-IM-A3U2                    TCGA-IM-A3U3 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-IM-A41Y                    TCGA-IM-A41Z 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-IM-A420                    TCGA-IM-A4EB 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-J8-A3NZ                    TCGA-J8-A3O0 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-J8-A3O1                    TCGA-J8-A3O2 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-J8-A3YD                    TCGA-J8-A3YE 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-J8-A3YF                    TCGA-J8-A3YG 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-J8-A3YH                    TCGA-J8-A42S 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-J8-A4HW                    TCGA-J8-A4HY 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-KS-A41F                    TCGA-KS-A41I 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-KS-A41J                    TCGA-KS-A41L 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-KS-A4I1                    TCGA-KS-A4I3 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-KS-A4I5                    TCGA-KS-A4I7 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-KS-A4I9                    TCGA-KS-A4IB 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-KS-A4IC                    TCGA-KS-A4ID 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-L6-A4EP                    TCGA-L6-A4EQ 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-L6-A4ET                    TCGA-L6-A4EU 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-MK-A4N6                    TCGA-MK-A4N7 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-MK-A4N9                    TCGA-MK-A84Z 
"DEL PEAK 14(8P23.2) WILD-TYPE" "DEL PEAK 14(8P23.2) WILD-TYPE" 
                   TCGA-QD-A8IV 
"DEL PEAK 14(8P23.2) WILD-TYPE" 
D74V17, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.2) MUTATED     0   2
  DEL PEAK 14(8P23.2) WILD-TYPE  38 348
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.2) MUTATED      0    2
  DEL PEAK 14(8P23.2) WILD-TYPE   38  348
                        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                           348
[1] 2 2
[1] FALSE

Clustering(75) Variable = DEL PEAK 15(8P22) MUTATION ANALYSIS
D75V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 15(8P22) MUTATED     4   0
  DEL PEAK 15(8P22) WILD-TYPE 473  14
  DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE 
                          4                         487 
  DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE 
                          0                          14 
$`DEL PEAK 15(8P22) MUTATED`
TCGA-BJ-A190 TCGA-DJ-A2Q0 TCGA-EM-A3O9 TCGA-EM-A3SY 
       20.58         8.12         9.24        13.51 

$`DEL PEAK 15(8P22) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
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        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.78         8.42         9.34         6.77         9.21         9.44 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
        9.90         8.61        10.09         7.07        10.36        12.43 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        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        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04         1.15        22.29 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        12.36        18.05        19.79        19.46        54.21 
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        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        10.49        13.15        22.16        13.84        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       17.59        12.07        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 
       17.46        18.97        15.68        14.14        19.63        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        16.44        16.77        27.95        23.77        16.80 
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        11.15         7.33        12.53        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       11.51        16.41        15.62        12.79        70.65        16.90 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        9.01         4.83         8.61         8.38         9.80         5.03 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       37.87        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       29.49        54.05        22.09        12.26        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       65.36        84.89        98.56        61.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        59.15        28.24         5.85         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        24.69        68.22       102.90        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       81.34        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        46.06         4.08         0.89        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10        91.17         1.25         1.15        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        1.64         0.99         1.51         0.76         0.03         4.67 
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         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74        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         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE 
                       8.12                        0.03 
  DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE 
                      20.58                      158.83 
  DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE 
                     11.375                      16.640 
[1] "8.1 - 20.6 (11.4)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "1200000"
D75V2, 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     278       49       109        2        45
                             vv
clus                          STAGE IVC
  DEL PEAK 15(8P22) MUTATED           0
  DEL PEAK 15(8P22) WILD-TYPE         6
D75V3, multiclass
           clus
vv          DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE
  STAGE I                           2                         278
  STAGE II                          2                          49
  STAGE III                         0                         109
  STAGE IV                          0                           2
  STAGE IVA                         0                          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 15(8P22) MUTATED     1   2   1   0
  DEL PEAK 15(8P22) WILD-TYPE 139 164 164  21
D75V4, multiclass
    clus
vv   DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE
  T1                         1                         139
  T2                         2                         164
  T3                         1                         164
  T4                         0                          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"
D75V5, binary
                             cls
clus                            0   1
  DEL PEAK 15(8P22) MUTATED     3   0
  DEL PEAK 15(8P22) WILD-TYPE 220 222
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(8P22) MUTATED      3    0
  DEL PEAK 15(8P22) WILD-TYPE  220  222
   clus
vv  DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE
  0                         3                         220
  1                         0                         222
[1] 2 2
[1] FALSE
                             vv
clus                           M0  M1  MX
  DEL PEAK 15(8P22) MUTATED     1   0   3
  DEL PEAK 15(8P22) WILD-TYPE 272   9 209
D75V6, multiclass
    clus
vv   DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE
  M0                         1                         272
  M1                         0                           9
  MX                         3                         209
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V7, binary
                             cls
clus                            0   1
  DEL PEAK 15(8P22) MUTATED     1   3
  DEL PEAK 15(8P22) WILD-TYPE 363 128
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(8P22) MUTATED      1    3
  DEL PEAK 15(8P22) WILD-TYPE  363  128
        clus
vv       DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE
  FEMALE                         1                         363
  MALE                           3                         128
[1] 2 2
[1] FALSE
                             vv
clus                          OTHER  SPECIFY
  DEL PEAK 15(8P22) MUTATED                0
  DEL PEAK 15(8P22) WILD-TYPE              9
                             vv
clus                          THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 15(8P22) MUTATED                                               2
  DEL PEAK 15(8P22) WILD-TYPE                                           351
                             vv
clus                          THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 15(8P22) MUTATED                                                                        2
  DEL PEAK 15(8P22) WILD-TYPE                                                                     96
                             vv
clus                          THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 15(8P22) MUTATED                                                                     0
  DEL PEAK 15(8P22) WILD-TYPE                                                                  35
D75V8, 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                                                                                   9
  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"
D75V9, binary
                             cls
clus                            0   1
  DEL PEAK 15(8P22) MUTATED     0   4
  DEL PEAK 15(8P22) WILD-TYPE  14 477
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(8P22) MUTATED      0    4
  DEL PEAK 15(8P22) WILD-TYPE   14  477
     clus
vv    DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE
  NO                          0                          14
  YES                         4                         477
[1] 2 2
[1] FALSE
D75V10, binary
                             cls
clus                            0   1
  DEL PEAK 15(8P22) MUTATED     4   0
  DEL PEAK 15(8P22) WILD-TYPE 413  17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(8P22) MUTATED      4    0
  DEL PEAK 15(8P22) WILD-TYPE  413   17
     clus
vv    DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE
  NO                          4                         413
  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          130                      16  324
                             vv
clus                          VERY ADVANCED (T4B)
  DEL PEAK 15(8P22) MUTATED                     0
  DEL PEAK 15(8P22) WILD-TYPE                   1
D75V11, multiclass
                         clus
vv                        DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE
  MINIMAL (T3)                                    0                         130
  MODERATE/ADVANCED (T4A)                         0                          16
  NONE                                            4                         324
  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 374  51   4  30
D75V12, multiclass
    clus
vv   DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE
  R0                         4                         374
  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"
D75V13, continuous
D75V14, binary
                             cls
clus                            0   1
  DEL PEAK 15(8P22) MUTATED     2   2
  DEL PEAK 15(8P22) WILD-TYPE 222 259
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(8P22) MUTATED      2    2
  DEL PEAK 15(8P22) WILD-TYPE  222  259
            clus
vv           DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE
  MULTIFOCAL                         2                         222
  UNIFOCAL                           2                         259
[1] 2 2
[1] FALSE
D75V15, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(8P22) MUTATED                                  0     0
  DEL PEAK 15(8P22) WILD-TYPE                                1    49
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(8P22) MUTATED                           0     2
  DEL PEAK 15(8P22) WILD-TYPE                        26   319
D75V16, multiclass
[1] "Remove cluster labels:"    "DEL PEAK 15(8P22) MUTATED"
clus
  DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE 
                          2                         395 
                 TCGA-BJ-A0YZ                  TCGA-BJ-A0Z2 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A0Z3                  TCGA-BJ-A0Z5 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A0Z9                  TCGA-BJ-A0ZA 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A0ZB                  TCGA-BJ-A0ZC 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A0ZE                  TCGA-BJ-A0ZG 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A0ZH                  TCGA-BJ-A0ZJ 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A18Y                  TCGA-BJ-A18Z 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A191                  TCGA-BJ-A192 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A28R                  TCGA-BJ-A28S 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A28T                  TCGA-BJ-A28V 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A28W                  TCGA-BJ-A28X 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A28Z                  TCGA-BJ-A290 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A291                  TCGA-BJ-A2N7 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A2N8                  TCGA-BJ-A2N9 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A2NA                  TCGA-BJ-A2P4 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A3EZ                  TCGA-BJ-A3F0 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A3PR                  TCGA-BJ-A3PT 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A3PU                  TCGA-BJ-A45C 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A45D                  TCGA-BJ-A45E 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A45F                  TCGA-BJ-A45G 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A45H                  TCGA-BJ-A45I 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A45J                  TCGA-BJ-A45K 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-BJ-A4O8                  TCGA-BJ-A4O9 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-CE-A13K                  TCGA-CE-A27D 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-CE-A3MD                  TCGA-CE-A3ME 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-CE-A481                  TCGA-CE-A482 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-CE-A483                  TCGA-CE-A484 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-CE-A485                  TCGA-DE-A0XZ 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DE-A0Y2                  TCGA-DE-A0Y3 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DE-A2OL                  TCGA-DE-A3KN 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DE-A4M8                  TCGA-DE-A4M9 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DE-A4MA                  TCGA-DE-A4MB 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DE-A4MC                  TCGA-DE-A4MD 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DE-A69J                  TCGA-DE-A69K 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DE-A7U5                  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-A2PT                  TCGA-DJ-A2PU 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A2PV                  TCGA-DJ-A2PW 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A2PX                  TCGA-DJ-A2PY 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A2PZ                  TCGA-DJ-A2Q1 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A2Q2                  TCGA-DJ-A2Q3 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A2Q4                  TCGA-DJ-A2Q5 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A2Q6                  TCGA-DJ-A2Q7 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A2Q9                  TCGA-DJ-A2QA 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A2QB                  TCGA-DJ-A3UK 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A3UM                  TCGA-DJ-A3UN 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A3UO                  TCGA-DJ-A3UQ 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A3UR                  TCGA-DJ-A3US 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A3UT                  TCGA-DJ-A3UU 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A3UW                  TCGA-DJ-A3UX 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A3UY                  TCGA-DJ-A3UZ 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A3V2                  TCGA-DJ-A3V3 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A3V4                  TCGA-DJ-A3V5 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A3V7                  TCGA-DJ-A3V8 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A3V9                  TCGA-DJ-A3VD 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A3VE                  TCGA-DJ-A3VF 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A3VG                  TCGA-DJ-A3VJ 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A3VL                  TCGA-DJ-A3VM 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-DJ-A4UL                  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-A2JQ                  TCGA-E8-A3X7 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-E8-A413                  TCGA-E8-A414 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-E8-A415                  TCGA-E8-A416 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-E8-A417                  TCGA-E8-A418 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-E8-A419                  TCGA-E8-A432 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-E8-A433                  TCGA-E8-A434 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-E8-A436                  TCGA-E8-A437 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-E8-A438                  TCGA-E8-A44K 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-E8-A44M                  TCGA-EL-A3CL 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3CM                  TCGA-EL-A3CN 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3CO                  TCGA-EL-A3CP 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3CR                  TCGA-EL-A3CS 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3CT                  TCGA-EL-A3CU 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3CV                  TCGA-EL-A3CW 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3CX                  TCGA-EL-A3CY 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3CZ                  TCGA-EL-A3D0 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3D1                  TCGA-EL-A3D4 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3D5                  TCGA-EL-A3D6 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3GO                  TCGA-EL-A3GP 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3GQ                  TCGA-EL-A3GR 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3GS                  TCGA-EL-A3GU 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3GV                  TCGA-EL-A3GW 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3GX                  TCGA-EL-A3GY 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3GZ                  TCGA-EL-A3H1 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3H2                  TCGA-EL-A3H3 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3H4                  TCGA-EL-A3H5 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3H7                  TCGA-EL-A3H8 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3MW                  TCGA-EL-A3MX 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3MY                  TCGA-EL-A3MZ 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3N2                  TCGA-EL-A3N3 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3T0                  TCGA-EL-A3T1 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3T2                  TCGA-EL-A3T3 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3T6                  TCGA-EL-A3T7 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3T8                  TCGA-EL-A3T9 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3TA                  TCGA-EL-A3TB 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3ZG                  TCGA-EL-A3ZH 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3ZK                  TCGA-EL-A3ZL 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3ZN                  TCGA-EL-A3ZO 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3ZP                  TCGA-EL-A3ZQ 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3ZR                  TCGA-EL-A3ZS 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A3ZT                  TCGA-EL-A4JV 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A4JW                  TCGA-EL-A4JX 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A4JZ                  TCGA-EL-A4K0 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A4K1                  TCGA-EL-A4K2 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A4K4                  TCGA-EL-A4K6 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A4K7                  TCGA-EL-A4K9 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A4KD                  TCGA-EL-A4KG 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-EL-A4KH                  TCGA-EL-A4KI 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A25G                  TCGA-ET-A25I 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A25J                  TCGA-ET-A25K 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A25L                  TCGA-ET-A25M 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A25N                  TCGA-ET-A25O 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A25P                  TCGA-ET-A25R 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A2MX                  TCGA-ET-A2MY 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A2MZ                  TCGA-ET-A2N0 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A2N1                  TCGA-ET-A2N3 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A2N4                  TCGA-ET-A2N5 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A39I                  TCGA-ET-A39J 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A39K                  TCGA-ET-A39M 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A39N                  TCGA-ET-A39O 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A39P                  TCGA-ET-A39R 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A39S                  TCGA-ET-A39T 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A3BN                  TCGA-ET-A3BO 
"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-A3DO                  TCGA-ET-A3DP 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A3DQ                  TCGA-ET-A3DR 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A3DS                  TCGA-ET-A3DT 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A3DU                  TCGA-ET-A3DV 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A3DW                  TCGA-ET-A40P 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A40Q                  TCGA-ET-A40R 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A40S                  TCGA-ET-A40T 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-ET-A4KN                  TCGA-ET-A4KQ 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FE-A22Z                  TCGA-FE-A230 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FE-A231                  TCGA-FE-A232 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FE-A233                  TCGA-FE-A234 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FE-A235                  TCGA-FE-A236 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FE-A237                  TCGA-FE-A238 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FE-A239                  TCGA-FE-A23A 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FE-A3PA                  TCGA-FE-A3PB 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FE-A3PC                  TCGA-FE-A3PD 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FK-A3S3                  TCGA-FK-A3SB 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FK-A3SD                  TCGA-FK-A3SE 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FK-A3SG                  TCGA-FK-A3SH 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FK-A4UB                  TCGA-FY-A2QD 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FY-A3BL                  TCGA-FY-A3I4 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FY-A3I5                  TCGA-FY-A3NM 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FY-A3ON                  TCGA-FY-A3R6 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FY-A3R7                  TCGA-FY-A3R8 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FY-A3R9                  TCGA-FY-A3RA 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FY-A3W9                  TCGA-FY-A3WA 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FY-A3YR                  TCGA-FY-A40K 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FY-A40L                  TCGA-FY-A40M 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FY-A40N                  TCGA-FY-A4B0 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FY-A4B3                  TCGA-FY-A4B4 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-FY-A76V                  TCGA-GE-A2C6 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-H2-A26U                  TCGA-H2-A2K9 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-H2-A3RH                  TCGA-H2-A3RI 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-H2-A421                  TCGA-H2-A422 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-IM-A3EB                  TCGA-IM-A3ED 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-IM-A3U2                  TCGA-IM-A3U3 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-IM-A41Y                  TCGA-IM-A41Z 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-IM-A420                  TCGA-IM-A4EB 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-J8-A3NZ                  TCGA-J8-A3O0 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-J8-A3O1                  TCGA-J8-A3O2 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-J8-A3YD                  TCGA-J8-A3YE 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-J8-A3YF                  TCGA-J8-A3YG 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-J8-A3YH                  TCGA-J8-A42S 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-J8-A4HW                  TCGA-J8-A4HY 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-KS-A41F                  TCGA-KS-A41I 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-KS-A41J                  TCGA-KS-A41L 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-KS-A4I1                  TCGA-KS-A4I3 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-KS-A4I5                  TCGA-KS-A4I7 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-KS-A4I9                  TCGA-KS-A4IB 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-KS-A4IC                  TCGA-KS-A4ID 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-L6-A4EP                  TCGA-L6-A4EQ 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-L6-A4ET                  TCGA-L6-A4EU 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-MK-A4N6                  TCGA-MK-A4N7 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-MK-A4N9                  TCGA-MK-A84Z 
"DEL PEAK 15(8P22) WILD-TYPE" "DEL PEAK 15(8P22) WILD-TYPE" 
                 TCGA-QD-A8IV 
"DEL PEAK 15(8P22) WILD-TYPE" 
D75V17, binary
                             cls
clus                            0   1
  DEL PEAK 15(8P22) MUTATED     0   2
  DEL PEAK 15(8P22) WILD-TYPE  38 348
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(8P22) MUTATED      0    2
  DEL PEAK 15(8P22) WILD-TYPE   38  348
                        clus
vv                       DEL PEAK 15(8P22) MUTATED DEL PEAK 15(8P22) WILD-TYPE
  HISPANIC OR LATINO                             0                          38
  NOT HISPANIC OR LATINO                         2                         348
[1] 2 2
[1] FALSE

Clustering(76) Variable = DEL PEAK 16(8P12) MUTATION ANALYSIS
D76V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 16(8P12) MUTATED     4   0
  DEL PEAK 16(8P12) WILD-TYPE 473  14
  DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE 
                          4                         487 
  DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE 
                          0                          14 
$`DEL PEAK 16(8P12) MUTATED`
TCGA-BJ-A190 TCGA-DJ-A2Q0 TCGA-EM-A3O9 TCGA-EM-A3SY 
       20.58         8.12         9.24        13.51 

$`DEL PEAK 16(8P12) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
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        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.78         8.42         9.34         6.77         9.21         9.44 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
        9.90         8.61        10.09         7.07        10.36        12.43 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        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        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04         1.15        22.29 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        12.36        18.05        19.79        19.46        54.21 
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        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        10.49        13.15        22.16        13.84        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       17.59        12.07        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 
       17.46        18.97        15.68        14.14        19.63        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        16.44        16.77        27.95        23.77        16.80 
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        11.15         7.33        12.53        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       11.51        16.41        15.62        12.79        70.65        16.90 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        9.01         4.83         8.61         8.38         9.80         5.03 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       37.87        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       29.49        54.05        22.09        12.26        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       65.36        84.89        98.56        61.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        59.15        28.24         5.85         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        24.69        68.22       102.90        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       81.34        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        46.06         4.08         0.89        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10        91.17         1.25         1.15        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        1.64         0.99         1.51         0.76         0.03         4.67 
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         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74        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         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE 
                       8.12                        0.03 
  DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE 
                      20.58                      158.83 
  DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE 
                     11.375                      16.640 
[1] "8.1 - 20.6 (11.4)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "1200000"
D76V2, 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     278       49       109        2        45
                             vv
clus                          STAGE IVC
  DEL PEAK 16(8P12) MUTATED           0
  DEL PEAK 16(8P12) WILD-TYPE         6
D76V3, multiclass
           clus
vv          DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE
  STAGE I                           2                         278
  STAGE II                          2                          49
  STAGE III                         0                         109
  STAGE IV                          0                           2
  STAGE IVA                         0                          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 16(8P12) MUTATED     1   2   1   0
  DEL PEAK 16(8P12) WILD-TYPE 139 164 164  21
D76V4, multiclass
    clus
vv   DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE
  T1                         1                         139
  T2                         2                         164
  T3                         1                         164
  T4                         0                          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"
D76V5, binary
                             cls
clus                            0   1
  DEL PEAK 16(8P12) MUTATED     3   0
  DEL PEAK 16(8P12) WILD-TYPE 220 222
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(8P12) MUTATED      3    0
  DEL PEAK 16(8P12) WILD-TYPE  220  222
   clus
vv  DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE
  0                         3                         220
  1                         0                         222
[1] 2 2
[1] FALSE
                             vv
clus                           M0  M1  MX
  DEL PEAK 16(8P12) MUTATED     1   0   3
  DEL PEAK 16(8P12) WILD-TYPE 272   9 209
D76V6, multiclass
    clus
vv   DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE
  M0                         1                         272
  M1                         0                           9
  MX                         3                         209
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V7, binary
                             cls
clus                            0   1
  DEL PEAK 16(8P12) MUTATED     1   3
  DEL PEAK 16(8P12) WILD-TYPE 363 128
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(8P12) MUTATED      1    3
  DEL PEAK 16(8P12) WILD-TYPE  363  128
        clus
vv       DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE
  FEMALE                         1                         363
  MALE                           3                         128
[1] 2 2
[1] FALSE
                             vv
clus                          OTHER  SPECIFY
  DEL PEAK 16(8P12) MUTATED                0
  DEL PEAK 16(8P12) WILD-TYPE              9
                             vv
clus                          THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 16(8P12) MUTATED                                               2
  DEL PEAK 16(8P12) WILD-TYPE                                           351
                             vv
clus                          THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 16(8P12) MUTATED                                                                        2
  DEL PEAK 16(8P12) WILD-TYPE                                                                     96
                             vv
clus                          THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 16(8P12) MUTATED                                                                     0
  DEL PEAK 16(8P12) WILD-TYPE                                                                  35
D76V8, 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                                                                                   9
  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"
D76V9, binary
                             cls
clus                            0   1
  DEL PEAK 16(8P12) MUTATED     0   4
  DEL PEAK 16(8P12) WILD-TYPE  14 477
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(8P12) MUTATED      0    4
  DEL PEAK 16(8P12) WILD-TYPE   14  477
     clus
vv    DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE
  NO                          0                          14
  YES                         4                         477
[1] 2 2
[1] FALSE
D76V10, binary
                             cls
clus                            0   1
  DEL PEAK 16(8P12) MUTATED     4   0
  DEL PEAK 16(8P12) WILD-TYPE 413  17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(8P12) MUTATED      4    0
  DEL PEAK 16(8P12) WILD-TYPE  413   17
     clus
vv    DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE
  NO                          4                         413
  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          130                      16  324
                             vv
clus                          VERY ADVANCED (T4B)
  DEL PEAK 16(8P12) MUTATED                     0
  DEL PEAK 16(8P12) WILD-TYPE                   1
D76V11, multiclass
                         clus
vv                        DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE
  MINIMAL (T3)                                    0                         130
  MODERATE/ADVANCED (T4A)                         0                          16
  NONE                                            4                         324
  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 374  51   4  30
D76V12, multiclass
    clus
vv   DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE
  R0                         4                         374
  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"
D76V13, continuous
D76V14, binary
                             cls
clus                            0   1
  DEL PEAK 16(8P12) MUTATED     2   2
  DEL PEAK 16(8P12) WILD-TYPE 222 259
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(8P12) MUTATED      2    2
  DEL PEAK 16(8P12) WILD-TYPE  222  259
            clus
vv           DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE
  MULTIFOCAL                         2                         222
  UNIFOCAL                           2                         259
[1] 2 2
[1] FALSE
D76V15, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(8P12) MUTATED                                  0     0
  DEL PEAK 16(8P12) WILD-TYPE                                1    49
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(8P12) MUTATED                           0     2
  DEL PEAK 16(8P12) WILD-TYPE                        26   319
D76V16, multiclass
[1] "Remove cluster labels:"    "DEL PEAK 16(8P12) MUTATED"
clus
  DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE 
                          2                         395 
                 TCGA-BJ-A0YZ                  TCGA-BJ-A0Z2 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A0Z3                  TCGA-BJ-A0Z5 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A0Z9                  TCGA-BJ-A0ZA 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A0ZB                  TCGA-BJ-A0ZC 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A0ZE                  TCGA-BJ-A0ZG 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A0ZH                  TCGA-BJ-A0ZJ 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A18Y                  TCGA-BJ-A18Z 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A191                  TCGA-BJ-A192 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A28R                  TCGA-BJ-A28S 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A28T                  TCGA-BJ-A28V 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A28W                  TCGA-BJ-A28X 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A28Z                  TCGA-BJ-A290 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A291                  TCGA-BJ-A2N7 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A2N8                  TCGA-BJ-A2N9 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A2NA                  TCGA-BJ-A2P4 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A3EZ                  TCGA-BJ-A3F0 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A3PR                  TCGA-BJ-A3PT 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A3PU                  TCGA-BJ-A45C 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A45D                  TCGA-BJ-A45E 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A45F                  TCGA-BJ-A45G 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A45H                  TCGA-BJ-A45I 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A45J                  TCGA-BJ-A45K 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-BJ-A4O8                  TCGA-BJ-A4O9 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-CE-A13K                  TCGA-CE-A27D 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-CE-A3MD                  TCGA-CE-A3ME 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-CE-A481                  TCGA-CE-A482 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-CE-A483                  TCGA-CE-A484 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-CE-A485                  TCGA-DE-A0XZ 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DE-A0Y2                  TCGA-DE-A0Y3 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DE-A2OL                  TCGA-DE-A3KN 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DE-A4M8                  TCGA-DE-A4M9 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DE-A4MA                  TCGA-DE-A4MB 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DE-A4MC                  TCGA-DE-A4MD 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DE-A69J                  TCGA-DE-A69K 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DE-A7U5                  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-A2PT                  TCGA-DJ-A2PU 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A2PV                  TCGA-DJ-A2PW 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A2PX                  TCGA-DJ-A2PY 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A2PZ                  TCGA-DJ-A2Q1 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A2Q2                  TCGA-DJ-A2Q3 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A2Q4                  TCGA-DJ-A2Q5 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A2Q6                  TCGA-DJ-A2Q7 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A2Q9                  TCGA-DJ-A2QA 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A2QB                  TCGA-DJ-A3UK 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A3UM                  TCGA-DJ-A3UN 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A3UO                  TCGA-DJ-A3UQ 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A3UR                  TCGA-DJ-A3US 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A3UT                  TCGA-DJ-A3UU 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A3UW                  TCGA-DJ-A3UX 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A3UY                  TCGA-DJ-A3UZ 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A3V2                  TCGA-DJ-A3V3 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A3V4                  TCGA-DJ-A3V5 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A3V7                  TCGA-DJ-A3V8 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A3V9                  TCGA-DJ-A3VD 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A3VE                  TCGA-DJ-A3VF 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A3VG                  TCGA-DJ-A3VJ 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A3VL                  TCGA-DJ-A3VM 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-DJ-A4UL                  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-A2JQ                  TCGA-E8-A3X7 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-E8-A413                  TCGA-E8-A414 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-E8-A415                  TCGA-E8-A416 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-E8-A417                  TCGA-E8-A418 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-E8-A419                  TCGA-E8-A432 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-E8-A433                  TCGA-E8-A434 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-E8-A436                  TCGA-E8-A437 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-E8-A438                  TCGA-E8-A44K 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-E8-A44M                  TCGA-EL-A3CL 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3CM                  TCGA-EL-A3CN 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3CO                  TCGA-EL-A3CP 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3CR                  TCGA-EL-A3CS 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3CT                  TCGA-EL-A3CU 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3CV                  TCGA-EL-A3CW 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3CX                  TCGA-EL-A3CY 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3CZ                  TCGA-EL-A3D0 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3D1                  TCGA-EL-A3D4 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3D5                  TCGA-EL-A3D6 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3GO                  TCGA-EL-A3GP 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3GQ                  TCGA-EL-A3GR 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3GS                  TCGA-EL-A3GU 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3GV                  TCGA-EL-A3GW 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3GX                  TCGA-EL-A3GY 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3GZ                  TCGA-EL-A3H1 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3H2                  TCGA-EL-A3H3 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3H4                  TCGA-EL-A3H5 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3H7                  TCGA-EL-A3H8 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3MW                  TCGA-EL-A3MX 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3MY                  TCGA-EL-A3MZ 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3N2                  TCGA-EL-A3N3 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3T0                  TCGA-EL-A3T1 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3T2                  TCGA-EL-A3T3 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3T6                  TCGA-EL-A3T7 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3T8                  TCGA-EL-A3T9 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3TA                  TCGA-EL-A3TB 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3ZG                  TCGA-EL-A3ZH 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3ZK                  TCGA-EL-A3ZL 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3ZN                  TCGA-EL-A3ZO 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3ZP                  TCGA-EL-A3ZQ 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3ZR                  TCGA-EL-A3ZS 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A3ZT                  TCGA-EL-A4JV 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A4JW                  TCGA-EL-A4JX 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A4JZ                  TCGA-EL-A4K0 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A4K1                  TCGA-EL-A4K2 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A4K4                  TCGA-EL-A4K6 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A4K7                  TCGA-EL-A4K9 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A4KD                  TCGA-EL-A4KG 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-EL-A4KH                  TCGA-EL-A4KI 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A25G                  TCGA-ET-A25I 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A25J                  TCGA-ET-A25K 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A25L                  TCGA-ET-A25M 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A25N                  TCGA-ET-A25O 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A25P                  TCGA-ET-A25R 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A2MX                  TCGA-ET-A2MY 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A2MZ                  TCGA-ET-A2N0 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A2N1                  TCGA-ET-A2N3 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A2N4                  TCGA-ET-A2N5 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A39I                  TCGA-ET-A39J 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A39K                  TCGA-ET-A39M 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A39N                  TCGA-ET-A39O 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A39P                  TCGA-ET-A39R 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A39S                  TCGA-ET-A39T 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A3BN                  TCGA-ET-A3BO 
"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-A3DO                  TCGA-ET-A3DP 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A3DQ                  TCGA-ET-A3DR 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A3DS                  TCGA-ET-A3DT 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A3DU                  TCGA-ET-A3DV 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A3DW                  TCGA-ET-A40P 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A40Q                  TCGA-ET-A40R 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A40S                  TCGA-ET-A40T 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-ET-A4KN                  TCGA-ET-A4KQ 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FE-A22Z                  TCGA-FE-A230 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FE-A231                  TCGA-FE-A232 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FE-A233                  TCGA-FE-A234 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FE-A235                  TCGA-FE-A236 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FE-A237                  TCGA-FE-A238 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FE-A239                  TCGA-FE-A23A 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FE-A3PA                  TCGA-FE-A3PB 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FE-A3PC                  TCGA-FE-A3PD 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FK-A3S3                  TCGA-FK-A3SB 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FK-A3SD                  TCGA-FK-A3SE 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FK-A3SG                  TCGA-FK-A3SH 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FK-A4UB                  TCGA-FY-A2QD 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FY-A3BL                  TCGA-FY-A3I4 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FY-A3I5                  TCGA-FY-A3NM 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FY-A3ON                  TCGA-FY-A3R6 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FY-A3R7                  TCGA-FY-A3R8 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FY-A3R9                  TCGA-FY-A3RA 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FY-A3W9                  TCGA-FY-A3WA 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FY-A3YR                  TCGA-FY-A40K 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FY-A40L                  TCGA-FY-A40M 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FY-A40N                  TCGA-FY-A4B0 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FY-A4B3                  TCGA-FY-A4B4 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-FY-A76V                  TCGA-GE-A2C6 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-H2-A26U                  TCGA-H2-A2K9 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-H2-A3RH                  TCGA-H2-A3RI 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-H2-A421                  TCGA-H2-A422 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-IM-A3EB                  TCGA-IM-A3ED 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-IM-A3U2                  TCGA-IM-A3U3 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-IM-A41Y                  TCGA-IM-A41Z 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-IM-A420                  TCGA-IM-A4EB 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-J8-A3NZ                  TCGA-J8-A3O0 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-J8-A3O1                  TCGA-J8-A3O2 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-J8-A3YD                  TCGA-J8-A3YE 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-J8-A3YF                  TCGA-J8-A3YG 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-J8-A3YH                  TCGA-J8-A42S 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-J8-A4HW                  TCGA-J8-A4HY 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-KS-A41F                  TCGA-KS-A41I 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-KS-A41J                  TCGA-KS-A41L 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-KS-A4I1                  TCGA-KS-A4I3 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-KS-A4I5                  TCGA-KS-A4I7 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-KS-A4I9                  TCGA-KS-A4IB 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-KS-A4IC                  TCGA-KS-A4ID 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-L6-A4EP                  TCGA-L6-A4EQ 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-L6-A4ET                  TCGA-L6-A4EU 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-MK-A4N6                  TCGA-MK-A4N7 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-MK-A4N9                  TCGA-MK-A84Z 
"DEL PEAK 16(8P12) WILD-TYPE" "DEL PEAK 16(8P12) WILD-TYPE" 
                 TCGA-QD-A8IV 
"DEL PEAK 16(8P12) WILD-TYPE" 
D76V17, binary
                             cls
clus                            0   1
  DEL PEAK 16(8P12) MUTATED     0   2
  DEL PEAK 16(8P12) WILD-TYPE  38 348
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(8P12) MUTATED      0    2
  DEL PEAK 16(8P12) WILD-TYPE   38  348
                        clus
vv                       DEL PEAK 16(8P12) MUTATED DEL PEAK 16(8P12) WILD-TYPE
  HISPANIC OR LATINO                             0                          38
  NOT HISPANIC OR LATINO                         2                         348
[1] 2 2
[1] FALSE

Clustering(77) Variable = DEL PEAK 17(8Q24.22) MUTATION ANALYSIS
D77V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 17(8Q24.22) MUTATED     7   0
  DEL PEAK 17(8Q24.22) WILD-TYPE 470  14
  DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE 
                             7                            484 
  DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE 
                             0                             14 
$`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         8.09         7.20         8.12        17.29         9.24 
TCGA-EM-A3SY 
       13.51 

$`DEL PEAK 17(8Q24.22) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A28R TCGA-BJ-A28S 
       17.69        23.34        20.71         4.83         4.87        21.04 
TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 
        2.79         5.10        11.31        17.52         1.22        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        15.48        23.31        18.64         5.75 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
        6.48         0.03         3.45         6.35         7.82         6.18 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
        5.06         8.98         4.93         5.98         0.53         0.10 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
        0.20         0.23        11.38        10.68         0.10         0.39 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.10        20.22        15.42        36.46         5.98        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-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
        4.27         3.22         2.76        17.26        14.07       137.88 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
        3.39         8.71        25.35        13.41        11.90        14.60 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        7.99        11.01       100.01        18.51        13.12         7.99 
TCGA-DJ-A1QI TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       14.96         1.45         8.88         1.02         5.95        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT 
        7.99         5.33         8.48        10.45         1.51         9.60 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       12.56         8.28         7.69         5.52         8.78         8.42 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
        9.34         6.77         9.21         9.44         9.90         8.61 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.07        10.36        12.43        10.85        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        12.49        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        24.23        17.69        43.00        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       21.37        12.76        25.02        20.22        30.61        14.56 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20         9.83        21.27        20.48        11.93        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL 
       21.01        18.97         7.76         8.32        17.36        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       27.62        18.21        10.78        10.98        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       17.82         3.12        15.81        24.33        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 
       30.31        14.04         1.15        22.29        19.59        13.61 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 
       14.27        13.81        14.07        14.27         3.02        14.43 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
       14.70        14.10        14.96         7.69        20.68        13.78 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
       13.58        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 
       80.91         4.18        58.82         1.45        74.30        45.40 
TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR 
       33.47       108.36        39.32         1.41        30.18       102.84 
TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY 
       65.39       124.04        50.37        37.25       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        38.66        52.73 
TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ 
      139.00       131.15       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 
       12.16       147.42       130.72       129.57        32.48       116.91 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
       98.24        41.29        95.38         5.72        66.90        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO 
       77.36        78.97        31.50        50.33        53.06        47.38 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       52.50        45.53        48.16         7.07        44.65        45.80 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       19.30        45.96        37.94        31.04        19.59        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       33.60        28.73        41.13        37.78        29.95        13.32 
TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       11.87         8.71        26.86        18.18        20.91        12.36 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
       18.05        19.79        19.46        54.21        57.01        54.08 
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 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT 
       23.51         6.05         2.99        12.30        15.19        10.49 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        13.84        19.73        17.59        12.07 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.59        17.46        14.60        17.46        18.97        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR 
       14.14        19.63        13.38         8.35        16.44        16.77 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        16.80        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        11.15         7.33 
TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
       12.53        13.91         7.82        11.51        16.41        15.62 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        70.65        16.90         9.01         4.83         8.61 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
        8.38         9.80         5.03        37.87        12.72         0.95 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       47.47        48.20        29.69        32.35        14.79        12.33 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       14.79        27.09        18.38        29.49        54.05        22.09 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       12.26        16.08        29.19        19.76         2.66        58.22 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
       13.74        71.01        80.02        65.36        84.89        98.56 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
       61.02        58.72        57.11        55.10        59.15        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
        5.85         4.18         2.43         5.56        24.72        38.30 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       42.25         2.37         4.50        80.81        69.24        59.87 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       43.50         0.30        17.98        25.32       132.36        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
        3.22         7.17         4.80         5.03         2.14         4.01 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
        1.94        73.74        59.70        31.59        44.25        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       102.90        66.77        81.34        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        46.06 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.08         0.89        22.03         0.92        48.10        91.17 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON 
        1.25         1.15        17.82         1.64         0.99         1.51 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        0.76         0.03         4.67        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         6.87         4.14         6.58         4.54 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
        0.89         1.35         1.15         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        10.26        16.90         9.80         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        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        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       12.43         6.74        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         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

  DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE 
                          7.20                           0.03 
  DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE 
                         20.58                         158.83 
  DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE 
                         9.240                         16.685 
[1] "7.2 - 20.6 (9.2)"   "0.0 - 158.8 (16.7)"
[1] "hr="     "1200000"
D77V2, 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     278       48       107        2        45
                                vv
clus                             STAGE IVC
  DEL PEAK 17(8Q24.22) MUTATED           0
  DEL PEAK 17(8Q24.22) WILD-TYPE         6
D77V3, multiclass
           clus
vv          DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE
  STAGE I                              2                            278
  STAGE II                             3                             48
  STAGE III                            2                            107
  STAGE IV                             0                              2
  STAGE IVA                            0                             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 17(8Q24.22) MUTATED     1   3   3   0
  DEL PEAK 17(8Q24.22) WILD-TYPE 139 163 162  21
D77V4, multiclass
    clus
vv   DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE
  T1                            1                            139
  T2                            3                            163
  T3                            3                            162
  T4                            0                             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"
D77V5, binary
                                cls
clus                               0   1
  DEL PEAK 17(8Q24.22) MUTATED     5   0
  DEL PEAK 17(8Q24.22) WILD-TYPE 218 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(8Q24.22) MUTATED      5    0
  DEL PEAK 17(8Q24.22) WILD-TYPE  218  222
   clus
vv  DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE
  0                            5                            218
  1                            0                            222
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 17(8Q24.22) MUTATED     3   0   4
  DEL PEAK 17(8Q24.22) WILD-TYPE 270   9 208
D77V6, multiclass
    clus
vv   DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE
  M0                            3                            270
  M1                            0                              9
  MX                            4                            208
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V7, binary
                                cls
clus                               0   1
  DEL PEAK 17(8Q24.22) MUTATED     2   5
  DEL PEAK 17(8Q24.22) WILD-TYPE 362 126
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(8Q24.22) MUTATED      2    5
  DEL PEAK 17(8Q24.22) WILD-TYPE  362  126
        clus
vv       DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE
  FEMALE                            2                            362
  MALE                              5                            126
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 17(8Q24.22) MUTATED                0
  DEL PEAK 17(8Q24.22) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 17(8Q24.22) MUTATED                                               3
  DEL PEAK 17(8Q24.22) WILD-TYPE                                           350
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 17(8Q24.22) MUTATED                                                                        4
  DEL PEAK 17(8Q24.22) WILD-TYPE                                                                     94
                                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                                                                  35
D77V8, 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                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             94
  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"
D77V9, binary
                                cls
clus                               0   1
  DEL PEAK 17(8Q24.22) MUTATED     0   7
  DEL PEAK 17(8Q24.22) WILD-TYPE  14 474
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(8Q24.22) MUTATED      0    7
  DEL PEAK 17(8Q24.22) WILD-TYPE   14  474
     clus
vv    DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE
  NO                             0                             14
  YES                            7                            474
[1] 2 2
[1] FALSE
D77V10, binary
                                cls
clus                               0   1
  DEL PEAK 17(8Q24.22) MUTATED     7   0
  DEL PEAK 17(8Q24.22) WILD-TYPE 410  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(8Q24.22) MUTATED      7    0
  DEL PEAK 17(8Q24.22) WILD-TYPE  410   17
     clus
vv    DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE
  NO                             7                            410
  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          129                      16  322
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 17(8Q24.22) MUTATED                     0
  DEL PEAK 17(8Q24.22) WILD-TYPE                   1
D77V11, 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)                                       129
  MODERATE/ADVANCED (T4A)                             16
  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 17(8Q24.22) MUTATED     6   0   0   1
  DEL PEAK 17(8Q24.22) WILD-TYPE 372  51   4  29
D77V12, multiclass
    clus
vv   DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE
  R0                            6                            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"
D77V13, continuous
D77V14, binary
                                cls
clus                               0   1
  DEL PEAK 17(8Q24.22) MUTATED     3   4
  DEL PEAK 17(8Q24.22) WILD-TYPE 221 257
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(8Q24.22) MUTATED      3    4
  DEL PEAK 17(8Q24.22) WILD-TYPE  221  257
            clus
vv           DEL PEAK 17(8Q24.22) MUTATED DEL PEAK 17(8Q24.22) WILD-TYPE
  MULTIFOCAL                            3                            221
  UNIFOCAL                              4                            257
[1] 2 2
[1] FALSE
D77V15, 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    49
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(8Q24.22) MUTATED                           0     3
  DEL PEAK 17(8Q24.22) WILD-TYPE                        26   318
D77V16, 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                                                        49
  BLACK OR AFRICAN AMERICAN                                    26
  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"
D77V17, binary
                                cls
clus                               0   1
  DEL PEAK 17(8Q24.22) MUTATED     0   3
  DEL PEAK 17(8Q24.22) WILD-TYPE  38 347
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(8Q24.22) MUTATED      0    3
  DEL PEAK 17(8Q24.22) WILD-TYPE   38  347
                        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                            347
[1] 2 2
[1] FALSE

Clustering(78) Variable = DEL PEAK 18(9P21.3) MUTATION ANALYSIS
D78V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 18(9P21.3) MUTATED    17   2
  DEL PEAK 18(9P21.3) WILD-TYPE 460  12
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                           19                           472 
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                            2                            12 
$`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         8.12         2.33        14.43         1.41        57.63 
TCGA-EL-A3T9 TCGA-EL-A3ZK TCGA-EL-A3ZO TCGA-EL-A4K6 TCGA-EL-A4KI TCGA-EM-A1YE 
        5.72        31.50        47.38        28.73         8.71        54.08 
TCGA-EM-A2OY TCGA-EM-A3O3 TCGA-EM-A3O9 TCGA-EM-A3SY TCGA-ET-A39N TCGA-FY-A3W9 
       17.59        14.50         9.24        13.51        98.56         0.76 
TCGA-FY-A40M 
        4.54 

$`DEL PEAK 18(9P21.3) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
        1.22        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        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.78         8.42         9.34         6.77         9.21         9.44 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
        9.90         8.61        10.09         7.07        10.36        12.43 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        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        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       54.90        21.53        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        30.31        14.04         1.15        22.29        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
       14.70        14.10        14.96         7.69        20.68        13.78 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
       13.58        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 
       80.91         4.18        58.82         1.45        74.30        45.40 
TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS 
       33.47       108.36        39.32        30.18       102.84        65.39 
TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
      124.04        50.37        37.25       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        38.66        52.73       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 
      131.15       108.66        17.52        52.50        12.16       147.42 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      130.72       129.57        32.48       116.91        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZL 
       95.38        66.90        82.82        77.36        78.97        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       53.06        52.50        45.53        48.16         7.07        44.65 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       45.80        19.30        45.96        37.94        31.04        19.59 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       30.51        33.60        41.13        37.78        29.95        13.32 
TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       11.87        26.86        18.18        20.91        12.36        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J 
       19.79        19.46        54.21        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        11.74        11.15 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        16.44        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        2.99        12.30        15.19        10.49        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       13.84        19.73        12.07        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        17.46        18.97        15.68        14.14        19.63 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        16.44        16.77        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        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        11.15         7.33        12.53        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       11.51        16.41        15.62        12.79        70.65        16.90 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        9.01         4.83         8.61         8.38         9.80         5.03 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       37.87        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       29.49        54.05        22.09        12.26        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        61.02        58.72        57.11        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       59.15        28.24         5.85         4.18         2.43         5.56 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       24.72        38.30        42.25         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       69.24        59.87        43.50         0.30        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       102.90        66.77        81.34 
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        46.06         4.08         0.89        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 
       48.10        91.17         1.25         1.15        17.82         1.64 
TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
        0.99         1.51         0.76         0.03         4.67        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         6.87         4.14         6.58 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
        0.89         1.35         1.15         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        10.26        16.90         9.80         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        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        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       12.43         6.74        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         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                         0.76                          0.03 
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                        98.56                        158.83 
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                        14.43                         16.75 
[1] "0.8 - 98.6 (14.4)"  "0.0 - 158.8 (16.8)"
[1] "hr=" "4.7"
D78V2, 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     273       46       105        0        44
                               vv
clus                            STAGE IVC
  DEL PEAK 18(9P21.3) MUTATED           1
  DEL PEAK 18(9P21.3) WILD-TYPE         5
D78V3, multiclass
           clus
vv          DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  STAGE I                             7                           273
  STAGE II                            5                            46
  STAGE III                           4                           105
  STAGE IV                            2                             0
  STAGE IVA                           1                            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 18(9P21.3) MUTATED     5   7   5   3
  DEL PEAK 18(9P21.3) WILD-TYPE 135 159 160  18
D78V4, multiclass
    clus
vv   DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  T1                           5                           135
  T2                           7                           159
  T3                           5                           160
  T4                           3                            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"
D78V5, binary
                               cls
clus                              0   1
  DEL PEAK 18(9P21.3) MUTATED     9   8
  DEL PEAK 18(9P21.3) WILD-TYPE 214 214
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(9P21.3) MUTATED      9    8
  DEL PEAK 18(9P21.3) WILD-TYPE  214  214
   clus
vv  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  0                           9                           214
  1                           8                           214
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  DEL PEAK 18(9P21.3) MUTATED     6   1  13
  DEL PEAK 18(9P21.3) WILD-TYPE 267   8 199
D78V6, multiclass
    clus
vv   DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  M0                           6                           267
  M1                           1                             8
  MX                          13                           199
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V7, binary
                               cls
clus                              0   1
  DEL PEAK 18(9P21.3) MUTATED    13   7
  DEL PEAK 18(9P21.3) WILD-TYPE 351 124
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(9P21.3) MUTATED     13    7
  DEL PEAK 18(9P21.3) WILD-TYPE  351  124
        clus
vv       DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  FEMALE                          13                           351
  MALE                             7                           124
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  DEL PEAK 18(9P21.3) MUTATED                0
  DEL PEAK 18(9P21.3) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 18(9P21.3) MUTATED                                              15
  DEL PEAK 18(9P21.3) WILD-TYPE                                           338
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 18(9P21.3) MUTATED                                                                        5
  DEL PEAK 18(9P21.3) WILD-TYPE                                                                     93
                               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                                                                  35
D78V8, 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                                                                                     9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    338
  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"
D78V9, binary
                               cls
clus                              0   1
  DEL PEAK 18(9P21.3) MUTATED     0  20
  DEL PEAK 18(9P21.3) WILD-TYPE  14 461
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(9P21.3) MUTATED      0   20
  DEL PEAK 18(9P21.3) WILD-TYPE   14  461
     clus
vv    DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  NO                            0                            14
  YES                          20                           461
[1] 2 2
[1] FALSE
D78V10, binary
                               cls
clus                              0   1
  DEL PEAK 18(9P21.3) MUTATED    19   0
  DEL PEAK 18(9P21.3) WILD-TYPE 398  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(9P21.3) MUTATED     19    0
  DEL PEAK 18(9P21.3) WILD-TYPE  398   17
     clus
vv    DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  NO                           19                           398
  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          126                      16  314
                               vv
clus                            VERY ADVANCED (T4B)
  DEL PEAK 18(9P21.3) MUTATED                     1
  DEL PEAK 18(9P21.3) WILD-TYPE                   0
D78V11, 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)                                      126
  MODERATE/ADVANCED (T4A)                            16
  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
  DEL PEAK 18(9P21.3) MUTATED    14   3   0   2
  DEL PEAK 18(9P21.3) WILD-TYPE 364  48   4  28
D78V12, multiclass
    clus
vv   DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  R0                          14                           364
  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"
D78V13, continuous
D78V14, binary
                               cls
clus                              0   1
  DEL PEAK 18(9P21.3) MUTATED     6  14
  DEL PEAK 18(9P21.3) WILD-TYPE 218 247
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(9P21.3) MUTATED      6   14
  DEL PEAK 18(9P21.3) WILD-TYPE  218  247
            clus
vv           DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  MULTIFOCAL                           6                           218
  UNIFOCAL                            14                           247
[1] 2 2
[1] FALSE
D78V15, 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    48
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(9P21.3) MUTATED                           1    13
  DEL PEAK 18(9P21.3) WILD-TYPE                        25   308
D78V16, 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                                                       48
  BLACK OR AFRICAN AMERICAN                                   25
  WHITE                                                      308
[1] 4 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 18(9P21.3) MUTATED     0  15
  DEL PEAK 18(9P21.3) WILD-TYPE  38 335
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(9P21.3) MUTATED      0   15
  DEL PEAK 18(9P21.3) WILD-TYPE   38  335
                        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                           335
[1] 2 2
[1] FALSE

Clustering(79) Variable = DEL PEAK 19(9Q22.33) MUTATION ANALYSIS
D79V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 19(9Q22.33) MUTATED    22   2
  DEL PEAK 19(9Q22.33) WILD-TYPE 455  12
  DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE 
                            24                            467 
  DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE 
                             2                             12 
$`DEL PEAK 19(9Q22.33) MUTATED`
TCGA-BJ-A2N8 TCGA-CE-A484 TCGA-DE-A4MB TCGA-DJ-A2Q0 TCGA-DO-A2HM TCGA-E8-A432 
       16.57         0.39        11.57         8.12         2.33        14.43 
TCGA-EL-A3GP TCGA-EL-A3MX TCGA-EL-A3T9 TCGA-EL-A3ZK TCGA-EL-A3ZO TCGA-EL-A4K6 
        1.41        57.63         5.72        31.50        47.38        28.73 
TCGA-EL-A4KI TCGA-EM-A1YB TCGA-EM-A1YE TCGA-EM-A2OY TCGA-EM-A3O3 TCGA-EM-A3O9 
        8.71        19.46        54.08        17.59        14.50         9.24 
TCGA-EM-A3SY TCGA-ET-A39N TCGA-FE-A231 TCGA-FK-A3SG TCGA-FY-A40M TCGA-IM-A3U2 
       13.51        98.56        31.59         0.92         4.54        10.26 

$`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        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
        1.22        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        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.10        20.22        15.42        36.46         5.98        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         4.27 
TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
        3.22         2.76        17.26        14.07       137.88         3.39 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        25.35        13.41        11.90        14.60         7.99 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       11.01       100.01        18.51        13.12         7.99        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
        7.20         1.45         8.88         1.02         5.95        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT 
        7.99         5.33         8.48        10.45         1.51         9.60 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       12.56         8.28         7.69         5.52         8.78         8.42 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
        9.34         6.77         9.21         9.44         9.90         8.61 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.07        10.36        12.43        10.85        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        12.49        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        24.23        17.69        43.00        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       21.37        12.76        25.02        20.22        30.61        14.56 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20         9.83        21.27        20.48        11.93        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL 
       21.01        18.97         7.76         8.32        17.36        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       27.62        18.21        10.78        10.98        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       17.82         3.12        15.81        24.33        54.90        21.53 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       31.07        12.07        66.38        40.21        63.19        30.31 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       14.04         1.15        22.29        19.59        13.61        14.27 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A433 TCGA-E8-A434 
       13.81        14.07        14.27         3.02        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        13.78        13.58        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        80.91         4.18 
TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 
       58.82         1.45        74.30        45.40        33.47       108.36 
TCGA-EL-A3GO TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       39.32        30.18       102.84        65.39       124.04        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       37.25       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        38.66        52.73       139.00       131.15       108.66 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA 
       32.48       116.91        98.24        41.29        95.38        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZP 
       82.82        77.36        78.97        50.33        53.06        52.50 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       45.53        48.16         7.07        44.65        45.80        19.30 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        37.94        31.04        19.59        30.51        33.60 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS 
       41.13        37.78        29.95        13.32        11.87        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YC 
       18.18        20.91        12.36        18.05        19.79        54.21 
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        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ 
       10.49        13.15        22.16        13.84        19.73        12.07 
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        17.46        18.97 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        19.63        13.38         8.35        16.44 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       16.77        27.95        23.77        16.80        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        11.15         7.33 
TCGA-EM-A3O8 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
       12.53        13.91         7.82        11.51        16.41        15.62 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        70.65        16.90         9.01         4.83         8.61 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
        8.38         9.80         5.03        37.87        12.72         0.95 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       47.47        48.20        29.69        32.35        14.79        12.33 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       14.79        27.09        18.38        29.49        54.05        22.09 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       12.26        16.08        29.19        19.76         2.66        58.22 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O 
       13.74        71.01        80.02        65.36        84.89        61.02 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       58.72        57.11        55.10        59.15        28.24         5.85 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
        4.18         2.43         5.56        24.72        38.30        42.25 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
        2.37         4.50        80.81        69.24        59.87        43.50 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
        0.30        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       73.74        59.70        44.25        24.69        68.22       102.90 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
       66.77        81.34        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        46.06         4.08         0.89 
TCGA-FK-A3SE TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
       22.03        48.10        91.17         1.25         1.15        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        1.64         0.99         1.51         0.76         0.03         4.67 
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         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        4.14         6.58         0.89         1.35         1.15         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-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z 
       18.61        48.92        47.41        16.90         9.80         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        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        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        12.43         6.74        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         0.72 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       16.64        32.45         8.71        10.98         5.19 

  DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE 
                          0.39                           0.03 
  DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE 
                         98.56                         158.83 
  DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE 
                         13.97                          16.77 
[1] "0.4 - 98.6 (14.0)"  "0.0 - 158.8 (16.8)"
[1] "hr=" "4.3"
D79V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 19(9Q22.33) MUTATED         9        5         4        2         4
  DEL PEAK 19(9Q22.33) WILD-TYPE     271       46       105        0        41
                                vv
clus                             STAGE IVC
  DEL PEAK 19(9Q22.33) MUTATED           1
  DEL PEAK 19(9Q22.33) WILD-TYPE         5
D79V3, multiclass
           clus
vv          DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE
  STAGE I                              9                            271
  STAGE II                             5                             46
  STAGE III                            4                            105
  STAGE IV                             2                              0
  STAGE IVA                            4                             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     5   9   8   3
  DEL PEAK 19(9Q22.33) WILD-TYPE 135 157 157  18
D79V4, multiclass
    clus
vv   DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE
  T1                            5                            135
  T2                            9                            157
  T3                            8                            157
  T4                            3                             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"
D79V5, binary
                                cls
clus                               0   1
  DEL PEAK 19(9Q22.33) MUTATED     8  13
  DEL PEAK 19(9Q22.33) WILD-TYPE 215 209
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(9Q22.33) MUTATED      8   13
  DEL PEAK 19(9Q22.33) WILD-TYPE  215  209
   clus
vv  DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE
  0                            8                            215
  1                           13                            209
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 19(9Q22.33) MUTATED     8   1  16
  DEL PEAK 19(9Q22.33) WILD-TYPE 265   8 196
D79V6, multiclass
    clus
vv   DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE
  M0                            8                            265
  M1                            1                              8
  MX                           16                            196
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V7, binary
                                cls
clus                               0   1
  DEL PEAK 19(9Q22.33) MUTATED    17   8
  DEL PEAK 19(9Q22.33) WILD-TYPE 347 123
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(9Q22.33) MUTATED     17    8
  DEL PEAK 19(9Q22.33) WILD-TYPE  347  123
        clus
vv       DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE
  FEMALE                           17                            347
  MALE                              8                            123
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 19(9Q22.33) MUTATED                0
  DEL PEAK 19(9Q22.33) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 19(9Q22.33) MUTATED                                              19
  DEL PEAK 19(9Q22.33) WILD-TYPE                                           334
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 19(9Q22.33) MUTATED                                                                        5
  DEL PEAK 19(9Q22.33) WILD-TYPE                                                                     93
                                vv
clus                             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 19(9Q22.33) MUTATED                                                                     1
  DEL PEAK 19(9Q22.33) WILD-TYPE                                                                  34
D79V8, multiclass
                                                                        clus
vv                                                                       DEL PEAK 19(9Q22.33) MUTATED
  OTHER  SPECIFY                                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    19
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            5
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               1
                                                                        clus
vv                                                                       DEL PEAK 19(9Q22.33) WILD-TYPE
  OTHER  SPECIFY                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     334
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             93
  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"
D79V9, binary
                                cls
clus                               0   1
  DEL PEAK 19(9Q22.33) MUTATED     1  24
  DEL PEAK 19(9Q22.33) WILD-TYPE  13 457
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(9Q22.33) MUTATED      1   24
  DEL PEAK 19(9Q22.33) WILD-TYPE   13  457
     clus
vv    DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE
  NO                             1                             13
  YES                           24                            457
[1] 2 2
[1] FALSE
D79V10, binary
                                cls
clus                               0   1
  DEL PEAK 19(9Q22.33) MUTATED    23   1
  DEL PEAK 19(9Q22.33) WILD-TYPE 394  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(9Q22.33) MUTATED     23    1
  DEL PEAK 19(9Q22.33) WILD-TYPE  394   16
     clus
vv    DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE
  NO                            23                            394
  YES                            1                             16
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 19(9Q22.33) MUTATED              6                       0   17
  DEL PEAK 19(9Q22.33) WILD-TYPE          124                      16  311
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 19(9Q22.33) MUTATED                     1
  DEL PEAK 19(9Q22.33) WILD-TYPE                   0
D79V11, multiclass
                         clus
vv                        DEL PEAK 19(9Q22.33) MUTATED
  MINIMAL (T3)                                       6
  MODERATE/ADVANCED (T4A)                            0
  NONE                                              17
  VERY ADVANCED (T4B)                                1
                         clus
vv                        DEL PEAK 19(9Q22.33) WILD-TYPE
  MINIMAL (T3)                                       124
  MODERATE/ADVANCED (T4A)                             16
  NONE                                               311
  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    19   3   0   2
  DEL PEAK 19(9Q22.33) WILD-TYPE 359  48   4  28
D79V12, multiclass
    clus
vv   DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE
  R0                           19                            359
  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"
D79V13, continuous
D79V14, binary
                                cls
clus                               0   1
  DEL PEAK 19(9Q22.33) MUTATED    10  15
  DEL PEAK 19(9Q22.33) WILD-TYPE 214 246
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(9Q22.33) MUTATED     10   15
  DEL PEAK 19(9Q22.33) WILD-TYPE  214  246
            clus
vv           DEL PEAK 19(9Q22.33) MUTATED DEL PEAK 19(9Q22.33) WILD-TYPE
  MULTIFOCAL                           10                            214
  UNIFOCAL                             15                            246
[1] 2 2
[1] FALSE
D79V15, 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    47
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(9Q22.33) MUTATED                           1    16
  DEL PEAK 19(9Q22.33) WILD-TYPE                        25   305
D79V16, multiclass
                                  clus
vv                                 DEL PEAK 19(9Q22.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                      16
                                  clus
vv                                 DEL PEAK 19(9Q22.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        47
  BLACK OR AFRICAN AMERICAN                                    25
  WHITE                                                       305
[1] 4 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 19(9Q22.33) MUTATED     2  17
  DEL PEAK 19(9Q22.33) WILD-TYPE  36 333
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(9Q22.33) MUTATED      2   17
  DEL PEAK 19(9Q22.33) WILD-TYPE   36  333
                        clus
vv                       DEL PEAK 19(9Q22.33) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           17
                        clus
vv                       DEL PEAK 19(9Q22.33) WILD-TYPE
  HISPANIC OR LATINO                                 36
  NOT HISPANIC OR LATINO                            333
[1] 2 2
[1] FALSE

Clustering(80) Variable = DEL PEAK 20(10P12.31) MUTATION ANALYSIS
D80V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 20(10P12.31) MUTATED     7   0
  DEL PEAK 20(10P12.31) WILD-TYPE 470  14
  DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE 
                              7                             484 
  DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE 
                              0                              14 
$`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        14.43         8.71         9.24        98.56         0.30 
TCGA-FY-A3I5 
        1.64 

$`DEL PEAK 20(10P12.31) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
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        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
       14.27         3.02        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       29.95        13.32        11.87        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
       12.36        18.05        19.79        19.46        54.21        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        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       10.49        13.15        22.16        13.84        19.73        17.59 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       12.07        17.59        17.46        17.29        14.60        17.46 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       18.97        15.68        14.14        19.63        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       16.44        16.77        27.95        23.77        16.80        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 
       11.15         7.33        12.53        13.91         7.82        11.51 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       16.41        15.62        13.51        12.79        70.65        16.90 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        9.01         4.83         8.61         8.38         9.80         5.03 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       37.87        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       29.49        54.05        22.09        12.26        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        61.02        58.72        57.11        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       59.15        28.24         5.85         4.18         2.43         5.56 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       24.72        38.30        42.25         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       69.24        59.87        43.50        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        4.01         1.94        73.74        59.70        31.59        44.25 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       102.90        66.77        81.34        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 
       46.06         4.08         0.89        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON 
       91.17         1.25         1.15        17.82         0.99         1.51 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        0.76         0.03         4.67        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         6.87         4.14         6.58         4.54 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
        0.89         1.35         1.15         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        10.26        16.90         9.80         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        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        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       12.43         6.74        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         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

  DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE 
                           0.30                            0.03 
  DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE 
                          98.56                          158.83 
  DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE 
                          9.240                          16.685 
[1] "0.3 - 98.6 (9.2)"   "0.0 - 158.8 (16.7)"
[1] "hr="     "9200000"
D80V2, 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     277       49       107        2        45
                                 vv
clus                              STAGE IVC
  DEL PEAK 20(10P12.31) MUTATED           0
  DEL PEAK 20(10P12.31) WILD-TYPE         6
D80V3, multiclass
           clus
vv          DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE
  STAGE I                               3                             277
  STAGE II                              2                              49
  STAGE III                             2                             107
  STAGE IV                              0                               2
  STAGE IVA                             0                              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 20(10P12.31) MUTATED     1   2   4   0
  DEL PEAK 20(10P12.31) WILD-TYPE 139 164 161  21
D80V4, multiclass
    clus
vv   DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE
  T1                             1                             139
  T2                             2                             164
  T3                             4                             161
  T4                             0                              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"
D80V5, binary
                                 cls
clus                                0   1
  DEL PEAK 20(10P12.31) MUTATED     6   0
  DEL PEAK 20(10P12.31) WILD-TYPE 217 222
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(10P12.31) MUTATED      6    0
  DEL PEAK 20(10P12.31) WILD-TYPE  217  222
   clus
vv  DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE
  0                             6                             217
  1                             0                             222
[1] 2 2
[1] FALSE
                                 vv
clus                               M0  M1  MX
  DEL PEAK 20(10P12.31) MUTATED     1   0   6
  DEL PEAK 20(10P12.31) WILD-TYPE 272   9 206
D80V6, multiclass
    clus
vv   DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE
  M0                             1                             272
  M1                             0                               9
  MX                             6                             206
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V7, binary
                                 cls
clus                                0   1
  DEL PEAK 20(10P12.31) MUTATED     4   3
  DEL PEAK 20(10P12.31) WILD-TYPE 360 128
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(10P12.31) MUTATED      4    3
  DEL PEAK 20(10P12.31) WILD-TYPE  360  128
        clus
vv       DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE
  FEMALE                             4                             360
  MALE                               3                             128
[1] 2 2
[1] FALSE
                                 vv
clus                              OTHER  SPECIFY
  DEL PEAK 20(10P12.31) MUTATED                0
  DEL PEAK 20(10P12.31) WILD-TYPE              9
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 20(10P12.31) MUTATED                                               5
  DEL PEAK 20(10P12.31) WILD-TYPE                                           348
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 20(10P12.31) MUTATED                                                                        2
  DEL PEAK 20(10P12.31) WILD-TYPE                                                                     96
                                 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                                                                  35
D80V8, 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                                                                                       9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      348
  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"
D80V9, binary
                                 cls
clus                                0   1
  DEL PEAK 20(10P12.31) MUTATED     0   7
  DEL PEAK 20(10P12.31) WILD-TYPE  14 474
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(10P12.31) MUTATED      0    7
  DEL PEAK 20(10P12.31) WILD-TYPE   14  474
     clus
vv    DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE
  NO                              0                              14
  YES                             7                             474
[1] 2 2
[1] FALSE
D80V10, binary
                                 cls
clus                                0   1
  DEL PEAK 20(10P12.31) MUTATED     6   0
  DEL PEAK 20(10P12.31) WILD-TYPE 411  17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(10P12.31) MUTATED      6    0
  DEL PEAK 20(10P12.31) WILD-TYPE  411   17
     clus
vv    DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE
  NO                              6                             411
  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          129                      16  322
                                 vv
clus                              VERY ADVANCED (T4B)
  DEL PEAK 20(10P12.31) MUTATED                     0
  DEL PEAK 20(10P12.31) WILD-TYPE                   1
D80V11, 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)                                        129
  MODERATE/ADVANCED (T4A)                              16
  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 20(10P12.31) MUTATED     7   0   0   0
  DEL PEAK 20(10P12.31) WILD-TYPE 371  51   4  30
D80V12, multiclass
    clus
vv   DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE
  R0                             7                             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 20(10P12.31) MUTATED     4   3
  DEL PEAK 20(10P12.31) WILD-TYPE 220 258
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(10P12.31) MUTATED      4    3
  DEL PEAK 20(10P12.31) WILD-TYPE  220  258
            clus
vv           DEL PEAK 20(10P12.31) MUTATED DEL PEAK 20(10P12.31) WILD-TYPE
  MULTIFOCAL                             4                             220
  UNIFOCAL                               3                             258
[1] 2 2
[1] FALSE
D80V15, 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    48
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(10P12.31) MUTATED                           0     5
  DEL PEAK 20(10P12.31) WILD-TYPE                        26   316
D80V16, 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                                                         48
  BLACK OR AFRICAN AMERICAN                                     26
  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"
D80V17, binary
                                 cls
clus                                0   1
  DEL PEAK 20(10P12.31) MUTATED     0   6
  DEL PEAK 20(10P12.31) WILD-TYPE  38 344
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(10P12.31) MUTATED      0    6
  DEL PEAK 20(10P12.31) WILD-TYPE   38  344
                        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                             344
[1] 2 2
[1] FALSE

Clustering(81) Variable = DEL PEAK 21(10Q21.2) MUTATION ANALYSIS
D81V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 21(10Q21.2) MUTATED    12   0
  DEL PEAK 21(10Q21.2) WILD-TYPE 465  14
  DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE 
                            12                            479 
  DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE 
                             0                             14 
$`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         1.22        15.85        54.90        14.43 
TCGA-EL-A3ZS TCGA-EL-A4KI TCGA-EM-A3O9 TCGA-ET-A39N TCGA-ET-A3DQ TCGA-FY-A3I5 
        7.07         8.71         9.24        98.56        59.87         1.64 

$`DEL PEAK 21(10Q21.2) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ 
       18.87         4.01        16.73         7.56        15.12        17.69 
TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S 
       23.34        20.71         4.83         8.09         4.87        21.04 
TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A290 TCGA-BJ-A291 
        2.79         5.10        11.31        17.52        30.21        22.88 
TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ 
       18.38        16.57        20.48        18.97         7.04        16.01 
TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D 
       13.94        15.48        23.31        18.64         5.75         6.48 
TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J 
        0.03         3.45         6.35         7.82         6.18         5.06 
TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD 
        8.98         4.93         5.98         0.53         0.10         0.20 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 
        0.23        11.38        10.68         0.10         0.39         0.10 
TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A4M8 TCGA-DE-A4M9 
       20.22        15.42        36.46         5.98        18.54        18.84 
TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K 
       30.12        11.57        30.02        25.12         4.27         3.22 
TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        2.76        17.26        14.07       137.88         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       25.35        13.41        11.90        14.60         7.99        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      100.01        18.51        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45         8.88         1.02         5.95        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33         8.48        10.45         1.51         9.60        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
        8.28         7.69         5.52         8.78         8.42         8.12 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
        9.34         6.77         9.21         9.44         9.90         8.61 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.07        10.36        12.43        10.85        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        12.49        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        24.23        17.69        43.00        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       21.37        12.76        25.02        20.22        30.61        14.56 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20         9.83        21.27        20.48        11.93        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL 
       21.01        18.97         7.76         8.32        17.36        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       27.62        18.21        10.78        10.98        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1K0 TCGA-DO-A2HM 
       17.82         3.12        15.81        24.33        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       31.07        12.07        66.38        40.21        63.19        30.31 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       14.04         1.15        22.29        19.59        13.61        14.27 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A433 TCGA-E8-A434 
       13.81        14.07        14.27         3.02        14.70        14.10 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.96         7.69        20.68        13.78        13.58        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        80.91         4.18 
TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 
       58.82         1.45        74.30        45.40        33.47       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
       39.32         1.41        30.18       102.84        65.39       124.04 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        37.25       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        38.66        52.73       139.00       131.15 
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        12.16       147.42 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      130.72       129.57        32.48       116.91        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
       95.38         5.72        66.90        82.82        77.36        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       31.50        50.33        53.06        47.38        52.50        45.53 
TCGA-EL-A3ZR TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
       48.16        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT 
       37.78        29.95        13.32        11.87        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        12.36        18.05        19.79        19.46        54.21 
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        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        10.49        13.15        22.16        13.84        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       17.59        12.07        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 
       17.46        18.97        15.68        14.14        19.63        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        16.44        16.77        27.95        23.77        16.80 
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        11.15         7.33        12.53        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        16.41        15.62        13.51        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       80.02        65.36        84.89        61.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        59.15        28.24         5.85         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       80.81        69.24        43.50         0.30        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       102.90        66.77        81.34 
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        46.06         4.08         0.89        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM 
       48.10        91.17         1.25         1.15        17.82         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
        1.51         0.76         0.03         4.67        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         6.87         4.14         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
        4.54         0.89         1.35         1.15         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        10.26        16.90         9.80         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        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        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        12.43         6.74        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         0.72 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       16.64        32.45         8.71        10.98         5.19 

  DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE 
                          1.22                           0.03 
  DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE 
                         98.56                         158.83 
  DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE 
                         13.00                          16.73 
[1] "1.2 - 98.6 (13.0)"  "0.0 - 158.8 (16.7)"
[1] "hr="     "2.5e+07"
D81V2, 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     274       49       106        2        44
                                vv
clus                             STAGE IVC
  DEL PEAK 21(10Q21.2) MUTATED           0
  DEL PEAK 21(10Q21.2) WILD-TYPE         6
D81V3, multiclass
           clus
vv          DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE
  STAGE I                              6                            274
  STAGE II                             2                             49
  STAGE III                            3                            106
  STAGE IV                             0                              2
  STAGE IVA                            1                             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 21(10Q21.2) MUTATED     3   3   6   0
  DEL PEAK 21(10Q21.2) WILD-TYPE 137 163 159  21
D81V4, multiclass
    clus
vv   DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE
  T1                            3                            137
  T2                            3                            163
  T3                            6                            159
  T4                            0                             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"
D81V5, binary
                                cls
clus                               0   1
  DEL PEAK 21(10Q21.2) MUTATED     7   3
  DEL PEAK 21(10Q21.2) WILD-TYPE 216 219
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10Q21.2) MUTATED      7    3
  DEL PEAK 21(10Q21.2) WILD-TYPE  216  219
   clus
vv  DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE
  0                            7                            216
  1                            3                            219
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 21(10Q21.2) MUTATED     5   0   7
  DEL PEAK 21(10Q21.2) WILD-TYPE 268   9 205
D81V6, multiclass
    clus
vv   DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE
  M0                            5                            268
  M1                            0                              9
  MX                            7                            205
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V7, binary
                                cls
clus                               0   1
  DEL PEAK 21(10Q21.2) MUTATED     8   4
  DEL PEAK 21(10Q21.2) WILD-TYPE 356 127
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10Q21.2) MUTATED      8    4
  DEL PEAK 21(10Q21.2) WILD-TYPE  356  127
        clus
vv       DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE
  FEMALE                            8                            356
  MALE                              4                            127
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 21(10Q21.2) MUTATED                0
  DEL PEAK 21(10Q21.2) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 21(10Q21.2) MUTATED                                               8
  DEL PEAK 21(10Q21.2) WILD-TYPE                                           345
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 21(10Q21.2) MUTATED                                                                        4
  DEL PEAK 21(10Q21.2) WILD-TYPE                                                                     94
                                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                                                                  35
D81V8, 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                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     345
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             94
  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"
D81V9, binary
                                cls
clus                               0   1
  DEL PEAK 21(10Q21.2) MUTATED     1  11
  DEL PEAK 21(10Q21.2) WILD-TYPE  13 470
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10Q21.2) MUTATED      1   11
  DEL PEAK 21(10Q21.2) WILD-TYPE   13  470
     clus
vv    DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE
  NO                             1                             13
  YES                           11                            470
[1] 2 2
[1] FALSE
D81V10, binary
                                cls
clus                               0   1
  DEL PEAK 21(10Q21.2) MUTATED    10   0
  DEL PEAK 21(10Q21.2) WILD-TYPE 407  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10Q21.2) MUTATED     10    0
  DEL PEAK 21(10Q21.2) WILD-TYPE  407   17
     clus
vv    DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE
  NO                            10                            407
  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          127                      16  319
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 21(10Q21.2) MUTATED                     0
  DEL PEAK 21(10Q21.2) WILD-TYPE                   1
D81V11, 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)                                       127
  MODERATE/ADVANCED (T4A)                             16
  NONE                                               319
  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 368  50   4  30
D81V12, multiclass
    clus
vv   DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE
  R0                           10                            368
  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"
D81V13, continuous
D81V14, binary
                                cls
clus                               0   1
  DEL PEAK 21(10Q21.2) MUTATED     6   5
  DEL PEAK 21(10Q21.2) WILD-TYPE 218 256
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10Q21.2) MUTATED      6    5
  DEL PEAK 21(10Q21.2) WILD-TYPE  218  256
            clus
vv           DEL PEAK 21(10Q21.2) MUTATED DEL PEAK 21(10Q21.2) WILD-TYPE
  MULTIFOCAL                            6                            218
  UNIFOCAL                              5                            256
[1] 2 2
[1] FALSE
D81V15, 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    48
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(10Q21.2) MUTATED                           1     9
  DEL PEAK 21(10Q21.2) WILD-TYPE                        25   312
D81V16, 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                                                        48
  BLACK OR AFRICAN AMERICAN                                    25
  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"
D81V17, binary
                                cls
clus                               0   1
  DEL PEAK 21(10Q21.2) MUTATED     0  11
  DEL PEAK 21(10Q21.2) WILD-TYPE  38 339
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10Q21.2) MUTATED      0   11
  DEL PEAK 21(10Q21.2) WILD-TYPE   38  339
                        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                            339
[1] 2 2
[1] FALSE

Clustering(82) Variable = DEL PEAK 22(10Q23.31) MUTATION ANALYSIS
D82V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 22(10Q23.31) MUTATED    12   0
  DEL PEAK 22(10Q23.31) WILD-TYPE 465  14
  DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE 
                             12                             479 
  DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE 
                              0                              14 
$`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        14.43         8.71 
TCGA-EM-A1YE TCGA-EM-A3O6 TCGA-EM-A3O9 TCGA-ET-A39N TCGA-ET-A3DQ TCGA-FY-A3I5 
       54.08        11.15         9.24        98.56        59.87         1.64 

$`DEL PEAK 22(10Q23.31) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       24.79        18.21        16.34        14.73         8.25        18.87 
TCGA-BJ-A0ZB TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y 
        4.01        16.73         7.56        15.12        17.69        23.34 
TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.71         4.83         8.09         4.87        21.04         2.79 
TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 
        5.10        11.31        17.52         1.22        30.21        22.88 
TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ 
       18.38        16.57        20.48        18.97         7.04        16.01 
TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D 
       13.94        15.48        23.31        18.64         5.75         6.48 
TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J 
        0.03         3.45         6.35         7.82         6.18         5.06 
TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD 
        8.98         4.93         5.98         0.53         0.10         0.20 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 
        0.23        11.38        10.68         0.10         0.39         0.10 
TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A4M8 TCGA-DE-A4M9 
       20.22        15.42        36.46         5.98        18.54        18.84 
TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K 
       30.12        11.57        30.02        25.12         4.27         3.22 
TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S 
        2.76        17.26        14.07       137.88         3.39         8.71 
TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD 
       25.35        13.41        11.90        14.60         7.99        11.01 
TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
      100.01        18.51        13.12         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45         8.88         1.02         5.95        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        5.33         8.48        10.45         1.51         9.60        12.56 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
        8.28         7.69         5.52         8.78         8.42         8.12 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
        9.34         6.77         9.21         9.44         9.90         8.61 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.07        10.36        12.43        10.85        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        12.49        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        24.23        17.69        43.00        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 
       21.37        12.76        25.02        20.22        30.61        14.56 
TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       19.20         9.83        21.27        20.48        11.93        22.92 
TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL 
       21.01        18.97         7.76         8.32        17.36        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW 
       27.62        18.21        10.78        10.98        14.14        14.70 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       17.82         3.12        15.81        24.33        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        31.07        12.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 
       30.31        14.04         1.15        22.29        19.59        13.61 
TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A433 
       14.27        13.81        14.07        14.27         3.02        14.70 
TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M 
       14.10        14.96         7.69        20.68        13.78        13.58 
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        80.91 
TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 
        4.18        58.82         1.45        74.30        45.40        33.47 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS 
      108.36        39.32         1.41        30.18       102.84        65.39 
TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
      124.04        50.37        37.25       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        38.66        52.73       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 
      131.15       108.66        57.63        17.52        52.50        12.16 
TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
      147.42       130.72       129.57        32.48       116.91        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG 
       41.29        95.38         5.72        66.90        82.82        77.36 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP 
       78.97        31.50        50.33        53.06        47.38        52.50 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       45.53        48.16         7.07        44.65        45.80        19.30 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 
       45.96        37.94        31.04        19.59        30.51        33.60 
TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       28.73        41.13        37.78        29.95        13.32        11.87 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        12.36        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       19.46        54.21        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        11.74        11.15        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       16.44        17.88        13.18        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
       12.30        15.19        10.49        13.15        22.16        13.84 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        17.59        12.07        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        17.46        18.97        15.68        14.14        19.63 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        16.44        16.77        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        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        12.53        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        16.41        15.62        13.51        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       80.02        65.36        84.89        61.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        59.15        28.24         5.85         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       80.81        69.24        43.50         0.30        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       102.90        66.77        81.34 
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        46.06         4.08         0.89        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM 
       48.10        91.17         1.25         1.15        17.82         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
        1.51         0.76         0.03         4.67        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         6.87         4.14         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
        4.54         0.89         1.35         1.15         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        10.26        16.90         9.80         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        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        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        12.43         6.74        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         0.72 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       16.64        32.45         8.71        10.98         5.19 

  DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE 
                           1.64                            0.03 
  DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE 
                          98.56                          158.83 
  DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE 
                         14.105                          16.730 
[1] "1.6 - 98.6 (14.1)"  "0.0 - 158.8 (16.7)"
[1] "hr="     "2.5e+07"
D82V2, 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     276       46       107        2        44
                                 vv
clus                              STAGE IVC
  DEL PEAK 22(10Q23.31) MUTATED           0
  DEL PEAK 22(10Q23.31) WILD-TYPE         6
D82V3, multiclass
           clus
vv          DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE
  STAGE I                               4                             276
  STAGE II                              5                              46
  STAGE III                             2                             107
  STAGE IV                              0                               2
  STAGE IVA                             1                              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 22(10Q23.31) MUTATED     2   5   5   0
  DEL PEAK 22(10Q23.31) WILD-TYPE 138 161 160  21
D82V4, multiclass
    clus
vv   DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE
  T1                             2                             138
  T2                             5                             161
  T3                             5                             160
  T4                             0                              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"
D82V5, binary
                                 cls
clus                                0   1
  DEL PEAK 22(10Q23.31) MUTATED     9   1
  DEL PEAK 22(10Q23.31) WILD-TYPE 214 221
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(10Q23.31) MUTATED      9    1
  DEL PEAK 22(10Q23.31) WILD-TYPE  214  221
   clus
vv  DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE
  0                             9                             214
  1                             1                             221
[1] 2 2
[1] FALSE
                                 vv
clus                               M0  M1  MX
  DEL PEAK 22(10Q23.31) MUTATED     3   0   9
  DEL PEAK 22(10Q23.31) WILD-TYPE 270   9 203
D82V6, multiclass
    clus
vv   DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE
  M0                             3                             270
  M1                             0                               9
  MX                             9                             203
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V7, binary
                                 cls
clus                                0   1
  DEL PEAK 22(10Q23.31) MUTATED     7   5
  DEL PEAK 22(10Q23.31) WILD-TYPE 357 126
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(10Q23.31) MUTATED      7    5
  DEL PEAK 22(10Q23.31) WILD-TYPE  357  126
        clus
vv       DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE
  FEMALE                             7                             357
  MALE                               5                             126
[1] 2 2
[1] FALSE
                                 vv
clus                              OTHER  SPECIFY
  DEL PEAK 22(10Q23.31) MUTATED                0
  DEL PEAK 22(10Q23.31) WILD-TYPE              9
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 22(10Q23.31) MUTATED                                               7
  DEL PEAK 22(10Q23.31) WILD-TYPE                                           346
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 22(10Q23.31) MUTATED                                                                        5
  DEL PEAK 22(10Q23.31) WILD-TYPE                                                                     93
                                 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                                                                  35
D82V8, 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                                                                                       9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      346
  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"
D82V9, binary
                                 cls
clus                                0   1
  DEL PEAK 22(10Q23.31) MUTATED     0  12
  DEL PEAK 22(10Q23.31) WILD-TYPE  14 469
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(10Q23.31) MUTATED      0   12
  DEL PEAK 22(10Q23.31) WILD-TYPE   14  469
     clus
vv    DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE
  NO                              0                              14
  YES                            12                             469
[1] 2 2
[1] FALSE
D82V10, binary
                                 cls
clus                                0   1
  DEL PEAK 22(10Q23.31) MUTATED    10   0
  DEL PEAK 22(10Q23.31) WILD-TYPE 407  17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(10Q23.31) MUTATED     10    0
  DEL PEAK 22(10Q23.31) WILD-TYPE  407   17
     clus
vv    DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE
  NO                             10                             407
  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          128                      16  318
                                 vv
clus                              VERY ADVANCED (T4B)
  DEL PEAK 22(10Q23.31) MUTATED                     0
  DEL PEAK 22(10Q23.31) WILD-TYPE                   1
D82V11, 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)                                        128
  MODERATE/ADVANCED (T4A)                              16
  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 22(10Q23.31) MUTATED    12   0   0   0
  DEL PEAK 22(10Q23.31) WILD-TYPE 366  51   4  30
D82V12, multiclass
    clus
vv   DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE
  R0                            12                             366
  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"
D82V13, continuous
D82V14, binary
                                 cls
clus                                0   1
  DEL PEAK 22(10Q23.31) MUTATED     5   6
  DEL PEAK 22(10Q23.31) WILD-TYPE 219 255
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(10Q23.31) MUTATED      5    6
  DEL PEAK 22(10Q23.31) WILD-TYPE  219  255
            clus
vv           DEL PEAK 22(10Q23.31) MUTATED DEL PEAK 22(10Q23.31) WILD-TYPE
  MULTIFOCAL                             5                             219
  UNIFOCAL                               6                             255
[1] 2 2
[1] FALSE
D82V15, 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    48
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(10Q23.31) MUTATED                           0     7
  DEL PEAK 22(10Q23.31) WILD-TYPE                        26   314
D82V16, 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                                                         48
  BLACK OR AFRICAN AMERICAN                                     26
  WHITE                                                        314
[1] 4 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 22(10Q23.31) MUTATED     0   9
  DEL PEAK 22(10Q23.31) WILD-TYPE  38 341
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(10Q23.31) MUTATED      0    9
  DEL PEAK 22(10Q23.31) WILD-TYPE   38  341
                        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                             341
[1] 2 2
[1] FALSE

Clustering(83) Variable = DEL PEAK 23(11P15.1) MUTATION ANALYSIS
D83V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(11P15.1) MUTATED     6   1
  DEL PEAK 23(11P15.1) WILD-TYPE 471  13
  DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE 
                             7                            484 
  DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE 
                             1                             13 
$`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         1.41        28.73         8.71        10.65        33.63 
TCGA-FY-A3I5 
        1.64 

$`DEL PEAK 23(11P15.1) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
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        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
        1.45        74.30        45.40        33.47       108.36        39.32 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       19.59        30.51        33.60        41.13        37.78        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       13.32        11.87        26.86        18.18        20.91        12.36 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
       18.05        19.79        19.46        54.21        57.01        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        11.74 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.15        14.24        16.44        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
        6.05         2.99        12.30        15.19        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        13.84        19.73        17.59        12.07        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        17.46        18.97        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR 
       14.14        19.63        13.38         8.35        16.44        16.77 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        16.80        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        11.15         7.33 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
       12.53         9.24        13.91         7.82        11.51        16.41 
TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       15.62        13.51        12.79        70.65        16.90         9.01 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        4.83         8.61         8.38         9.80         5.03        37.87 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       12.72         0.95        47.47        48.20        29.69        32.35 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       14.79        12.33        14.79        27.09        18.38        29.49 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       54.05        22.09        12.26        16.08        29.19        19.76 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        58.22        13.74        71.01        80.02        65.36 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       84.89        98.56        61.02        58.72        57.11        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       59.15        28.24         5.85         4.18         2.43         5.56 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       24.72        38.30        42.25         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       69.24        59.87        43.50         0.30        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       102.90        66.77        81.34 
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 
       46.06         4.08         0.89        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON 
       91.17         1.25         1.15        17.82         0.99         1.51 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        0.76         0.03         4.67        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         6.87         4.14         6.58         4.54 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
        0.89         1.35         1.15         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        10.26        16.90         9.80         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        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        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       12.43         6.74        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         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

  DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE 
                          1.41                           0.03 
  DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE 
                         33.63                         158.83 
  DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE 
                        10.650                         16.605 
[1] "1.4 - 33.6 (10.7)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "15" 
D83V2, 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     279       50       105        1        45
                                vv
clus                             STAGE IVC
  DEL PEAK 23(11P15.1) MUTATED           0
  DEL PEAK 23(11P15.1) WILD-TYPE         6
D83V3, multiclass
           clus
vv          DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE
  STAGE I                              1                            279
  STAGE II                             1                             50
  STAGE III                            4                            105
  STAGE IV                             1                              1
  STAGE IVA                            0                             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 23(11P15.1) MUTATED     1   1   4   1
  DEL PEAK 23(11P15.1) WILD-TYPE 139 165 161  20
D83V4, multiclass
    clus
vv   DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE
  T1                            1                            139
  T2                            1                            165
  T3                            4                            161
  T4                            1                             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"
D83V5, binary
                                cls
clus                               0   1
  DEL PEAK 23(11P15.1) MUTATED     5   2
  DEL PEAK 23(11P15.1) WILD-TYPE 218 220
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11P15.1) MUTATED      5    2
  DEL PEAK 23(11P15.1) WILD-TYPE  218  220
   clus
vv  DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE
  0                            5                            218
  1                            2                            220
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 23(11P15.1) MUTATED     1   0   6
  DEL PEAK 23(11P15.1) WILD-TYPE 272   9 206
D83V6, multiclass
    clus
vv   DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE
  M0                            1                            272
  M1                            0                              9
  MX                            6                            206
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V7, binary
                                cls
clus                               0   1
  DEL PEAK 23(11P15.1) MUTATED     2   5
  DEL PEAK 23(11P15.1) WILD-TYPE 362 126
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11P15.1) MUTATED      2    5
  DEL PEAK 23(11P15.1) WILD-TYPE  362  126
        clus
vv       DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE
  FEMALE                            2                            362
  MALE                              5                            126
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 23(11P15.1) MUTATED                0
  DEL PEAK 23(11P15.1) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 23(11P15.1) MUTATED                                               5
  DEL PEAK 23(11P15.1) WILD-TYPE                                           348
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 23(11P15.1) MUTATED                                                                        2
  DEL PEAK 23(11P15.1) WILD-TYPE                                                                     96
                                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                                                                  35
D83V8, 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                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     348
  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"
D83V9, binary
                                cls
clus                               0   1
  DEL PEAK 23(11P15.1) MUTATED     1   6
  DEL PEAK 23(11P15.1) WILD-TYPE  13 475
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11P15.1) MUTATED      1    6
  DEL PEAK 23(11P15.1) WILD-TYPE   13  475
     clus
vv    DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE
  NO                             1                             13
  YES                            6                            475
[1] 2 2
[1] FALSE
D83V10, binary
                                cls
clus                               0   1
  DEL PEAK 23(11P15.1) MUTATED     6   0
  DEL PEAK 23(11P15.1) WILD-TYPE 411  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11P15.1) MUTATED      6    0
  DEL PEAK 23(11P15.1) WILD-TYPE  411   17
     clus
vv    DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE
  NO                             6                            411
  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          127                      16  324
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 23(11P15.1) MUTATED                     0
  DEL PEAK 23(11P15.1) WILD-TYPE                   1
D83V11, 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)                                       127
  MODERATE/ADVANCED (T4A)                             16
  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 23(11P15.1) MUTATED     6   0   0   1
  DEL PEAK 23(11P15.1) WILD-TYPE 372  51   4  29
D83V12, multiclass
    clus
vv   DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE
  R0                            6                            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"
D83V13, continuous
D83V14, binary
                                cls
clus                               0   1
  DEL PEAK 23(11P15.1) MUTATED     4   3
  DEL PEAK 23(11P15.1) WILD-TYPE 220 258
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11P15.1) MUTATED      4    3
  DEL PEAK 23(11P15.1) WILD-TYPE  220  258
            clus
vv           DEL PEAK 23(11P15.1) MUTATED DEL PEAK 23(11P15.1) WILD-TYPE
  MULTIFOCAL                            4                            220
  UNIFOCAL                              3                            258
[1] 2 2
[1] FALSE
D83V15, 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    49
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(11P15.1) MUTATED                           1     5
  DEL PEAK 23(11P15.1) WILD-TYPE                        25   316
D83V16, 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                                                        49
  BLACK OR AFRICAN AMERICAN                                    25
  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"
D83V17, binary
                                cls
clus                               0   1
  DEL PEAK 23(11P15.1) MUTATED     0   6
  DEL PEAK 23(11P15.1) WILD-TYPE  38 344
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11P15.1) MUTATED      0    6
  DEL PEAK 23(11P15.1) WILD-TYPE   38  344
                        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                            344
[1] 2 2
[1] FALSE

Clustering(84) Variable = DEL PEAK 24(13Q12.13) MUTATION ANALYSIS
D84V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 24(13Q12.13) MUTATED    16   1
  DEL PEAK 24(13Q12.13) WILD-TYPE 461  13
  DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE 
                             17                             474 
  DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE 
                              1                              13 
$`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         5.75       137.88         6.77        21.37       130.72 
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        16.41 
TCGA-ET-A39N TCGA-ET-A40S TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3W9 
       98.56         5.03        33.63         1.64         0.76 

$`DEL PEAK 24(13Q12.13) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
       18.97         7.04        16.01        15.48        23.31        18.64 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
        6.48         0.03         3.45         6.35         7.82         6.18 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
        5.06         8.98         4.93         5.98         0.53         0.10 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
        0.20         0.23        11.38        10.68         0.10         0.39 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.10        20.22        15.42        36.46         5.98        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-A13M TCGA-DJ-A13O TCGA-DJ-A13R 
        4.27         3.22         2.76        17.26        14.07         3.39 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        25.35        13.41        11.90        14.60         7.99 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       11.01       100.01        18.51        13.12         7.99        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
        7.20         1.45         8.88         1.02         5.95        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT 
        7.99         5.33         8.48        10.45         1.51         9.60 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       12.56         8.28         7.69         5.52         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
        8.12         9.34         9.21         9.44         9.90         8.61 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.07        10.36        12.43        10.85        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        12.49        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        24.23        17.69        43.00        11.34 
TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 
       12.76        25.02        20.22        30.61        14.56        19.20 
TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD 
        9.83        21.27        20.48        11.93        22.92        21.01 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76         8.32        17.36        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       18.21        10.78        10.98        14.14        14.70        17.82 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        24.33        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       31.07        12.07        66.38        40.21        63.19        30.31 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       14.04         1.15        22.29        19.59        13.61        14.27 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 
       13.81        14.07        14.27         3.02        14.43        14.70 
TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M 
       14.10        14.96         7.69        20.68        13.78        13.58 
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        80.91 
TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 
        4.18        58.82         1.45        74.30        45.40        33.47 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS 
      108.36        39.32         1.41        30.18       102.84        65.39 
TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ 
      124.04        50.37        37.25       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        38.66        52.73       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 
      131.15       108.66        57.63        17.52        52.50        12.16 
TCGA-EL-A3N3 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      147.42       129.57        32.48       116.91        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH 
       95.38         5.72        66.90        82.82        77.36        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ 
       31.50        50.33        53.06        47.38        52.50        45.53 
TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       48.16         7.07        44.65        45.80        19.30        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       37.94        31.04        19.59        30.51        33.60        28.73 
TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       41.13        37.78        29.95        13.32        11.87         8.71 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        12.36        18.05        19.79 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K 
       54.21        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        11.74        11.15        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OY TCGA-EM-A2OZ 
       10.49        13.15        22.16        13.84        17.59        12.07 
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        17.46        18.97 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        19.63        13.38         8.35        16.44 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       16.77        27.95        23.77        16.80        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        11.15         7.33 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SX 
       12.53         9.24        13.91         7.82        11.51        15.62 
TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       13.51        12.79        70.65        16.90         9.01         4.83 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
        8.61         8.38         9.80         5.03        37.87        12.72 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L 
        0.95        47.47        48.20        29.69        32.35        14.79 
TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX 
       12.33        14.79        27.09        18.38        29.49        54.05 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 
       22.09        12.26        16.08        29.19        19.76         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       58.22        13.74        71.01        80.02        65.36        84.89 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
       61.02        58.72        57.11        55.10        59.15        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
        5.85         4.18         2.43         5.56        24.72        38.30 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       42.25         2.37         4.50        80.81        69.24        59.87 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       43.50         0.30        17.98        25.32       132.36        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        3.22         7.17         4.80         2.14         4.01         1.94 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        59.70        31.59        44.25        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA 
      102.90        66.77        81.34        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        46.06         4.08         0.89 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10        91.17         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       17.82         0.99         1.51         0.76         0.03         4.67 
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         6.87         4.14 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58         4.54         0.89         1.35         1.15         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        10.26        16.90         9.80 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
        9.63         2.96         8.65        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 
       86.70         6.02        12.43         6.74        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 
        0.72        16.64        32.45         8.71        10.98         5.19 

  DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE 
                           0.76                            0.03 
  DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE 
                         137.88                          158.83 
  DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE 
                         14.530                          16.685 
[1] "0.8 - 137.9 (14.5)" "0.0 - 158.8 (16.7)"
[1] "hr=" "1.7"
D84V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 24(13Q12.13) MUTATED         7        3         7        0         1
  DEL PEAK 24(13Q12.13) WILD-TYPE     273       48       102        2        44
                                 vv
clus                              STAGE IVC
  DEL PEAK 24(13Q12.13) MUTATED           0
  DEL PEAK 24(13Q12.13) WILD-TYPE         6
D84V3, multiclass
           clus
vv          DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE
  STAGE I                               7                             273
  STAGE II                              3                              48
  STAGE III                             7                             102
  STAGE IV                              0                               2
  STAGE IVA                             1                              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 24(13Q12.13) MUTATED     5   5   8   0
  DEL PEAK 24(13Q12.13) WILD-TYPE 135 161 157  21
D84V4, multiclass
    clus
vv   DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE
  T1                             5                             135
  T2                             5                             161
  T3                             8                             157
  T4                             0                              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"
D84V5, binary
                                 cls
clus                                0   1
  DEL PEAK 24(13Q12.13) MUTATED    11   4
  DEL PEAK 24(13Q12.13) WILD-TYPE 212 218
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(13Q12.13) MUTATED     11    4
  DEL PEAK 24(13Q12.13) WILD-TYPE  212  218
   clus
vv  DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE
  0                            11                             212
  1                             4                             218
[1] 2 2
[1] FALSE
                                 vv
clus                               M0  M1  MX
  DEL PEAK 24(13Q12.13) MUTATED     6   0  12
  DEL PEAK 24(13Q12.13) WILD-TYPE 267   9 200
D84V6, multiclass
    clus
vv   DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE
  M0                             6                             267
  M1                             0                               9
  MX                            12                             200
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V7, binary
                                 cls
clus                                0   1
  DEL PEAK 24(13Q12.13) MUTATED    11   7
  DEL PEAK 24(13Q12.13) WILD-TYPE 353 124
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(13Q12.13) MUTATED     11    7
  DEL PEAK 24(13Q12.13) WILD-TYPE  353  124
        clus
vv       DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE
  FEMALE                            11                             353
  MALE                               7                             124
[1] 2 2
[1] FALSE
                                 vv
clus                              OTHER  SPECIFY
  DEL PEAK 24(13Q12.13) MUTATED                0
  DEL PEAK 24(13Q12.13) WILD-TYPE              9
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 24(13Q12.13) MUTATED                                              13
  DEL PEAK 24(13Q12.13) WILD-TYPE                                           340
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 24(13Q12.13) MUTATED                                                                        5
  DEL PEAK 24(13Q12.13) WILD-TYPE                                                                     93
                                 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                                                                  35
D84V8, 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                                                                                       9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      340
  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"
D84V9, binary
                                 cls
clus                                0   1
  DEL PEAK 24(13Q12.13) MUTATED     1  17
  DEL PEAK 24(13Q12.13) WILD-TYPE  13 464
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(13Q12.13) MUTATED      1   17
  DEL PEAK 24(13Q12.13) WILD-TYPE   13  464
     clus
vv    DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE
  NO                              1                              13
  YES                            17                             464
[1] 2 2
[1] FALSE
D84V10, binary
                                 cls
clus                                0   1
  DEL PEAK 24(13Q12.13) MUTATED    13   4
  DEL PEAK 24(13Q12.13) WILD-TYPE 404  13
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(13Q12.13) MUTATED     13    4
  DEL PEAK 24(13Q12.13) WILD-TYPE  404   13
     clus
vv    DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE
  NO                             13                             404
  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          127                      16  313
                                 vv
clus                              VERY ADVANCED (T4B)
  DEL PEAK 24(13Q12.13) MUTATED                     0
  DEL PEAK 24(13Q12.13) WILD-TYPE                   1
D84V11, 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)                                        127
  MODERATE/ADVANCED (T4A)                              16
  NONE                                                313
  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 364  49   4  29
D84V12, multiclass
    clus
vv   DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE
  R0                            14                             364
  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"
D84V13, continuous
D84V14, binary
                                 cls
clus                                0   1
  DEL PEAK 24(13Q12.13) MUTATED     9   9
  DEL PEAK 24(13Q12.13) WILD-TYPE 215 252
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(13Q12.13) MUTATED      9    9
  DEL PEAK 24(13Q12.13) WILD-TYPE  215  252
            clus
vv           DEL PEAK 24(13Q12.13) MUTATED DEL PEAK 24(13Q12.13) WILD-TYPE
  MULTIFOCAL                             9                             215
  UNIFOCAL                               9                             252
[1] 2 2
[1] FALSE
D84V15, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 24(13Q12.13) MUTATED                                  0     0
  DEL PEAK 24(13Q12.13) WILD-TYPE                                1    49
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(13Q12.13) MUTATED                           1    11
  DEL PEAK 24(13Q12.13) WILD-TYPE                        25   310
D84V16, multiclass
                                  clus
vv                                 DEL PEAK 24(13Q12.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                    1
  WHITE                                                       11
                                  clus
vv                                 DEL PEAK 24(13Q12.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         49
  BLACK OR AFRICAN AMERICAN                                     25
  WHITE                                                        310
[1] 4 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 24(13Q12.13) MUTATED     0  11
  DEL PEAK 24(13Q12.13) WILD-TYPE  38 339
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(13Q12.13) MUTATED      0   11
  DEL PEAK 24(13Q12.13) WILD-TYPE   38  339
                        clus
vv                       DEL PEAK 24(13Q12.13) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            11
                        clus
vv                       DEL PEAK 24(13Q12.13) WILD-TYPE
  HISPANIC OR LATINO                                  38
  NOT HISPANIC OR LATINO                             339
[1] 2 2
[1] FALSE

Clustering(85) Variable = DEL PEAK 25(13Q22.1) MUTATION ANALYSIS
D85V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(13Q22.1) MUTATED    17   1
  DEL PEAK 25(13Q22.1) WILD-TYPE 460  13
  DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE 
                            18                            473 
  DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE 
                             1                             13 
$`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         5.75         0.53       137.88         8.88 
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        98.56 
TCGA-ET-A40S TCGA-FE-A235 TCGA-FE-A239 TCGA-FY-A3I5 TCGA-FY-A3W9 TCGA-L6-A4EP 
        5.03       102.90        33.63         1.64         0.76        33.40 

$`DEL PEAK 25(13Q22.1) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2NA 
        1.22        30.21        22.88        18.38        16.57        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45D 
        7.04        16.01        15.48        23.31        18.64         6.48 
TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J 
        0.03         3.45         6.35         7.82         6.18         5.06 
TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME 
        8.98         4.93         5.98         0.10         0.20         0.23 
TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ 
       11.38        10.68         0.10         0.39         0.10        20.22 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 
       15.42        36.46         5.98        15.85        18.54        18.84 
TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD TCGA-DE-A69J TCGA-DE-A69K 
       30.12        11.57        30.02        25.12         4.27         3.22 
TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
        2.76        17.26        14.07         3.39         8.71        25.35 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       13.41        11.90        14.60         7.99        11.01       100.01 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       18.51        13.12         7.99        14.96         7.20         1.45 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 
        5.52         8.78         8.42         8.12         9.34         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
        1.45        74.30        45.40        33.47       108.36        39.32 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        30.18       102.84        65.39       124.04        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       37.25       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        38.66        52.73       139.00       131.15       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        12.16       147.42       130.72 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       116.91        98.24        41.29        95.38 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       50.33        53.06        47.38        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       37.78        29.95        13.32        11.87         8.71        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YC 
       18.18        20.91        12.36        18.05        19.79        54.21 
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-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       10.65        11.74        11.15        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT 
       23.51         6.05         2.99        12.30        15.19        10.49 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       13.15        22.16        13.84        17.59        12.07        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        17.46        18.97        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR 
       14.14        19.63        13.38         8.35        16.44        16.77 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        16.80        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        11.15         7.33 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
       12.53         9.24        13.91         7.82        11.51        16.41 
TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       15.62        13.51        12.79        70.65        16.90         9.01 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        4.83         8.61         8.38         9.80         5.03        37.87 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       12.72         0.95        47.47        48.20        29.69        32.35 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       14.79        12.33        14.79        27.09        18.38        29.49 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       54.05        22.09        12.26        16.08        29.19        19.76 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        58.22        13.74        71.01        80.02        65.36 
TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       84.89        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24         5.85         4.18         2.43         5.56        24.72 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       38.30        42.25         2.37         4.50        80.81        69.24 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       59.87        43.50         0.30        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40T TCGA-ET-A4KN 
       24.72         3.22         7.17         4.80         2.14         4.01 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
        1.94        73.74        59.70        31.59        44.25        24.69 
TCGA-FE-A234 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A23A TCGA-FE-A3PA 
       68.22        66.77        81.34        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        46.06         4.08         0.89 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL 
       22.03         0.92        48.10        91.17         1.25         1.15 
TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
       17.82         0.99         1.51         0.76         0.03         4.67 
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         6.87         4.14 
TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V 
        6.58         4.54         0.89         1.35         1.15         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        10.26        16.90         9.80 
TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
        9.63         2.96         8.65        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 
       86.70         6.02        12.43         6.74        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         0.72 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       16.64        32.45         8.71        10.98         5.19 

  DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE 
                          0.53                           0.03 
  DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE 
                        137.88                         158.83 
  DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE 
                        14.385                         16.640 
[1] "0.5 - 137.9 (14.4)" "0.0 - 158.8 (16.6)"
[1] "hr=" "1.7"
D85V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 25(13Q22.1) MUTATED        10        3         5        0         1
  DEL PEAK 25(13Q22.1) WILD-TYPE     270       48       104        2        44
                                vv
clus                             STAGE IVC
  DEL PEAK 25(13Q22.1) MUTATED           0
  DEL PEAK 25(13Q22.1) WILD-TYPE         6
D85V3, multiclass
           clus
vv          DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE
  STAGE I                             10                            270
  STAGE II                             3                             48
  STAGE III                            5                            104
  STAGE IV                             0                              2
  STAGE IVA                            1                             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 25(13Q22.1) MUTATED     5   6   8   0
  DEL PEAK 25(13Q22.1) WILD-TYPE 135 160 157  21
D85V4, multiclass
    clus
vv   DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE
  T1                            5                            135
  T2                            6                            160
  T3                            8                            157
  T4                            0                             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 25(13Q22.1) MUTATED    13   3
  DEL PEAK 25(13Q22.1) WILD-TYPE 210 219
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(13Q22.1) MUTATED     13    3
  DEL PEAK 25(13Q22.1) WILD-TYPE  210  219
   clus
vv  DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE
  0                           13                            210
  1                            3                            219
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 25(13Q22.1) MUTATED     8   0  11
  DEL PEAK 25(13Q22.1) WILD-TYPE 265   9 201
D85V6, multiclass
    clus
vv   DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE
  M0                            8                            265
  M1                            0                              9
  MX                           11                            201
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V7, binary
                                cls
clus                               0   1
  DEL PEAK 25(13Q22.1) MUTATED    12   7
  DEL PEAK 25(13Q22.1) WILD-TYPE 352 124
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(13Q22.1) MUTATED     12    7
  DEL PEAK 25(13Q22.1) WILD-TYPE  352  124
        clus
vv       DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE
  FEMALE                           12                            352
  MALE                              7                            124
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 25(13Q22.1) MUTATED                0
  DEL PEAK 25(13Q22.1) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 25(13Q22.1) MUTATED                                              14
  DEL PEAK 25(13Q22.1) WILD-TYPE                                           339
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 25(13Q22.1) MUTATED                                                                        5
  DEL PEAK 25(13Q22.1) WILD-TYPE                                                                     93
                                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                                                                  35
D85V8, 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                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     339
  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"
D85V9, binary
                                cls
clus                               0   1
  DEL PEAK 25(13Q22.1) MUTATED     2  17
  DEL PEAK 25(13Q22.1) WILD-TYPE  12 464
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(13Q22.1) MUTATED      2   17
  DEL PEAK 25(13Q22.1) WILD-TYPE   12  464
     clus
vv    DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE
  NO                             2                             12
  YES                           17                            464
[1] 2 2
[1] FALSE
D85V10, binary
                                cls
clus                               0   1
  DEL PEAK 25(13Q22.1) MUTATED    13   4
  DEL PEAK 25(13Q22.1) WILD-TYPE 404  13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(13Q22.1) MUTATED     13    4
  DEL PEAK 25(13Q22.1) WILD-TYPE  404   13
     clus
vv    DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE
  NO                            13                            404
  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          127                      16  312
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 25(13Q22.1) MUTATED                     0
  DEL PEAK 25(13Q22.1) WILD-TYPE                   1
D85V11, 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)                                       127
  MODERATE/ADVANCED (T4A)                             16
  NONE                                               312
  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 364  48   4  29
D85V12, multiclass
    clus
vv   DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE
  R0                           14                            364
  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"
D85V13, continuous
D85V14, binary
                                cls
clus                               0   1
  DEL PEAK 25(13Q22.1) MUTATED    10   9
  DEL PEAK 25(13Q22.1) WILD-TYPE 214 252
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(13Q22.1) MUTATED     10    9
  DEL PEAK 25(13Q22.1) WILD-TYPE  214  252
            clus
vv           DEL PEAK 25(13Q22.1) MUTATED DEL PEAK 25(13Q22.1) WILD-TYPE
  MULTIFOCAL                           10                            214
  UNIFOCAL                              9                            252
[1] 2 2
[1] FALSE
D85V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 25(13Q22.1) MUTATED                                  0     2
  DEL PEAK 25(13Q22.1) WILD-TYPE                                1    47
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(13Q22.1) MUTATED                           1    11
  DEL PEAK 25(13Q22.1) WILD-TYPE                        25   310
D85V16, multiclass
                                  clus
vv                                 DEL PEAK 25(13Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                      11
                                  clus
vv                                 DEL PEAK 25(13Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        47
  BLACK OR AFRICAN AMERICAN                                    25
  WHITE                                                       310
[1] 4 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 25(13Q22.1) MUTATED     0  14
  DEL PEAK 25(13Q22.1) WILD-TYPE  38 336
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(13Q22.1) MUTATED      0   14
  DEL PEAK 25(13Q22.1) WILD-TYPE   38  336
                        clus
vv                       DEL PEAK 25(13Q22.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           14
                        clus
vv                       DEL PEAK 25(13Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 38
  NOT HISPANIC OR LATINO                            336
[1] 2 2
[1] FALSE

Clustering(86) Variable = DEL PEAK 27(15Q25.3) MUTATION ANALYSIS
D86V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(15Q25.3) MUTATED     9   0
  DEL PEAK 27(15Q25.3) WILD-TYPE 468  14
  DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE 
                             9                            482 
  DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE 
                             0                             14 
$`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        10.98        39.32        54.08        14.73        17.59 
TCGA-EM-A3O9 TCGA-ET-A39N TCGA-FY-A3I5 
        9.24        98.56         1.64 

$`DEL PEAK 27(15Q25.3) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        30.21        22.88        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
       18.97         7.04        16.01        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A13M TCGA-DJ-A13O 
       25.12         4.27         3.22         2.76        17.26        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      137.88         3.39         8.71        25.35        13.41        11.90 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         7.99        11.01       100.01        18.51        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45         8.88         1.02 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
        5.95        10.09         7.99         5.33         8.48        10.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
        1.51         9.60        12.56         8.28         7.69         5.52 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42         8.12         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04         1.15        22.29 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GP TCGA-EL-A3GQ 
       74.30        45.40        33.47       108.36         1.41        30.18 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
      102.84        65.39       124.04        50.37        37.25       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        38.66 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       52.73       139.00       131.15       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        12.16       147.42       130.72       129.57        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      116.91        98.24        41.29        95.38         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN 
       82.82        77.36        78.97        31.50        50.33        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT 
       47.38        52.50        45.53        48.16         7.07        44.65 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 
       45.80        19.30        45.96        37.94        31.04        19.59 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD 
       30.51        33.60        28.73        41.13        37.78        29.95 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       13.32        11.87         8.71        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
       12.36        18.05        19.79        19.46        54.21        57.01 
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        11.74 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.15        14.24        16.44        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
        6.05         2.99        12.30        15.19        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        13.84        19.73        12.07        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        17.46        18.97        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       19.63        13.38         8.35        16.44        16.77        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        16.80        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        11.15         7.33        12.53 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY 
       13.91         7.82        11.51        16.41        15.62        13.51 
TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN 
       12.79        70.65        16.90         9.01         4.83         8.61 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 
        8.38         9.80         5.03        37.87        12.72         0.95 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
       47.47        48.20        29.69        32.35        14.79        12.33 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       14.79        27.09        18.38        29.49        54.05        22.09 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       12.26        16.08        29.19        19.76         2.66        58.22 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O 
       13.74        71.01        80.02        65.36        84.89        61.02 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       58.72        57.11        55.10        59.15        28.24         5.85 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
        4.18         2.43         5.56        24.72        38.30        42.25 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
        2.37         4.50        80.81        69.24        59.87        43.50 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P 
        0.30        17.98        25.32       132.36        24.72         3.22 
TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ 
        7.17         4.80         5.03         2.14         4.01         1.94 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        59.70        31.59        44.25        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A 
      102.90        66.77        81.34        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        46.06         4.08 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD 
        0.89        22.03         0.92        48.10        91.17         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        1.15        17.82         0.99         1.51         0.76         0.03 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
        4.67        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 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
        1.15         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        10.26 
TCGA-IM-A3U3 TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ 
       16.90         9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74 
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         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE 
                          1.64                           0.03 
  DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE 
                         98.56                         158.83 
  DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE 
                        14.730                         16.605 
[1] "1.6 - 98.6 (14.7)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "9200000"
D86V2, 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     276       48       107        2        45
                                vv
clus                             STAGE IVC
  DEL PEAK 27(15Q25.3) MUTATED           0
  DEL PEAK 27(15Q25.3) WILD-TYPE         6
D86V3, multiclass
           clus
vv          DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE
  STAGE I                              4                            276
  STAGE II                             3                             48
  STAGE III                            2                            107
  STAGE IV                             0                              2
  STAGE IVA                            0                             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 27(15Q25.3) MUTATED     1   3   5   0
  DEL PEAK 27(15Q25.3) WILD-TYPE 139 163 160  21
D86V4, multiclass
    clus
vv   DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE
  T1                            1                            139
  T2                            3                            163
  T3                            5                            160
  T4                            0                             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 27(15Q25.3) MUTATED     7   1
  DEL PEAK 27(15Q25.3) WILD-TYPE 216 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q25.3) MUTATED      7    1
  DEL PEAK 27(15Q25.3) WILD-TYPE  216  221
   clus
vv  DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE
  0                            7                            216
  1                            1                            221
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 27(15Q25.3) MUTATED     2   1   6
  DEL PEAK 27(15Q25.3) WILD-TYPE 271   8 206
D86V6, multiclass
    clus
vv   DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE
  M0                            2                            271
  M1                            1                              8
  MX                            6                            206
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(15Q25.3) MUTATED     8   1
  DEL PEAK 27(15Q25.3) WILD-TYPE 356 130
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q25.3) MUTATED      8    1
  DEL PEAK 27(15Q25.3) WILD-TYPE  356  130
        clus
vv       DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE
  FEMALE                            8                            356
  MALE                              1                            130
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 27(15Q25.3) MUTATED                0
  DEL PEAK 27(15Q25.3) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 27(15Q25.3) MUTATED                                               4
  DEL PEAK 27(15Q25.3) WILD-TYPE                                           349
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 27(15Q25.3) MUTATED                                                                        5
  DEL PEAK 27(15Q25.3) WILD-TYPE                                                                     93
                                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                                                                  35
D86V8, 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                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     349
  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"
D86V9, binary
                                cls
clus                               0   1
  DEL PEAK 27(15Q25.3) MUTATED     0   9
  DEL PEAK 27(15Q25.3) WILD-TYPE  14 472
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q25.3) MUTATED      0    9
  DEL PEAK 27(15Q25.3) WILD-TYPE   14  472
     clus
vv    DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE
  NO                             0                             14
  YES                            9                            472
[1] 2 2
[1] FALSE
D86V10, binary
                                cls
clus                               0   1
  DEL PEAK 27(15Q25.3) MUTATED     8   0
  DEL PEAK 27(15Q25.3) WILD-TYPE 409  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q25.3) MUTATED      8    0
  DEL PEAK 27(15Q25.3) WILD-TYPE  409   17
     clus
vv    DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE
  NO                             8                            409
  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          128                      16  321
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 27(15Q25.3) MUTATED                     0
  DEL PEAK 27(15Q25.3) WILD-TYPE                   1
D86V11, 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)                                       128
  MODERATE/ADVANCED (T4A)                             16
  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 27(15Q25.3) MUTATED     8   1   0   0
  DEL PEAK 27(15Q25.3) WILD-TYPE 370  50   4  30
D86V12, multiclass
    clus
vv   DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE
  R0                            8                            370
  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"
D86V13, continuous
D86V14, binary
                                cls
clus                               0   1
  DEL PEAK 27(15Q25.3) MUTATED     4   5
  DEL PEAK 27(15Q25.3) WILD-TYPE 220 256
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q25.3) MUTATED      4    5
  DEL PEAK 27(15Q25.3) WILD-TYPE  220  256
            clus
vv           DEL PEAK 27(15Q25.3) MUTATED DEL PEAK 27(15Q25.3) WILD-TYPE
  MULTIFOCAL                            4                            220
  UNIFOCAL                              5                            256
[1] 2 2
[1] FALSE
D86V15, 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    48
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(15Q25.3) MUTATED                           0     4
  DEL PEAK 27(15Q25.3) WILD-TYPE                        26   317
D86V16, 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                                                        48
  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"
D86V17, binary
                                cls
clus                               0   1
  DEL PEAK 27(15Q25.3) MUTATED     1   4
  DEL PEAK 27(15Q25.3) WILD-TYPE  37 346
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q25.3) MUTATED      1    4
  DEL PEAK 27(15Q25.3) WILD-TYPE   37  346
                        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                            346
[1] 2 2
[1] FALSE

Clustering(87) Variable = DEL PEAK 29(16Q23.3) MUTATION ANALYSIS
D87V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(16Q23.3) MUTATED     5   1
  DEL PEAK 29(16Q23.3) WILD-TYPE 472  13
  DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE 
                             6                            485 
  DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE 
                             1                             13 
$`DEL PEAK 29(16Q23.3) MUTATED`
TCGA-DJ-A3V7 TCGA-EL-A3GP TCGA-EL-A3H5 TCGA-EL-A3MX TCGA-ET-A2N4 TCGA-ET-A3BT 
        9.83         1.41        52.73        57.63         2.66        24.72 

$`DEL PEAK 29(16Q23.3) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        5.52         8.78         8.42         8.12         9.34         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
        9.21         9.44         9.90         8.61        10.09         7.07 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       10.36        12.43        10.85        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        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 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V8 
       25.02        20.22        30.61        14.56        19.20        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
        1.45        74.30        45.40        33.47       108.36        39.32 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66       139.00       131.15       108.66        17.52        52.50 
TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       12.16       147.42       130.72       129.57        32.48       116.91 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
       98.24        41.29        95.38         5.72        66.90        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO 
       77.36        78.97        31.50        50.33        53.06        47.38 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       52.50        45.53        48.16         7.07        44.65        45.80 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       19.30        45.96        37.94        31.04        19.59        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       33.60        28.73        41.13        37.78        29.95        13.32 
TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       11.87         8.71        26.86        18.18        20.91        12.36 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
       18.05        19.79        19.46        54.21        57.01        54.08 
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 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT 
       23.51         6.05         2.99        12.30        15.19        10.49 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        13.84        19.73        17.59        12.07 
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        17.46        18.97 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        19.63        13.38         8.35        16.44 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       16.77        27.95        23.77        16.80        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        11.15 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33        12.53         9.24        13.91         7.82        11.51 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       16.41        15.62        13.51        12.79        70.65        16.90 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        9.01         4.83         8.61         8.38         9.80         5.03 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       37.87        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       29.49        54.05        22.09        12.26        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
       19.76        58.22        13.74        71.01        80.02        65.36 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       84.89        98.56        61.02        58.72        57.11        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       59.15        28.24         5.85         4.18         2.43         5.56 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       38.30        42.25         2.37         4.50        80.81        69.24 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       59.87        43.50         0.30        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T 
       24.72         3.22         7.17         4.80         5.03         2.14 
TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        4.01         1.94        73.74        59.70        31.59        44.25 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 
       24.69        68.22       102.90        66.77        81.34        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 
       46.06         4.08         0.89        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
       91.17         1.25         1.15        17.82         1.64         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
        1.51         0.76         0.03         4.67        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         6.87         4.14         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
        4.54         0.89         1.35         1.15         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        10.26        16.90         9.80         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        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        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        12.43         6.74        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         0.72 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       16.64        32.45         8.71        10.98         5.19 

  DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE 
                          1.41                           0.03 
  DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE 
                         57.63                         158.83 
  DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE 
                        17.275                         16.570 
[1] "1.4 - 57.6 (17.3)"  "0.0 - 158.8 (16.6)"
[1] "hr=" "5.3"
D87V2, 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     280       51       106        2        43
                                vv
clus                             STAGE IVC
  DEL PEAK 29(16Q23.3) MUTATED           1
  DEL PEAK 29(16Q23.3) WILD-TYPE         5
D87V3, multiclass
           clus
vv          DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE
  STAGE I                              0                            280
  STAGE II                             0                             51
  STAGE III                            3                            106
  STAGE IV                             0                              2
  STAGE IVA                            2                             43
  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 140 165 162  19
D87V4, multiclass
    clus
vv   DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE
  T1                            0                            140
  T2                            1                            165
  T3                            3                            162
  T4                            2                             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"
D87V5, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q23.3) MUTATED     2   4
  DEL PEAK 29(16Q23.3) WILD-TYPE 221 218
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q23.3) MUTATED      2    4
  DEL PEAK 29(16Q23.3) WILD-TYPE  221  218
   clus
vv  DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE
  0                            2                            221
  1                            4                            218
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 29(16Q23.3) MUTATED     3   1   2
  DEL PEAK 29(16Q23.3) WILD-TYPE 270   8 210
D87V6, multiclass
    clus
vv   DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE
  M0                            3                            270
  M1                            1                              8
  MX                            2                            210
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V7, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q23.3) MUTATED     5   1
  DEL PEAK 29(16Q23.3) WILD-TYPE 359 130
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q23.3) MUTATED      5    1
  DEL PEAK 29(16Q23.3) WILD-TYPE  359  130
        clus
vv       DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE
  FEMALE                            5                            359
  MALE                              1                            130
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 29(16Q23.3) MUTATED                0
  DEL PEAK 29(16Q23.3) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 29(16Q23.3) MUTATED                                               3
  DEL PEAK 29(16Q23.3) WILD-TYPE                                           350
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 29(16Q23.3) MUTATED                                                                        1
  DEL PEAK 29(16Q23.3) WILD-TYPE                                                                     97
                                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                                                                  33
D87V8, 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                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             97
  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"
D87V9, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q23.3) MUTATED     0   6
  DEL PEAK 29(16Q23.3) WILD-TYPE  14 475
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q23.3) MUTATED      0    6
  DEL PEAK 29(16Q23.3) WILD-TYPE   14  475
     clus
vv    DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE
  NO                             0                             14
  YES                            6                            475
[1] 2 2
[1] FALSE
D87V10, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q23.3) MUTATED     5   1
  DEL PEAK 29(16Q23.3) WILD-TYPE 412  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q23.3) MUTATED      5    1
  DEL PEAK 29(16Q23.3) WILD-TYPE  412   16
     clus
vv    DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE
  NO                             5                            412
  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          127                      15  326
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 29(16Q23.3) MUTATED                     0
  DEL PEAK 29(16Q23.3) WILD-TYPE                   1
D87V11, 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)                                       127
  MODERATE/ADVANCED (T4A)                             15
  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 29(16Q23.3) MUTATED     3   1   0   2
  DEL PEAK 29(16Q23.3) WILD-TYPE 375  50   4  28
D87V12, multiclass
    clus
vv   DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE
  R0                            3                            375
  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"
D87V13, continuous
D87V14, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q23.3) MUTATED     3   3
  DEL PEAK 29(16Q23.3) WILD-TYPE 221 258
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q23.3) MUTATED      3    3
  DEL PEAK 29(16Q23.3) WILD-TYPE  221  258
            clus
vv           DEL PEAK 29(16Q23.3) MUTATED DEL PEAK 29(16Q23.3) WILD-TYPE
  MULTIFOCAL                            3                            221
  UNIFOCAL                              3                            258
[1] 2 2
[1] FALSE
D87V15, 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    49
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(16Q23.3) MUTATED                           1     5
  DEL PEAK 29(16Q23.3) WILD-TYPE                        25   316
D87V16, 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                                                        49
  BLACK OR AFRICAN AMERICAN                                    25
  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"
D87V17, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q23.3) MUTATED     0   6
  DEL PEAK 29(16Q23.3) WILD-TYPE  38 344
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q23.3) MUTATED      0    6
  DEL PEAK 29(16Q23.3) WILD-TYPE   38  344
                        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                            344
[1] 2 2
[1] FALSE

Clustering(88) Variable = DEL PEAK 30(17P13.1) MUTATION ANALYSIS
D88V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(17P13.1) MUTATED     7   0
  DEL PEAK 30(17P13.1) WILD-TYPE 470  14
  DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE 
                             7                            484 
  DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE 
                             0                             14 
$`DEL PEAK 30(17P13.1) MUTATED`
TCGA-E8-A432 TCGA-EL-A3D5 TCGA-EM-A1YE TCGA-EM-A3O9 TCGA-EM-A3OB TCGA-FE-A22Z 
       14.43        33.47        54.08         9.24         7.82        73.74 
TCGA-FE-A238 
       39.95 

$`DEL PEAK 30(17P13.1) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        5.52         8.78         8.42         8.12         9.34         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
        9.21         9.44         9.90         8.61        10.09         7.07 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       10.36        12.43        10.85        15.88        15.09        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       12.49        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 
       24.23        17.69        43.00        11.34        21.37        12.76 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 
       25.02        20.22        30.61        14.56        19.20         9.83 
TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE 
       21.27        20.48        11.93        22.92        21.01        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76         8.32        17.36        17.23        27.62        18.21 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       10.78        10.98        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
        1.15        22.29        19.59        13.61        14.27        13.81 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.07        14.27         3.02        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
        1.45        74.30        45.40       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        12.36        18.05        19.79        19.46        54.21 
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        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       10.49        13.15        22.16        13.84        19.73        17.59 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       12.07        17.59        17.46        17.29        14.60        17.46 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       18.97        15.68        14.14        19.63        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       16.44        16.77        27.95        23.77        16.80        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-A3ST TCGA-EM-A3SU 
       11.15         7.33        12.53        13.91        11.51        16.41 
TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK 
       15.62        13.51        12.79        70.65        16.90         9.01 
TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU 
        4.83         8.61         8.38         9.80         5.03        37.87 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       12.72         0.95        47.47        48.20        29.69        32.35 
TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R 
       14.79        12.33        14.79        27.09        18.38        29.49 
TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       54.05        22.09        12.26        16.08        29.19        19.76 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        58.22        13.74        71.01        80.02        65.36 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       84.89        98.56        61.02        58.72        57.11        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       59.15        28.24         5.85         4.18         2.43         5.56 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       24.72        38.30        42.25         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       69.24        59.87        43.50         0.30        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        2.14         4.01         1.94        59.70        31.59        44.25 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A239 
       24.69        68.22       102.90        66.77        81.34        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        46.06 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.08         0.89        22.03         0.92        48.10        91.17 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON 
        1.25         1.15        17.82         1.64         0.99         1.51 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        0.76         0.03         4.67        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         6.87         4.14         6.58         4.54 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
        0.89         1.35         1.15         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        10.26        16.90         9.80         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        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        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       12.43         6.74        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         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

  DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE 
                          7.82                           0.03 
  DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE 
                         73.74                         158.83 
  DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE 
                         33.47                          16.57 
[1] "7.8 - 73.7 (33.5)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "9200000"
D88V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 30(17P13.1) MUTATED         4        2         0        0         1
  DEL PEAK 30(17P13.1) WILD-TYPE     276       49       109        2        44
                                vv
clus                             STAGE IVC
  DEL PEAK 30(17P13.1) MUTATED           0
  DEL PEAK 30(17P13.1) WILD-TYPE         6
D88V3, multiclass
           clus
vv          DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE
  STAGE I                              4                            276
  STAGE II                             2                             49
  STAGE III                            0                            109
  STAGE IV                             0                              2
  STAGE IVA                            1                             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   1
  DEL PEAK 30(17P13.1) WILD-TYPE 140 163 162  20
D88V4, multiclass
    clus
vv   DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE
  T1                            0                            140
  T2                            3                            163
  T3                            3                            162
  T4                            1                             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"
D88V5, binary
                                cls
clus                               0   1
  DEL PEAK 30(17P13.1) MUTATED     5   2
  DEL PEAK 30(17P13.1) WILD-TYPE 218 220
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(17P13.1) MUTATED      5    2
  DEL PEAK 30(17P13.1) WILD-TYPE  218  220
   clus
vv  DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE
  0                            5                            218
  1                            2                            220
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 30(17P13.1) MUTATED     2   0   5
  DEL PEAK 30(17P13.1) WILD-TYPE 271   9 207
D88V6, multiclass
    clus
vv   DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE
  M0                            2                            271
  M1                            0                              9
  MX                            5                            207
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(17P13.1) MUTATED     6   1
  DEL PEAK 30(17P13.1) WILD-TYPE 358 130
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(17P13.1) MUTATED      6    1
  DEL PEAK 30(17P13.1) WILD-TYPE  358  130
        clus
vv       DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE
  FEMALE                            6                            358
  MALE                              1                            130
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 30(17P13.1) MUTATED                0
  DEL PEAK 30(17P13.1) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 30(17P13.1) MUTATED                                               3
  DEL PEAK 30(17P13.1) WILD-TYPE                                           350
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 30(17P13.1) MUTATED                                                                        4
  DEL PEAK 30(17P13.1) WILD-TYPE                                                                     94
                                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                                                                  35
D88V8, multiclass
                                                                        clus
vv                                                                       DEL PEAK 30(17P13.1) 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 30(17P13.1) WILD-TYPE
  OTHER  SPECIFY                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     350
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             94
  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"
D88V9, binary
                                cls
clus                               0   1
  DEL PEAK 30(17P13.1) MUTATED     2   5
  DEL PEAK 30(17P13.1) WILD-TYPE  12 476
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(17P13.1) MUTATED      2    5
  DEL PEAK 30(17P13.1) WILD-TYPE   12  476
     clus
vv    DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE
  NO                             2                             12
  YES                            5                            476
[1] 2 2
[1] FALSE
D88V10, binary
                                cls
clus                               0   1
  DEL PEAK 30(17P13.1) MUTATED     6   1
  DEL PEAK 30(17P13.1) WILD-TYPE 411  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(17P13.1) MUTATED      6    1
  DEL PEAK 30(17P13.1) WILD-TYPE  411   16
     clus
vv    DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE
  NO                             6                            411
  YES                            1                             16
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 30(17P13.1) MUTATED              2                       1    4
  DEL PEAK 30(17P13.1) WILD-TYPE          128                      15  324
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 30(17P13.1) MUTATED                     0
  DEL PEAK 30(17P13.1) WILD-TYPE                   1
D88V11, multiclass
                         clus
vv                        DEL PEAK 30(17P13.1) MUTATED
  MINIMAL (T3)                                       2
  MODERATE/ADVANCED (T4A)                            1
  NONE                                               4
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK 30(17P13.1) WILD-TYPE
  MINIMAL (T3)                                       128
  MODERATE/ADVANCED (T4A)                             15
  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 30(17P13.1) MUTATED     6   1   0   0
  DEL PEAK 30(17P13.1) WILD-TYPE 372  50   4  30
D88V12, multiclass
    clus
vv   DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE
  R0                            6                            372
  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"
D88V13, continuous
D88V14, binary
                                cls
clus                               0   1
  DEL PEAK 30(17P13.1) MUTATED     3   4
  DEL PEAK 30(17P13.1) WILD-TYPE 221 257
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(17P13.1) MUTATED      3    4
  DEL PEAK 30(17P13.1) WILD-TYPE  221  257
            clus
vv           DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE
  MULTIFOCAL                            3                            221
  UNIFOCAL                              4                            257
[1] 2 2
[1] FALSE
D88V15, 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    48
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(17P13.1) MUTATED                           0     3
  DEL PEAK 30(17P13.1) WILD-TYPE                        26   318
D88V16, 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                                                        48
  BLACK OR AFRICAN AMERICAN                                    26
  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"
D88V17, binary
                                cls
clus                               0   1
  DEL PEAK 30(17P13.1) MUTATED     0   4
  DEL PEAK 30(17P13.1) WILD-TYPE  38 346
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(17P13.1) MUTATED      0    4
  DEL PEAK 30(17P13.1) WILD-TYPE   38  346
                        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                            346
[1] 2 2
[1] FALSE

Clustering(89) Variable = DEL PEAK 31(18Q12.3) MUTATION ANALYSIS
D89V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(18Q12.3) MUTATED     4   0
  DEL PEAK 31(18Q12.3) WILD-TYPE 473  14
  DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE 
                             4                            487 
  DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE 
                             0                             14 
$`DEL PEAK 31(18Q12.3) MUTATED`
TCGA-DJ-A2Q0 TCGA-EM-A1YE TCGA-EM-A3SY TCGA-ET-A3BP 
        8.12        54.08        13.51         4.18 

$`DEL PEAK 31(18Q12.3) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 
       17.69        23.34        20.71        20.58         4.83         8.09 
TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X 
        4.87        21.04         2.79         5.10        11.31        17.52 
TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
        1.22        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        15.48        23.31 
TCGA-BJ-A3PU TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       18.64         5.75         6.48         0.03         3.45         6.35 
TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        7.82         6.18         5.06         8.98         4.93         5.98 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 
        0.53         0.10         0.20         0.23        11.38        10.68 
TCGA-CE-A483 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
        0.10         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
        5.98        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-A13M 
       30.02        25.12         4.27         3.22         2.76        17.26 
TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U 
       14.07       137.88         3.39         8.71        25.35        13.41 
TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       11.90        14.60         7.99        11.01       100.01        18.51 
TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
       13.12         7.99        14.96         7.20         1.45         8.88 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ 
        1.02         5.95        10.09         7.99         5.33         8.48 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       10.45         1.51         9.60        12.56         8.28         7.69 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        5.52         8.78         8.42         9.34         6.77         9.21 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.44         9.90         8.61        10.09         7.07        10.36 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN 
       12.43        10.85        15.88        15.09        31.04        12.49 
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        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ 
        8.32        17.36        17.23        27.62        18.21        10.78 
TCGA-DJ-A4UR TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       10.98        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04         1.15 
TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 
       22.29        19.59        13.61        14.27        13.81        14.07 
TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 
       14.27         3.02        14.43        14.70        14.10        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
        7.69        20.68        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
        1.45        74.30        45.40        33.47       108.36        39.32 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        30.18       102.84        65.39       124.04        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       37.25       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        38.66        52.73       139.00       131.15       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        12.16       147.42       130.72 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       116.91        98.24        41.29        95.38 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK 
        5.72        66.90        82.82        77.36        78.97        31.50 
TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       50.33        53.06        47.38        52.50        45.53        48.16 
TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
        7.07        44.65        45.80        19.30        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 
       31.04        19.59        30.51        33.60        28.73        41.13 
TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       37.78        29.95        13.32        11.87         8.71        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        12.36        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       54.21        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        11.74        11.15        14.24        16.44 
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-A2CS TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       15.19        10.49        13.15        22.16        13.84        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       17.59        12.07        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 
       17.46        18.97        15.68        14.14        19.63        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        16.44        16.77        27.95        23.77        16.80 
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        11.15         7.33        12.53         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FF 
        7.82        11.51        16.41        15.62        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
       80.02        65.36        84.89        98.56        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BQ 
       57.11        55.10        59.15        28.24         5.85         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R 
       25.32       132.36        24.72         3.22         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        5.03         2.14         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        24.69        68.22       102.90        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       81.34        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        46.06         4.08         0.89        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10        91.17         1.25         1.15        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        1.64         0.99         1.51         0.76         0.03         4.67 
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         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74        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         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE 
                          4.18                           0.03 
  DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE 
                         54.08                         158.83 
  DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE 
                        10.815                         16.640 
[1] "4.2 - 54.1 (10.8)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "3300000"
D89V2, 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     278       49       109        2        45
                                vv
clus                             STAGE IVC
  DEL PEAK 31(18Q12.3) MUTATED           0
  DEL PEAK 31(18Q12.3) WILD-TYPE         6
D89V3, multiclass
           clus
vv          DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE
  STAGE I                              2                            278
  STAGE II                             2                             49
  STAGE III                            0                            109
  STAGE IV                             0                              2
  STAGE IVA                            0                             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 31(18Q12.3) MUTATED     1   3   0   0
  DEL PEAK 31(18Q12.3) WILD-TYPE 139 163 165  21
D89V4, multiclass
    clus
vv   DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE
  T1                            1                            139
  T2                            3                            163
  T3                            0                            165
  T4                            0                             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"
D89V5, binary
                                cls
clus                               0   1
  DEL PEAK 31(18Q12.3) MUTATED     2   1
  DEL PEAK 31(18Q12.3) WILD-TYPE 221 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(18Q12.3) MUTATED      2    1
  DEL PEAK 31(18Q12.3) WILD-TYPE  221  221
   clus
vv  DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE
  0                            2                            221
  1                            1                            221
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 31(18Q12.3) MUTATED     1   0   3
  DEL PEAK 31(18Q12.3) WILD-TYPE 272   9 209
D89V6, multiclass
    clus
vv   DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE
  M0                            1                            272
  M1                            0                              9
  MX                            3                            209
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V7, binary
                                cls
clus                               0   1
  DEL PEAK 31(18Q12.3) MUTATED     3   1
  DEL PEAK 31(18Q12.3) WILD-TYPE 361 130
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(18Q12.3) MUTATED      3    1
  DEL PEAK 31(18Q12.3) WILD-TYPE  361  130
        clus
vv       DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE
  FEMALE                            3                            361
  MALE                              1                            130
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 31(18Q12.3) MUTATED                0
  DEL PEAK 31(18Q12.3) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 31(18Q12.3) MUTATED                                               2
  DEL PEAK 31(18Q12.3) WILD-TYPE                                           351
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 31(18Q12.3) MUTATED                                                                        2
  DEL PEAK 31(18Q12.3) WILD-TYPE                                                                     96
                                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                                                                  35
D89V8, 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                                                                                      9
  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"
D89V9, binary
                                cls
clus                               0   1
  DEL PEAK 31(18Q12.3) MUTATED     0   4
  DEL PEAK 31(18Q12.3) WILD-TYPE  14 477
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(18Q12.3) MUTATED      0    4
  DEL PEAK 31(18Q12.3) WILD-TYPE   14  477
     clus
vv    DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE
  NO                             0                             14
  YES                            4                            477
[1] 2 2
[1] FALSE
D89V10, binary
                                cls
clus                               0   1
  DEL PEAK 31(18Q12.3) MUTATED     4   0
  DEL PEAK 31(18Q12.3) WILD-TYPE 413  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(18Q12.3) MUTATED      4    0
  DEL PEAK 31(18Q12.3) WILD-TYPE  413   17
     clus
vv    DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE
  NO                             4                            413
  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          130                      16  324
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 31(18Q12.3) MUTATED                     0
  DEL PEAK 31(18Q12.3) WILD-TYPE                   1
D89V11, 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)                                       130
  MODERATE/ADVANCED (T4A)                             16
  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 31(18Q12.3) MUTATED     4   0   0   0
  DEL PEAK 31(18Q12.3) WILD-TYPE 374  51   4  30
D89V12, multiclass
    clus
vv   DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE
  R0                            4                            374
  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"
D89V13, continuous
D89V14, binary
                                cls
clus                               0   1
  DEL PEAK 31(18Q12.3) MUTATED     1   3
  DEL PEAK 31(18Q12.3) WILD-TYPE 223 258
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(18Q12.3) MUTATED      1    3
  DEL PEAK 31(18Q12.3) WILD-TYPE  223  258
            clus
vv           DEL PEAK 31(18Q12.3) MUTATED DEL PEAK 31(18Q12.3) WILD-TYPE
  MULTIFOCAL                            1                            223
  UNIFOCAL                              3                            258
[1] 2 2
[1] FALSE
D89V15, 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    49
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(18Q12.3) MUTATED                           0     1
  DEL PEAK 31(18Q12.3) WILD-TYPE                        26   320
D89V16, 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 
                             1                            396 
                    TCGA-BJ-A0YZ                     TCGA-BJ-A0Z2 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A0Z3                     TCGA-BJ-A0Z5 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A0Z9                     TCGA-BJ-A0ZA 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A0ZB                     TCGA-BJ-A0ZC 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A0ZE                     TCGA-BJ-A0ZG 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A0ZH                     TCGA-BJ-A0ZJ 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A18Y                     TCGA-BJ-A18Z 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A190                     TCGA-BJ-A191 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A192                     TCGA-BJ-A28R 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A28S                     TCGA-BJ-A28T 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A28V                     TCGA-BJ-A28W 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A28X                     TCGA-BJ-A28Z 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A290                     TCGA-BJ-A291 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A2N7                     TCGA-BJ-A2N8 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A2N9                     TCGA-BJ-A2NA 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A2P4                     TCGA-BJ-A3EZ 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A3F0                     TCGA-BJ-A3PR 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A3PT                     TCGA-BJ-A3PU 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A45C                     TCGA-BJ-A45D 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A45E                     TCGA-BJ-A45F 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A45G                     TCGA-BJ-A45H 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A45I                     TCGA-BJ-A45J 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A45K                     TCGA-BJ-A4O8 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-BJ-A4O9                     TCGA-CE-A13K 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-CE-A27D                     TCGA-CE-A3MD 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-CE-A3ME                     TCGA-CE-A481 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-CE-A482                     TCGA-CE-A483 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-CE-A484                     TCGA-CE-A485 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DE-A0XZ                     TCGA-DE-A0Y2 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DE-A0Y3                     TCGA-DE-A2OL 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DE-A3KN                     TCGA-DE-A4M8 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DE-A4M9                     TCGA-DE-A4MA 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DE-A4MB                     TCGA-DE-A4MC 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DE-A4MD                     TCGA-DE-A69J 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DE-A69K                     TCGA-DE-A7U5 
"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-A2PT 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A2PU                     TCGA-DJ-A2PV 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A2PW                     TCGA-DJ-A2PX 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A2PY                     TCGA-DJ-A2PZ 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A2Q1                     TCGA-DJ-A2Q2 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A2Q3                     TCGA-DJ-A2Q4 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A2Q5                     TCGA-DJ-A2Q6 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A2Q7                     TCGA-DJ-A2Q9 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A2QA                     TCGA-DJ-A2QB 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A3UK                     TCGA-DJ-A3UM 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A3UN                     TCGA-DJ-A3UO 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A3UQ                     TCGA-DJ-A3UR 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A3US                     TCGA-DJ-A3UT 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A3UU                     TCGA-DJ-A3UW 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A3UX                     TCGA-DJ-A3UY 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A3UZ                     TCGA-DJ-A3V2 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A3V3                     TCGA-DJ-A3V4 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A3V5                     TCGA-DJ-A3V7 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A3V8                     TCGA-DJ-A3V9 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A3VD                     TCGA-DJ-A3VE 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A3VF                     TCGA-DJ-A3VG 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A3VJ                     TCGA-DJ-A3VL 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-DJ-A3VM                     TCGA-DJ-A4UL 
"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-A2JQ 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-E8-A3X7                     TCGA-E8-A413 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-E8-A414                     TCGA-E8-A415 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-E8-A416                     TCGA-E8-A417 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-E8-A418                     TCGA-E8-A419 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-E8-A432                     TCGA-E8-A433 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-E8-A434                     TCGA-E8-A436 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-E8-A437                     TCGA-E8-A438 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-E8-A44K                     TCGA-E8-A44M 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3CL                     TCGA-EL-A3CM 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3CN                     TCGA-EL-A3CO 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3CP                     TCGA-EL-A3CR 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3CS                     TCGA-EL-A3CT 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3CU                     TCGA-EL-A3CV 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3CW                     TCGA-EL-A3CX 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3CY                     TCGA-EL-A3CZ 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3D0                     TCGA-EL-A3D1 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3D4                     TCGA-EL-A3D5 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3D6                     TCGA-EL-A3GO 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3GP                     TCGA-EL-A3GQ 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3GR                     TCGA-EL-A3GS 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3GU                     TCGA-EL-A3GV 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3GW                     TCGA-EL-A3GX 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3GY                     TCGA-EL-A3GZ 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3H1                     TCGA-EL-A3H2 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3H3                     TCGA-EL-A3H4 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3H5                     TCGA-EL-A3H7 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3H8                     TCGA-EL-A3MW 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3MX                     TCGA-EL-A3MY 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3MZ                     TCGA-EL-A3N2 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3N3                     TCGA-EL-A3T0 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3T1                     TCGA-EL-A3T2 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3T3                     TCGA-EL-A3T6 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3T7                     TCGA-EL-A3T8 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3T9                     TCGA-EL-A3TA 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3TB                     TCGA-EL-A3ZG 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3ZH                     TCGA-EL-A3ZK 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3ZL                     TCGA-EL-A3ZN 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3ZO                     TCGA-EL-A3ZP 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3ZQ                     TCGA-EL-A3ZR 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A3ZS                     TCGA-EL-A3ZT 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A4JV                     TCGA-EL-A4JW 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A4JX                     TCGA-EL-A4JZ 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A4K0                     TCGA-EL-A4K1 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A4K2                     TCGA-EL-A4K4 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A4K6                     TCGA-EL-A4K7 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A4K9                     TCGA-EL-A4KD 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A4KG                     TCGA-EL-A4KH 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-EL-A4KI                     TCGA-ET-A25G 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A25I                     TCGA-ET-A25J 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A25K                     TCGA-ET-A25L 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A25M                     TCGA-ET-A25N 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A25O                     TCGA-ET-A25P 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A25R                     TCGA-ET-A2MX 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A2MY                     TCGA-ET-A2MZ 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A2N0                     TCGA-ET-A2N1 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A2N3                     TCGA-ET-A2N4 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A2N5                     TCGA-ET-A39I 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A39J                     TCGA-ET-A39K 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A39M                     TCGA-ET-A39N 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A39O                     TCGA-ET-A39P 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A39R                     TCGA-ET-A39S 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A39T                     TCGA-ET-A3BN 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A3BO                     TCGA-ET-A3BQ 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A3BS                     TCGA-ET-A3BT 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A3BU                     TCGA-ET-A3BV 
"DEL PEAK 31(18Q12.3) WILD-TYPE" "DEL PEAK 31(18Q12.3) WILD-TYPE" 
                    TCGA-ET-A3BW                     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" 
D89V17, binary
                                cls
clus                               0   1
  DEL PEAK 31(18Q12.3) MUTATED     1   1
  DEL PEAK 31(18Q12.3) WILD-TYPE  37 349
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(18Q12.3) MUTATED      1    1
  DEL PEAK 31(18Q12.3) WILD-TYPE   37  349
                        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                            349
[1] 2 2
[1] FALSE

Clustering(90) Variable = DEL PEAK 32(19P13.2) MUTATION ANALYSIS
D90V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 32(19P13.2) MUTATED     5   1
  DEL PEAK 32(19P13.2) WILD-TYPE 472  13
  DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE 
                             6                            485 
  DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE 
                             1                             13 
$`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         8.09        33.47        33.50        98.56        17.06 

$`DEL PEAK 32(19P13.2) WILD-TYPE`
TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       13.78        18.21        16.34        14.73         8.25        18.87 
TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ 
        4.01        11.57        16.73         7.56        15.12        17.69 
TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A28R TCGA-BJ-A28S 
       23.34        20.71        20.58         4.83         4.87        21.04 
TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 
        2.79         5.10        11.31        17.52         1.22        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        15.48        23.31        18.64         5.75 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
        6.48         0.03         3.45         6.35         7.82         6.18 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
        5.06         8.98         4.93         5.98         0.53         0.10 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
        0.20         0.23        11.38        10.68         0.10         0.39 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.10        20.22        15.42        36.46         5.98        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-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
        4.27         3.22         2.76        17.26        14.07       137.88 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
        3.39         8.71        25.35        13.41        11.90        14.60 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        7.99        11.01       100.01        18.51        13.12         7.99 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96         7.20         1.45         8.88         1.02         5.95 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS 
       10.09         7.99         5.33         8.48        10.45         1.51 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY 
        9.60        12.56         8.28         7.69         5.52         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.42         8.12         9.34         6.77         9.21         9.44 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
        9.90         8.61        10.09         7.07        10.36        12.43 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        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        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04         1.15        22.29 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       74.30        45.40       108.36        39.32         1.41        30.18 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
      102.84        65.39       124.04        50.37        37.25       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        38.66        52.73 
TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ 
      139.00       131.15       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 
       12.16       147.42       130.72       129.57        32.48       116.91 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
       98.24        41.29        95.38         5.72        66.90        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO 
       77.36        78.97        31.50        50.33        53.06        47.38 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       52.50        45.53        48.16         7.07        44.65        45.80 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       19.30        45.96        37.94        31.04        19.59        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       33.60        28.73        41.13        37.78        29.95        13.32 
TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       11.87         8.71        26.86        18.18        20.91        12.36 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
       18.05        19.79        19.46        54.21        57.01        54.08 
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 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT 
       23.51         6.05         2.99        12.30        15.19        10.49 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        13.84        19.73        17.59        12.07 
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        17.46        18.97 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        19.63        13.38         8.35        16.44 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       16.77        27.95        23.77        16.80        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        11.15 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33        12.53         9.24        13.91         7.82        11.51 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       16.41        15.62        13.51        12.79        70.65        16.90 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        9.01         4.83         8.61         8.38         9.80         5.03 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       37.87        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       29.49        54.05        22.09        12.26        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        61.02        58.72        57.11        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       59.15        28.24         5.85         4.18         2.43         5.56 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       24.72        38.30        42.25         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       69.24        59.87        43.50         0.30        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       102.90        66.77        81.34 
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        46.06         4.08         0.89        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 
       48.10        91.17         1.25         1.15        17.82         1.64 
TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
        0.99         1.51         0.76         0.03         4.67        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         6.87         4.14         6.58 
TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 
        4.54         0.89         1.35         1.15         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        10.26        16.90         9.80         9.63 
TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
        2.96         8.65        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        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
        6.02        12.43         6.74        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         0.72 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       16.64        32.45         8.71        10.98         5.19 

  DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE 
                          8.09                           0.03 
  DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE 
                         98.56                         158.83 
  DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE 
                         29.13                          16.44 
[1] "8.1 - 98.6 (29.1)"  "0.0 - 158.8 (16.4)"
[1] "hr=" "4.4"
D90V2, 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     276       49       108        2        45
                                vv
clus                             STAGE IVC
  DEL PEAK 32(19P13.2) MUTATED           0
  DEL PEAK 32(19P13.2) WILD-TYPE         6
D90V3, multiclass
           clus
vv          DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE
  STAGE I                              4                            276
  STAGE II                             2                             49
  STAGE III                            1                            108
  STAGE IV                             0                              2
  STAGE IVA                            0                             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 32(19P13.2) MUTATED     2   2   3   0
  DEL PEAK 32(19P13.2) WILD-TYPE 138 164 162  21
D90V4, multiclass
    clus
vv   DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE
  T1                            2                            138
  T2                            2                            164
  T3                            3                            162
  T4                            0                             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"
D90V5, binary
                                cls
clus                               0   1
  DEL PEAK 32(19P13.2) MUTATED     2   1
  DEL PEAK 32(19P13.2) WILD-TYPE 221 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(19P13.2) MUTATED      2    1
  DEL PEAK 32(19P13.2) WILD-TYPE  221  221
   clus
vv  DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE
  0                            2                            221
  1                            1                            221
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 32(19P13.2) MUTATED     3   0   4
  DEL PEAK 32(19P13.2) WILD-TYPE 270   9 208
D90V6, multiclass
    clus
vv   DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE
  M0                            3                            270
  M1                            0                              9
  MX                            4                            208
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V7, binary
                                cls
clus                               0   1
  DEL PEAK 32(19P13.2) MUTATED     4   3
  DEL PEAK 32(19P13.2) WILD-TYPE 360 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(19P13.2) MUTATED      4    3
  DEL PEAK 32(19P13.2) WILD-TYPE  360  128
        clus
vv       DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE
  FEMALE                            4                            360
  MALE                              3                            128
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 32(19P13.2) MUTATED                0
  DEL PEAK 32(19P13.2) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 32(19P13.2) MUTATED                                               6
  DEL PEAK 32(19P13.2) WILD-TYPE                                           347
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 32(19P13.2) MUTATED                                                                        1
  DEL PEAK 32(19P13.2) WILD-TYPE                                                                     97
                                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                                                                  35
D90V8, 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                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     347
  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"
D90V9, binary
                                cls
clus                               0   1
  DEL PEAK 32(19P13.2) MUTATED     0   7
  DEL PEAK 32(19P13.2) WILD-TYPE  14 474
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(19P13.2) MUTATED      0    7
  DEL PEAK 32(19P13.2) WILD-TYPE   14  474
     clus
vv    DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE
  NO                             0                             14
  YES                            7                            474
[1] 2 2
[1] FALSE
D90V10, binary
                                cls
clus                               0   1
  DEL PEAK 32(19P13.2) MUTATED     5   2
  DEL PEAK 32(19P13.2) WILD-TYPE 412  15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(19P13.2) MUTATED      5    2
  DEL PEAK 32(19P13.2) WILD-TYPE  412   15
     clus
vv    DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE
  NO                             5                            412
  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          128                      16  323
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 32(19P13.2) MUTATED                     0
  DEL PEAK 32(19P13.2) WILD-TYPE                   1
D90V11, 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)                                       128
  MODERATE/ADVANCED (T4A)                             16
  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 32(19P13.2) MUTATED     4   2   0   1
  DEL PEAK 32(19P13.2) WILD-TYPE 374  49   4  29
D90V12, multiclass
    clus
vv   DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE
  R0                            4                            374
  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"
D90V13, 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                            390 
                    TCGA-BJ-A0Z0                     TCGA-BJ-A0Z3 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A0Z9                     TCGA-BJ-A0ZA 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A0ZB                     TCGA-BJ-A0ZH 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A0ZJ                     TCGA-BJ-A18Y 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A18Z                     TCGA-BJ-A190 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A191                     TCGA-BJ-A28R 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A28T                     TCGA-BJ-A28W 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A28X                     TCGA-BJ-A28Z 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A290                     TCGA-BJ-A291 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A2N8                     TCGA-BJ-A2N9 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A2NA                     TCGA-BJ-A3EZ 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A3PR                     TCGA-BJ-A3PU 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A45C                     TCGA-BJ-A45D 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A45E                     TCGA-BJ-A45G 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A45I                     TCGA-BJ-A45J 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A45K                     TCGA-BJ-A4O8 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-BJ-A4O9                     TCGA-CE-A13K 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-CE-A3MD                     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-A13P                     TCGA-DJ-A13R 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A13T                     TCGA-DJ-A13U 
"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-A3VJ                     TCGA-DJ-A3VL 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A4UL                     TCGA-DJ-A4UQ 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A4UR                     TCGA-DJ-A4UW 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DJ-A4V2                     TCGA-DJ-A4V5 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-DO-A1K0                     TCGA-DO-A2HM 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-E3-A3DY                     TCGA-E3-A3DZ 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-E3-A3E0                     TCGA-E3-A3E1 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-E3-A3E2                     TCGA-E3-A3E3 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-E3-A3E5                     TCGA-E8-A242 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-E8-A2EA                     TCGA-E8-A2JQ 
"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-A3ZN 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3ZO                     TCGA-EL-A3ZP 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A3ZS                     TCGA-EL-A4JV 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A4JW                     TCGA-EL-A4JX 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A4JZ                     TCGA-EL-A4K0 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A4K1                     TCGA-EL-A4K2 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A4K4                     TCGA-EL-A4K6 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A4K7                     TCGA-EL-A4KD 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EL-A4KG                     TCGA-EL-A4KI 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A1CS                     TCGA-EM-A1CT 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A1CU                     TCGA-EM-A1CV 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A1CW                     TCGA-EM-A1YA 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A1YB                     TCGA-EM-A1YC 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A1YD                     TCGA-EM-A1YE 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A22I                     TCGA-EM-A22J 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A22K                     TCGA-EM-A22L 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A22M                     TCGA-EM-A22N 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A22O                     TCGA-EM-A22P 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A22Q                     TCGA-EM-A2CK 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A2CN                     TCGA-EM-A2CP 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A2CQ                     TCGA-EM-A2CS 
"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-A2OW 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A2OX                     TCGA-EM-A2OY 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A2OZ                     TCGA-EM-A2P0 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A2P1                     TCGA-EM-A2P2 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A2P3                     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-A3FL                     TCGA-EM-A3FM 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A3FN                     TCGA-EM-A3FO 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A3FP                     TCGA-EM-A3FQ 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A3FR                     TCGA-EM-A3O3 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A3O7                     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-A3SY                     TCGA-EM-A3SZ 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A4FF                     TCGA-EM-A4FH 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A4FK                     TCGA-EM-A4FM 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A4FN                     TCGA-EM-A4FO 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A4FQ                     TCGA-EM-A4FR 
"DEL PEAK 32(19P13.2) WILD-TYPE" "DEL PEAK 32(19P13.2) WILD-TYPE" 
                    TCGA-EM-A4FU                     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" 
D90V14, binary
                                cls
clus                               0   1
  DEL PEAK 32(19P13.2) MUTATED     2   5
  DEL PEAK 32(19P13.2) WILD-TYPE 222 256
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(19P13.2) MUTATED      2    5
  DEL PEAK 32(19P13.2) WILD-TYPE  222  256
            clus
vv           DEL PEAK 32(19P13.2) MUTATED DEL PEAK 32(19P13.2) WILD-TYPE
  MULTIFOCAL                            2                            222
  UNIFOCAL                              5                            256
[1] 2 2
[1] FALSE
D90V15, 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    49
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(19P13.2) MUTATED                           0     7
  DEL PEAK 32(19P13.2) WILD-TYPE                        26   314
D90V16, 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                                                        49
  BLACK OR AFRICAN AMERICAN                                    26
  WHITE                                                       314
[1] 4 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 32(19P13.2) MUTATED     0   6
  DEL PEAK 32(19P13.2) WILD-TYPE  38 344
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(19P13.2) MUTATED      0    6
  DEL PEAK 32(19P13.2) WILD-TYPE   38  344
                        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                            344
[1] 2 2
[1] FALSE

Clustering(91) Variable = DEL PEAK 33(19P13.12) MUTATION ANALYSIS
D91V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 33(19P13.12) MUTATED     6   1
  DEL PEAK 33(19P13.12) WILD-TYPE 471  13
  DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE 
                              7                             484 
  DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE 
                              1                              13 
$`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         4.27        33.47        33.50        98.56         1.25 
TCGA-FY-A3WA 
       17.06 

$`DEL PEAK 33(19P13.12) WILD-TYPE`
TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       13.78        18.21        16.34        14.73         8.25        18.87 
TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ 
        4.01        11.57        16.73         7.56        15.12        17.69 
TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A190 TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       23.34        20.71        20.58         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
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        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL 
        0.39         0.10        20.22        15.42        36.46         5.98 
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-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       25.12         3.22         2.76        17.26        14.07       137.88 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
        3.39         8.71        25.35        13.41        11.90        14.60 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        7.99        11.01       100.01        18.51        13.12         7.99 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96         7.20         1.45         8.88         1.02         5.95 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS 
       10.09         7.99         5.33         8.48        10.45         1.51 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY 
        9.60        12.56         8.28         7.69         5.52         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.42         8.12         9.34         6.77         9.21         9.44 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
        9.90         8.61        10.09         7.07        10.36        12.43 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        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        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04         1.15        22.29 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       74.30        45.40       108.36        39.32         1.41        30.18 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
      102.84        65.39       124.04        50.37        37.25       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        38.66        52.73 
TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ 
      139.00       131.15       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 
       12.16       147.42       130.72       129.57        32.48       116.91 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
       98.24        41.29        95.38         5.72        66.90        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO 
       77.36        78.97        31.50        50.33        53.06        47.38 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       52.50        45.53        48.16         7.07        44.65        45.80 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       19.30        45.96        37.94        31.04        19.59        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       33.60        28.73        41.13        37.78        29.95        13.32 
TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       11.87         8.71        26.86        18.18        20.91        12.36 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
       18.05        19.79        19.46        54.21        57.01        54.08 
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 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT 
       23.51         6.05         2.99        12.30        15.19        10.49 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        13.84        19.73        17.59        12.07 
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        17.46        18.97 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        19.63        13.38         8.35        16.44 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       16.77        27.95        23.77        16.80        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        11.15 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST 
        7.33        12.53         9.24        13.91         7.82        11.51 
TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH 
       16.41        15.62        13.51        12.79        70.65        16.90 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        9.01         4.83         8.61         8.38         9.80         5.03 
TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       37.87        12.72         0.95        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P 
       32.35        14.79        12.33        14.79        27.09        18.38 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       29.49        54.05        22.09        12.26        16.08        29.19 
TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       19.76         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       65.36        84.89        61.02        58.72        57.11        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       59.15        28.24         5.85         4.18         2.43         5.56 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       24.72        38.30        42.25         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       69.24        59.87        43.50         0.30        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S 
      132.36        24.72         3.22         7.17         4.80         5.03 
TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        2.14         4.01         1.94        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       102.90        66.77        81.34 
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        46.06         4.08         0.89        22.03         0.92 
TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
       48.10        91.17         1.15        17.82         1.64         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
        1.51         0.76         0.03         4.67        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         6.87         4.14         6.58         4.54 
TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U 
        0.89         1.35         1.15         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        10.26        16.90         9.80         9.63         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YD 
        8.65        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        86.70         6.02 
TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-KS-A4IC 
       12.43         6.74        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         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45         8.71        10.98         5.19 

  DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE 
                           1.25                            0.03 
  DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE 
                          98.56                          158.83 
  DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE 
                         24.790                          16.505 
[1] "1.2 - 98.6 (24.8)"  "0.0 - 158.8 (16.5)"
[1] "hr=" "4.5"
D91V2, 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     275       49       109        2        45
                                 vv
clus                              STAGE IVC
  DEL PEAK 33(19P13.12) MUTATED           0
  DEL PEAK 33(19P13.12) WILD-TYPE         6
D91V3, multiclass
           clus
vv          DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE
  STAGE I                               5                             275
  STAGE II                              2                              49
  STAGE III                             0                             109
  STAGE IV                              0                               2
  STAGE IVA                             0                              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 33(19P13.12) MUTATED     3   3   2   0
  DEL PEAK 33(19P13.12) WILD-TYPE 137 163 163  21
D91V4, multiclass
    clus
vv   DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE
  T1                             3                             137
  T2                             3                             163
  T3                             2                             163
  T4                             0                              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"
D91V5, binary
                                 cls
clus                                0   1
  DEL PEAK 33(19P13.12) MUTATED     3   1
  DEL PEAK 33(19P13.12) WILD-TYPE 220 221
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(19P13.12) MUTATED      3    1
  DEL PEAK 33(19P13.12) WILD-TYPE  220  221
   clus
vv  DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE
  0                             3                             220
  1                             1                             221
[1] 2 2
[1] FALSE
                                 vv
clus                               M0  M1  MX
  DEL PEAK 33(19P13.12) MUTATED     3   0   4
  DEL PEAK 33(19P13.12) WILD-TYPE 270   9 208
D91V6, multiclass
    clus
vv   DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE
  M0                             3                             270
  M1                             0                               9
  MX                             4                             208
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V7, binary
                                 cls
clus                                0   1
  DEL PEAK 33(19P13.12) MUTATED     5   3
  DEL PEAK 33(19P13.12) WILD-TYPE 359 128
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(19P13.12) MUTATED      5    3
  DEL PEAK 33(19P13.12) WILD-TYPE  359  128
        clus
vv       DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE
  FEMALE                             5                             359
  MALE                               3                             128
[1] 2 2
[1] FALSE
                                 vv
clus                              OTHER  SPECIFY
  DEL PEAK 33(19P13.12) MUTATED                0
  DEL PEAK 33(19P13.12) WILD-TYPE              9
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 33(19P13.12) MUTATED                                               7
  DEL PEAK 33(19P13.12) WILD-TYPE                                           346
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 33(19P13.12) MUTATED                                                                        1
  DEL PEAK 33(19P13.12) WILD-TYPE                                                                     97
                                 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                                                                  35
D91V8, 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                                                                                       9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      346
  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"
D91V9, binary
                                 cls
clus                                0   1
  DEL PEAK 33(19P13.12) MUTATED     0   8
  DEL PEAK 33(19P13.12) WILD-TYPE  14 473
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(19P13.12) MUTATED      0    8
  DEL PEAK 33(19P13.12) WILD-TYPE   14  473
     clus
vv    DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE
  NO                              0                              14
  YES                             8                             473
[1] 2 2
[1] FALSE
D91V10, binary
                                 cls
clus                                0   1
  DEL PEAK 33(19P13.12) MUTATED     5   2
  DEL PEAK 33(19P13.12) WILD-TYPE 412  15
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(19P13.12) MUTATED      5    2
  DEL PEAK 33(19P13.12) WILD-TYPE  412   15
     clus
vv    DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE
  NO                              5                             412
  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          129                      16  321
                                 vv
clus                              VERY ADVANCED (T4B)
  DEL PEAK 33(19P13.12) MUTATED                     0
  DEL PEAK 33(19P13.12) WILD-TYPE                   1
D91V11, 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)                                        129
  MODERATE/ADVANCED (T4A)                              16
  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 33(19P13.12) MUTATED     5   2   0   0
  DEL PEAK 33(19P13.12) WILD-TYPE 373  49   4  30
D91V12, multiclass
    clus
vv   DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE
  R0                             5                             373
  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"
D91V13, 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                             389 
                     TCGA-BJ-A0Z0                      TCGA-BJ-A0Z3 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A0Z9                      TCGA-BJ-A0ZA 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A0ZB                      TCGA-BJ-A0ZH 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A0ZJ                      TCGA-BJ-A18Y 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A18Z                      TCGA-BJ-A190 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A191                      TCGA-BJ-A28R 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A28T                      TCGA-BJ-A28W 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A28X                      TCGA-BJ-A28Z 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A290                      TCGA-BJ-A291 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A2N8                      TCGA-BJ-A2N9 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A2NA                      TCGA-BJ-A3EZ 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A3PR                      TCGA-BJ-A3PU 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A45C                      TCGA-BJ-A45D 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A45E                      TCGA-BJ-A45G 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A45I                      TCGA-BJ-A45J 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A45K                      TCGA-BJ-A4O8 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-BJ-A4O9                      TCGA-CE-A13K 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-CE-A3MD                      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-A13P                      TCGA-DJ-A13R 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A13T                      TCGA-DJ-A13U 
"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-A3VJ                      TCGA-DJ-A3VL 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A4UL                      TCGA-DJ-A4UQ 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A4UR                      TCGA-DJ-A4UW 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DJ-A4V2                      TCGA-DJ-A4V5 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-DO-A1K0                      TCGA-DO-A2HM 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-E3-A3DY                      TCGA-E3-A3DZ 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-E3-A3E0                      TCGA-E3-A3E1 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-E3-A3E2                      TCGA-E3-A3E3 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-E3-A3E5                      TCGA-E8-A242 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-E8-A2EA                      TCGA-E8-A2JQ 
"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-A3ZN 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3ZO                      TCGA-EL-A3ZP 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A3ZS                      TCGA-EL-A4JV 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A4JW                      TCGA-EL-A4JX 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A4JZ                      TCGA-EL-A4K0 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A4K1                      TCGA-EL-A4K2 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A4K4                      TCGA-EL-A4K6 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A4K7                      TCGA-EL-A4KD 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EL-A4KG                      TCGA-EL-A4KI 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A1CS                      TCGA-EM-A1CT 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A1CU                      TCGA-EM-A1CV 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A1CW                      TCGA-EM-A1YA 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A1YB                      TCGA-EM-A1YC 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A1YD                      TCGA-EM-A1YE 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A22I                      TCGA-EM-A22J 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A22K                      TCGA-EM-A22L 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A22M                      TCGA-EM-A22N 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A22O                      TCGA-EM-A22P 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A22Q                      TCGA-EM-A2CK 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A2CN                      TCGA-EM-A2CP 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A2CQ                      TCGA-EM-A2CS 
"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-A2OW 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A2OX                      TCGA-EM-A2OY 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A2OZ                      TCGA-EM-A2P0 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A2P1                      TCGA-EM-A2P2 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A2P3                      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-A3FL                      TCGA-EM-A3FM 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A3FN                      TCGA-EM-A3FO 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A3FP                      TCGA-EM-A3FQ 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A3FR                      TCGA-EM-A3O3 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A3O7                      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-A3SY                      TCGA-EM-A3SZ 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A4FF                      TCGA-EM-A4FH 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A4FK                      TCGA-EM-A4FM 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A4FN                      TCGA-EM-A4FO 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A4FQ                      TCGA-EM-A4FR 
"DEL PEAK 33(19P13.12) WILD-TYPE" "DEL PEAK 33(19P13.12) WILD-TYPE" 
                     TCGA-EM-A4FU                      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" 
D91V14, binary
                                 cls
clus                                0   1
  DEL PEAK 33(19P13.12) MUTATED     4   4
  DEL PEAK 33(19P13.12) WILD-TYPE 220 257
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(19P13.12) MUTATED      4    4
  DEL PEAK 33(19P13.12) WILD-TYPE  220  257
            clus
vv           DEL PEAK 33(19P13.12) MUTATED DEL PEAK 33(19P13.12) WILD-TYPE
  MULTIFOCAL                             4                             220
  UNIFOCAL                               4                             257
[1] 2 2
[1] FALSE
D91V15, 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    49
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(19P13.12) MUTATED                           2     6
  DEL PEAK 33(19P13.12) WILD-TYPE                        24   315
D91V16, 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                                                         49
  BLACK OR AFRICAN AMERICAN                                     24
  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"
D91V17, binary
                                 cls
clus                                0   1
  DEL PEAK 33(19P13.12) MUTATED     0   8
  DEL PEAK 33(19P13.12) WILD-TYPE  38 342
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(19P13.12) MUTATED      0    8
  DEL PEAK 33(19P13.12) WILD-TYPE   38  342
                        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                             342
[1] 2 2
[1] FALSE

Clustering(92) Variable = DEL PEAK 36(21Q21.1) MUTATION ANALYSIS
D92V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 36(21Q21.1) MUTATED     9   0
  DEL PEAK 36(21Q21.1) WILD-TYPE 468  14
  DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE 
                             9                            482 
  DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE 
                             0                             14 
$`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         0.10         8.12        14.43        11.15        17.59 
TCGA-ET-A25L TCGA-FY-A3I5 TCGA-J8-A4HW 
       14.79         1.64         2.60 

$`DEL PEAK 36(21Q21.1) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 
       24.79        13.78        18.21        16.34        14.73         8.25 
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         7.56        15.12 
TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R 
       17.69        23.34        20.71         4.83         8.09         4.87 
TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z 
       21.04         2.79         5.10        11.31        17.52         1.22 
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        15.48        23.31        18.64 
TCGA-BJ-A45C TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H 
        5.75         6.48         0.03         3.45         6.35         7.82 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18         5.06         8.98         4.93         5.98         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
        0.10         0.20         0.23        11.38        10.68         0.10 
TCGA-CE-A484 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.39        20.22        15.42        36.46         5.98        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-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
        4.27         3.22         2.76        17.26        14.07       137.88 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
        3.39         8.71        25.35        13.41        11.90        14.60 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        7.99        11.01       100.01        18.51        13.12         7.99 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96         7.20         1.45         8.88         1.02         5.95 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS 
       10.09         7.99         5.33         8.48        10.45         1.51 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY 
        9.60        12.56         8.28         7.69         5.52         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
        8.42         9.34         6.77         9.21         9.44         9.90 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
        8.61        10.09         7.07        10.36        12.43        10.85 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       15.88        15.09        31.04        12.49        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        24.23        17.69        43.00 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 
       11.34        21.37        12.76        25.02        20.22        30.61 
TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 TCGA-DJ-A3VA 
       14.56        19.20         9.83        21.27        20.48        11.93 
TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG TCGA-DJ-A3VJ 
       22.92        21.01        18.97         7.76         8.32        17.36 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UT 
       17.23        27.62        18.21        10.78        10.98        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 
       63.19        30.31        14.04         1.15        22.29        19.59 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 
       13.61        14.27        13.81        14.07        14.27         3.02 
TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K 
       14.70        14.10        14.96         7.69        20.68        13.78 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
       13.58        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 
       80.91         4.18        58.82         1.45        74.30        45.40 
TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR 
       33.47       108.36        39.32         1.41        30.18       102.84 
TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY 
       65.39       124.04        50.37        37.25       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        38.66        52.73 
TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ 
      139.00       131.15       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 
       12.16       147.42       130.72       129.57        32.48       116.91 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
       98.24        41.29        95.38         5.72        66.90        82.82 
TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL TCGA-EL-A3ZN TCGA-EL-A3ZO 
       77.36        78.97        31.50        50.33        53.06        47.38 
TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JV 
       52.50        45.53        48.16         7.07        44.65        45.80 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 
       19.30        45.96        37.94        31.04        19.59        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 TCGA-EL-A4KD TCGA-EL-A4KG 
       33.60        28.73        41.13        37.78        29.95        13.32 
TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       11.87         8.71        26.86        18.18        20.91        12.36 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
       18.05        19.79        19.46        54.21        57.01        54.08 
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-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.74        14.24        16.44        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-EM-A2CU 
        6.05         2.99        12.30        15.19        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        13.84        19.73        12.07        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        17.46        18.97        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       19.63        13.38         8.35        16.44        16.77        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        16.80        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        11.15         7.33        12.53 
TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX 
        9.24        13.91         7.82        11.51        16.41        15.62 
TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       13.51        12.79        70.65        16.90         9.01         4.83 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
        8.61         8.38         9.80         5.03        37.87        12.72 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25M 
        0.95        47.47        48.20        29.69        32.35        12.33 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY 
       14.79        27.09        18.38        29.49        54.05        22.09 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 
       12.26        16.08        29.19        19.76         2.66        58.22 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
       13.74        71.01        80.02        65.36        84.89        98.56 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
       61.02        58.72        57.11        55.10        59.15        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
        5.85         4.18         2.43         5.56        24.72        38.30 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       42.25         2.37         4.50        80.81        69.24        59.87 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       43.50         0.30        17.98        25.32       132.36        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
        3.22         7.17         4.80         5.03         2.14         4.01 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
        1.94        73.74        59.70        31.59        44.25        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
       68.22       102.90        66.77        81.34        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        46.06 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.08         0.89        22.03         0.92        48.10        91.17 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
        1.25         1.15        17.82         0.99         1.51         0.76 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 
        0.03         4.67        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         6.87         4.14         6.58         4.54         0.89 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-FY-A76V TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
        1.35         1.15         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 
       10.26        16.90         9.80         9.63         2.96         8.65 
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        86.70         6.02        12.43         6.74 
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         0.72        16.64        32.45         8.71 
TCGA-MK-A84Z TCGA-QD-A8IV 
       10.98         5.19 

  DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE 
                         20.58                         158.83 
  DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE 
                         11.15                          16.75 
[1] "0.1 - 20.6 (11.2)"  "0.0 - 158.8 (16.8)"
[1] "hr="     "1200000"
D92V2, 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     279       47       107        2        43
                                vv
clus                             STAGE IVC
  DEL PEAK 36(21Q21.1) MUTATED           0
  DEL PEAK 36(21Q21.1) WILD-TYPE         6
D92V3, multiclass
           clus
vv          DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE
  STAGE I                              1                            279
  STAGE II                             4                             47
  STAGE III                            2                            107
  STAGE IV                             0                              2
  STAGE IVA                            2                             43
  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 139 160 163  21
D92V4, multiclass
    clus
vv   DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE
  T1                            1                            139
  T2                            6                            160
  T3                            2                            163
  T4                            0                             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"
D92V5, binary
                                cls
clus                               0   1
  DEL PEAK 36(21Q21.1) MUTATED     5   4
  DEL PEAK 36(21Q21.1) WILD-TYPE 218 218
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(21Q21.1) MUTATED      5    4
  DEL PEAK 36(21Q21.1) WILD-TYPE  218  218
   clus
vv  DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE
  0                            5                            218
  1                            4                            218
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 36(21Q21.1) MUTATED     4   0   5
  DEL PEAK 36(21Q21.1) WILD-TYPE 269   9 207
D92V6, multiclass
    clus
vv   DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE
  M0                            4                            269
  M1                            0                              9
  MX                            5                            207
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V7, binary
                                cls
clus                               0   1
  DEL PEAK 36(21Q21.1) MUTATED     6   3
  DEL PEAK 36(21Q21.1) WILD-TYPE 358 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(21Q21.1) MUTATED      6    3
  DEL PEAK 36(21Q21.1) WILD-TYPE  358  128
        clus
vv       DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE
  FEMALE                            6                            358
  MALE                              3                            128
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 36(21Q21.1) MUTATED                0
  DEL PEAK 36(21Q21.1) WILD-TYPE              9
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 36(21Q21.1) MUTATED                                               6
  DEL PEAK 36(21Q21.1) WILD-TYPE                                           347
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 36(21Q21.1) MUTATED                                                                        2
  DEL PEAK 36(21Q21.1) WILD-TYPE                                                                     96
                                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                                                                  34
D92V8, 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                                                                                      9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     347
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             96
  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"
D92V9, binary
                                cls
clus                               0   1
  DEL PEAK 36(21Q21.1) MUTATED     0   9
  DEL PEAK 36(21Q21.1) WILD-TYPE  14 472
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(21Q21.1) MUTATED      0    9
  DEL PEAK 36(21Q21.1) WILD-TYPE   14  472
     clus
vv    DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE
  NO                             0                             14
  YES                            9                            472
[1] 2 2
[1] FALSE
D92V10, binary
                                cls
clus                               0   1
  DEL PEAK 36(21Q21.1) MUTATED     8   0
  DEL PEAK 36(21Q21.1) WILD-TYPE 409  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(21Q21.1) MUTATED      8    0
  DEL PEAK 36(21Q21.1) WILD-TYPE  409   17
     clus
vv    DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE
  NO                             8                            409
  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          129                      16  320
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 36(21Q21.1) MUTATED                     0
  DEL PEAK 36(21Q21.1) WILD-TYPE                   1
D92V11, 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)                                       129
  MODERATE/ADVANCED (T4A)                             16
  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 36(21Q21.1) MUTATED     7   2   0   0
  DEL PEAK 36(21Q21.1) WILD-TYPE 371  49   4  30
D92V12, multiclass
    clus
vv   DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE
  R0                            7                            371
  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"
D92V13, continuous
D92V14, binary
                                cls
clus                               0   1
  DEL PEAK 36(21Q21.1) MUTATED     6   3
  DEL PEAK 36(21Q21.1) WILD-TYPE 218 258
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(21Q21.1) MUTATED      6    3
  DEL PEAK 36(21Q21.1) WILD-TYPE  218  258
            clus
vv           DEL PEAK 36(21Q21.1) MUTATED DEL PEAK 36(21Q21.1) WILD-TYPE
  MULTIFOCAL                            6                            218
  UNIFOCAL                              3                            258
[1] 2 2
[1] FALSE
D92V15, 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    47
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(21Q21.1) MUTATED                           0     5
  DEL PEAK 36(21Q21.1) WILD-TYPE                        26   316
D92V16, 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                                                        47
  BLACK OR AFRICAN AMERICAN                                    26
  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"
D92V17, binary
                                cls
clus                               0   1
  DEL PEAK 36(21Q21.1) MUTATED     0   6
  DEL PEAK 36(21Q21.1) WILD-TYPE  38 344
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(21Q21.1) MUTATED      0    6
  DEL PEAK 36(21Q21.1) WILD-TYPE   38  344
                        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                            344
[1] 2 2
[1] FALSE

Clustering(93) Variable = DEL PEAK 37(22Q12.3) MUTATION ANALYSIS
D93V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 37(22Q12.3) MUTATED    87   1
  DEL PEAK 37(22Q12.3) WILD-TYPE 390  13
  DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE 
                            88                            403 
  DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE 
                             1                             13 
$`DEL PEAK 37(22Q12.3) MUTATED`
TCGA-BJ-A0Z2 TCGA-BJ-A0Z5 TCGA-BJ-A0ZH TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A2P4 
       18.21        14.73        15.12        23.34        20.58         7.04 
TCGA-BJ-A3PT TCGA-BJ-A45D TCGA-BJ-A45F TCGA-CE-A484 TCGA-DE-A0XZ TCGA-DE-A4M8 
       23.31         6.48         3.45         0.39        20.22        18.54 
TCGA-DJ-A13M TCGA-DJ-A13T TCGA-DJ-A1QG TCGA-DJ-A1QN TCGA-DJ-A2PS TCGA-DJ-A2Q0 
       17.26        25.35        13.12         8.88         1.51         8.12 
TCGA-DJ-A2Q7 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A3UK TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.09        12.43        10.85        15.09        12.49        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-E3-A3DZ TCGA-E3-A3E5 TCGA-E8-A432 
       16.41        27.62        10.98        12.07        14.04        14.43 
TCGA-E8-A434 TCGA-EL-A3CL TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3GP 
       14.10        31.66         1.45        74.30        45.40         1.41 
TCGA-EL-A3GW TCGA-EL-A3T2 TCGA-EL-A3ZL TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4JZ 
       37.25        32.48        50.33        48.16        45.80        37.94 
TCGA-EL-A4K6 TCGA-EL-A4K9 TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A22K TCGA-EM-A22L 
       28.73        37.78         8.71        26.86        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22P TCGA-EM-A2CJ TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A3AP 
       14.53        11.15        16.44        19.73        17.59         8.35 
TCGA-EM-A3FO TCGA-EM-A3O9 TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FO TCGA-EM-A4FR 
       17.49         9.24        15.62        12.79         8.38         5.03 
TCGA-EM-A4FU TCGA-ET-A25L TCGA-ET-A25O TCGA-ET-A2N4 TCGA-ET-A39L TCGA-ET-A39M 
       37.87        14.79        27.09         2.66        65.36        84.89 
TCGA-ET-A39N TCGA-ET-A3BP TCGA-ET-A3DS TCGA-ET-A40P TCGA-ET-A40T TCGA-FE-A237 
       98.56         4.18         0.30         3.22         2.14        81.34 
TCGA-FE-A3PB TCGA-FY-A3R7 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A4B4 TCGA-GE-A2C6 
       85.15         0.03         0.76        17.06         1.15        12.53 
TCGA-IM-A3U3 TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3YD TCGA-J8-A3YH TCGA-KS-A41I 
       16.90         9.63        43.17        31.82         5.75        15.98 
TCGA-KS-A4I7 TCGA-KS-A4IB TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45        84.72        10.98         5.19 

$`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         8.25        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         7.56        17.69        20.71         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
        8.09         4.87        21.04         2.79         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        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        15.48        18.64 
TCGA-BJ-A45C TCGA-BJ-A45E TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J 
        5.75         0.03         6.35         7.82         6.18         5.06 
TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD 
        8.98         4.93         5.98         0.53         0.10         0.20 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A485 TCGA-DE-A0Y2 
        0.23        11.38        10.68         0.10         0.10        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       36.46         5.98        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-A13O 
       30.02        25.12         4.27         3.22         2.76        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
      137.88         3.39         8.71        13.41        11.90        14.60 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QH TCGA-DJ-A1QI 
        7.99        11.01       100.01        18.51         7.99        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        7.20         1.45         1.02         5.95        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
        5.33         8.48        10.45         9.60        12.56         8.28 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        7.69         5.52         8.78         8.42         9.34         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.21         9.44         9.90         8.61         7.07        10.36 
TCGA-DJ-A2QC TCGA-DJ-A3UM TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       15.88        31.04        19.56        36.33        32.81        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UT 
        8.32        17.36        17.23        18.21        10.78        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
       21.53         2.33        31.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       30.31         1.15        22.29        19.59        13.61        14.27 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A433 TCGA-E8-A436 
       13.81        14.07        14.27         3.02        14.70        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CM TCGA-EL-A3CN 
        7.69        20.68        13.78        13.58        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-A3D5 
       37.94        57.01        80.91         4.18        58.82        33.47 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
      108.36        39.32        30.18       102.84        65.39       124.04 
TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.37       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        38.66        52.73       139.00       131.15       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        12.16       147.42       130.72 
TCGA-EL-A3T1 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
      129.57       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZN 
       66.90        82.82        77.36        78.97        31.50        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JW 
       47.38        52.50        45.53         7.07        44.65        19.30 
TCGA-EL-A4JX TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K7 
       45.96        31.04        19.59        30.51        33.60        41.13 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       29.95        13.32        11.87        18.18        20.91        12.36 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
       18.05        19.79        19.46        54.21        57.01        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22Q TCGA-EM-A2CK 
       14.73        14.50        10.65        11.74        14.24        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OZ TCGA-EM-A2P0 
       10.49        13.15        22.16        13.84        12.07        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        17.46        18.97        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       14.14        19.63        13.38        16.44        16.77        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FP TCGA-EM-A3FQ 
       23.77        16.80        21.01        12.07        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        11.15         7.33        12.53        13.91 
TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SY TCGA-EM-A4FF TCGA-EM-A4FH 
        7.82        11.51        16.41        13.51        70.65        16.90 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-EM-A4G1 
        9.01         4.83         8.61         9.80        12.72         0.95 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25M TCGA-ET-A25N 
       47.47        48.20        29.69        32.35        12.33        14.79 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       29.19        19.76        58.22        13.74        71.01        80.02 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
       61.02        58.72        57.11        55.10        59.15        28.24 
TCGA-ET-A3BO TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
        5.85         2.43         5.56        24.72        38.30        42.25 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
        2.37         4.50        80.81        69.24        59.87        43.50 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40Q TCGA-ET-A40R 
       17.98        25.32       132.36        24.72         7.17         4.80 
TCGA-ET-A40S TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
        5.03         4.01         1.94        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A238 
       44.25        24.69        68.22       102.90        66.77        39.95 
TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
       33.63        81.83       106.36        85.68        78.77        46.06 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB 
        4.08         0.89        22.03         0.92        48.10        91.17 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON 
        1.25         1.15        17.82         1.64         0.99         1.51 
TCGA-FY-A3R6 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3YR 
        0.76         4.67        16.57        18.08         0.30         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A76V 
        4.14         6.58         4.54         0.89         1.35         1.68 
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-A41Y TCGA-IM-A420 TCGA-IM-A4EB 
       48.92        47.41        10.26         9.80         2.96         8.65 
TCGA-J8-A3NZ TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       17.23        27.19        11.24        27.85        24.69        22.29 
TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41J TCGA-KS-A41L 
        2.47         2.60         0.20       143.57        15.68        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IC TCGA-KS-A4ID 
        6.02        12.43         6.74        87.39        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         0.72        16.64        32.45 
TCGA-MK-A4N9 
        8.71 

  DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE 
                          0.03                           0.03 
  DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE 
                         98.56                         158.83 
  DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE 
                        15.105                         17.000 
[1] "0.0 - 98.6 (15.1)"  "0.0 - 158.8 (17.0)"
[1] "hr=" "1.9"
D93V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 37(22Q12.3) MUTATED        49       11        16        1        10
  DEL PEAK 37(22Q12.3) WILD-TYPE     231       40        93        1        35
                                vv
clus                             STAGE IVC
  DEL PEAK 37(22Q12.3) MUTATED           1
  DEL PEAK 37(22Q12.3) WILD-TYPE         5
D93V3, multiclass
           clus
vv          DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE
  STAGE I                             49                            231
  STAGE II                            11                             40
  STAGE III                           16                             93
  STAGE IV                             1                              1
  STAGE IVA                           10                             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    26  34  25   3
  DEL PEAK 37(22Q12.3) WILD-TYPE 114 132 140  18
D93V4, multiclass
    clus
vv   DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE
  T1                           26                            114
  T2                           34                            132
  T3                           25                            140
  T4                            3                             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"
D93V5, binary
                                cls
clus                               0   1
  DEL PEAK 37(22Q12.3) MUTATED    44  36
  DEL PEAK 37(22Q12.3) WILD-TYPE 179 186
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(22Q12.3) MUTATED     44   36
  DEL PEAK 37(22Q12.3) WILD-TYPE  179  186
   clus
vv  DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE
  0                           44                            179
  1                           36                            186
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 37(22Q12.3) MUTATED    43   2  43
  DEL PEAK 37(22Q12.3) WILD-TYPE 230   7 169
D93V6, multiclass
    clus
vv   DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE
  M0                           43                            230
  M1                            2                              7
  MX                           43                            169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V7, binary
                                cls
clus                               0   1
  DEL PEAK 37(22Q12.3) MUTATED    61  27
  DEL PEAK 37(22Q12.3) WILD-TYPE 303 104
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(22Q12.3) MUTATED     61   27
  DEL PEAK 37(22Q12.3) WILD-TYPE  303  104
        clus
vv       DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE
  FEMALE                           61                            303
  MALE                             27                            104
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 37(22Q12.3) MUTATED                1
  DEL PEAK 37(22Q12.3) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 37(22Q12.3) MUTATED                                              61
  DEL PEAK 37(22Q12.3) WILD-TYPE                                           292
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 37(22Q12.3) MUTATED                                                                       23
  DEL PEAK 37(22Q12.3) WILD-TYPE                                                                     75
                                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                                                                  32
D93V8, multiclass
                                                                        clus
vv                                                                       DEL PEAK 37(22Q12.3) MUTATED
  OTHER  SPECIFY                                                                                    1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    61
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           23
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               3
                                                                        clus
vv                                                                       DEL PEAK 37(22Q12.3) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     292
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             75
  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"
D93V9, binary
                                cls
clus                               0   1
  DEL PEAK 37(22Q12.3) MUTATED     1  87
  DEL PEAK 37(22Q12.3) WILD-TYPE  13 394
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(22Q12.3) MUTATED      1   87
  DEL PEAK 37(22Q12.3) WILD-TYPE   13  394
     clus
vv    DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE
  NO                             1                             13
  YES                           87                            394
[1] 2 2
[1] FALSE
D93V10, binary
                                cls
clus                               0   1
  DEL PEAK 37(22Q12.3) MUTATED    79   1
  DEL PEAK 37(22Q12.3) WILD-TYPE 338  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(22Q12.3) MUTATED     79    1
  DEL PEAK 37(22Q12.3) WILD-TYPE  338   16
     clus
vv    DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE
  NO                            79                            338
  YES                            1                             16
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 37(22Q12.3) MUTATED             18                       1   64
  DEL PEAK 37(22Q12.3) WILD-TYPE          112                      15  264
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 37(22Q12.3) MUTATED                     0
  DEL PEAK 37(22Q12.3) WILD-TYPE                   1
D93V11, multiclass
                         clus
vv                        DEL PEAK 37(22Q12.3) MUTATED
  MINIMAL (T3)                                      18
  MODERATE/ADVANCED (T4A)                            1
  NONE                                              64
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK 37(22Q12.3) WILD-TYPE
  MINIMAL (T3)                                       112
  MODERATE/ADVANCED (T4A)                             15
  NONE                                               264
  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    67   6   1   8
  DEL PEAK 37(22Q12.3) WILD-TYPE 311  45   3  22
D93V12, multiclass
    clus
vv   DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE
  R0                           67                            311
  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 37(22Q12.3) MUTATED    46  40
  DEL PEAK 37(22Q12.3) WILD-TYPE 178 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(22Q12.3) MUTATED     46   40
  DEL PEAK 37(22Q12.3) WILD-TYPE  178  221
            clus
vv           DEL PEAK 37(22Q12.3) MUTATED DEL PEAK 37(22Q12.3) WILD-TYPE
  MULTIFOCAL                           46                            178
  UNIFOCAL                             40                            221
[1] 2 2
[1] FALSE
D93V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 37(22Q12.3) MUTATED                                  0    10
  DEL PEAK 37(22Q12.3) WILD-TYPE                                1    39
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 37(22Q12.3) MUTATED                           6    51
  DEL PEAK 37(22Q12.3) WILD-TYPE                        20   270
D93V16, multiclass
                                  clus
vv                                 DEL PEAK 37(22Q12.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      10
  BLACK OR AFRICAN AMERICAN                                   6
  WHITE                                                      51
                                  clus
vv                                 DEL PEAK 37(22Q12.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        39
  BLACK OR AFRICAN AMERICAN                                    20
  WHITE                                                       270
[1] 4 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 37(22Q12.3) MUTATED     6  60
  DEL PEAK 37(22Q12.3) WILD-TYPE  32 290
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(22Q12.3) MUTATED      6   60
  DEL PEAK 37(22Q12.3) WILD-TYPE   32  290
                        clus
vv                       DEL PEAK 37(22Q12.3) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           60
                        clus
vv                       DEL PEAK 37(22Q12.3) WILD-TYPE
  HISPANIC OR LATINO                                 32
  NOT HISPANIC OR LATINO                            290
[1] 2 2
[1] FALSE

Clustering(94) Variable = DEL PEAK 38(22Q13.1) MUTATION ANALYSIS
D94V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 38(22Q13.1) MUTATED    86   1
  DEL PEAK 38(22Q13.1) WILD-TYPE 391  13
  DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE 
                            87                            404 
  DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE 
                             1                             13 
$`DEL PEAK 38(22Q13.1) MUTATED`
TCGA-BJ-A0Z2 TCGA-BJ-A0Z5 TCGA-BJ-A0ZH TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A2P4 
       18.21        14.73        15.12        23.34        20.58         7.04 
TCGA-BJ-A3PT TCGA-BJ-A45D TCGA-BJ-A45F TCGA-CE-A484 TCGA-DE-A0XZ TCGA-DE-A4M8 
       23.31         6.48         3.45         0.39        20.22        18.54 
TCGA-DJ-A13M TCGA-DJ-A13T TCGA-DJ-A1QG TCGA-DJ-A1QN TCGA-DJ-A2PS TCGA-DJ-A2Q0 
       17.26        25.35        13.12         8.88         1.51         8.12 
TCGA-DJ-A2Q7 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A3UK TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.09        12.43        10.85        15.09        12.49        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-E3-A3DZ TCGA-E3-A3E5 TCGA-E8-A432 
       16.41        27.62        10.98        12.07        14.04        14.43 
TCGA-E8-A434 TCGA-EL-A3CL TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3GP 
       14.10        31.66         1.45        74.30        45.40         1.41 
TCGA-EL-A3GW TCGA-EL-A3T2 TCGA-EL-A3ZL TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4JZ 
       37.25        32.48        50.33        48.16        45.80        37.94 
TCGA-EL-A4K6 TCGA-EL-A4K9 TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A22K TCGA-EM-A22L 
       28.73        37.78         8.71        26.86        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22P TCGA-EM-A2CJ TCGA-EM-A2OY TCGA-EM-A3AP TCGA-EM-A3FO 
       14.53        11.15        16.44        17.59         8.35        17.49 
TCGA-EM-A3O9 TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FO TCGA-EM-A4FR TCGA-EM-A4FU 
        9.24        15.62        12.79         8.38         5.03        37.87 
TCGA-ET-A25L TCGA-ET-A25O TCGA-ET-A2N4 TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
       14.79        27.09         2.66        65.36        84.89        98.56 
TCGA-ET-A3BP TCGA-ET-A3DS TCGA-ET-A40P TCGA-ET-A40T TCGA-FE-A237 TCGA-FE-A3PB 
        4.18         0.30         3.22         2.14        81.34        85.15 
TCGA-FY-A3R7 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-IM-A3U3 
        0.03         0.76        17.06         1.15        12.53        16.90 
TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3YD TCGA-J8-A3YH TCGA-KS-A41I TCGA-KS-A4I7 
        9.63        43.17        31.82         5.75        15.98        32.45 
TCGA-KS-A4IB TCGA-MK-A84Z TCGA-QD-A8IV 
       84.72        10.98         5.19 

$`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         8.25        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         7.56        17.69        20.71         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
        8.09         4.87        21.04         2.79         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        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        15.48        18.64 
TCGA-BJ-A45C TCGA-BJ-A45E TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J 
        5.75         0.03         6.35         7.82         6.18         5.06 
TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD 
        8.98         4.93         5.98         0.53         0.10         0.20 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A485 TCGA-DE-A0Y2 
        0.23        11.38        10.68         0.10         0.10        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       36.46         5.98        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-A13O 
       30.02        25.12         4.27         3.22         2.76        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
      137.88         3.39         8.71        13.41        11.90        14.60 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QH TCGA-DJ-A1QI 
        7.99        11.01       100.01        18.51         7.99        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        7.20         1.45         1.02         5.95        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
        5.33         8.48        10.45         9.60        12.56         8.28 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        7.69         5.52         8.78         8.42         9.34         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.21         9.44         9.90         8.61         7.07        10.36 
TCGA-DJ-A2QC TCGA-DJ-A3UM TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       15.88        31.04        19.56        36.33        32.81        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UT 
        8.32        17.36        17.23        18.21        10.78        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
       21.53         2.33        31.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       30.31         1.15        22.29        19.59        13.61        14.27 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A433 TCGA-E8-A436 
       13.81        14.07        14.27         3.02        14.70        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CM TCGA-EL-A3CN 
        7.69        20.68        13.78        13.58        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-A3D5 
       37.94        57.01        80.91         4.18        58.82        33.47 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
      108.36        39.32        30.18       102.84        65.39       124.04 
TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.37       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        38.66        52.73       139.00       131.15       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        12.16       147.42       130.72 
TCGA-EL-A3T1 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
      129.57       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZN 
       66.90        82.82        77.36        78.97        31.50        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JW 
       47.38        52.50        45.53         7.07        44.65        19.30 
TCGA-EL-A4JX TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K7 
       45.96        31.04        19.59        30.51        33.60        41.13 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       29.95        13.32        11.87        18.18        20.91        12.36 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
       18.05        19.79        19.46        54.21        57.01        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22Q TCGA-EM-A2CK 
       14.73        14.50        10.65        11.74        14.24        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ 
       10.49        13.15        22.16        13.84        19.73        12.07 
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        17.46        18.97 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AQ TCGA-EM-A3AR 
       15.68        14.14        19.63        13.38        16.44        16.77 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FP 
       27.95        23.77        16.80        21.01        12.07        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        11.15         7.33        12.53 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SY TCGA-EM-A4FF 
       13.91         7.82        11.51        16.41        13.51        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FV 
       16.90         9.01         4.83         8.61         9.80        12.72 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25M 
        0.95        47.47        48.20        29.69        32.35        12.33 
TCGA-ET-A25N TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       14.79        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       16.08        29.19        19.76        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       80.02        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
       28.24         5.85         2.43         5.56        24.72        38.30 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       42.25         2.37         4.50        80.81        69.24        59.87 
TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40Q 
       43.50        17.98        25.32       132.36        24.72         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        4.80         5.03         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        24.69        68.22       102.90        66.77 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FE-A3PD 
       39.95        33.63        81.83       106.36        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       46.06         4.08         0.89        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
       91.17         1.25         1.15        17.82         1.64         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        1.51         0.76         4.67        16.57        18.08         0.30 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A76V TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
        1.68        17.00        21.67        12.46         2.99        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A41Y TCGA-IM-A420 
       18.61        48.92        47.41        10.26         9.80         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YE TCGA-J8-A3YF 
        8.65        17.23        27.19        11.24        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41J 
       22.29         2.47         2.60         0.20       143.57        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IC 
       86.70         6.02        12.43         6.74        87.39        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         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 
       32.45         8.71 

  DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE 
                          0.03                           0.03 
  DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE 
                         98.56                         158.83 
  DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE 
                        15.090                         17.115 
[1] "0.0 - 98.6 (15.1)"  "0.0 - 158.8 (17.1)"
[1] "hr=" "1.9"
D94V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 38(22Q13.1) MUTATED        49       11        16        1         9
  DEL PEAK 38(22Q13.1) WILD-TYPE     231       40        93        1        36
                                vv
clus                             STAGE IVC
  DEL PEAK 38(22Q13.1) MUTATED           1
  DEL PEAK 38(22Q13.1) WILD-TYPE         5
D94V3, multiclass
           clus
vv          DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE
  STAGE I                             49                            231
  STAGE II                            11                             40
  STAGE III                           16                             93
  STAGE IV                             1                              1
  STAGE IVA                            9                             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    25  34  25   3
  DEL PEAK 38(22Q13.1) WILD-TYPE 115 132 140  18
D94V4, multiclass
    clus
vv   DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE
  T1                           25                            115
  T2                           34                            132
  T3                           25                            140
  T4                            3                             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"
D94V5, binary
                                cls
clus                               0   1
  DEL PEAK 38(22Q13.1) MUTATED    44  35
  DEL PEAK 38(22Q13.1) WILD-TYPE 179 187
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(22Q13.1) MUTATED     44   35
  DEL PEAK 38(22Q13.1) WILD-TYPE  179  187
   clus
vv  DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE
  0                           44                            179
  1                           35                            187
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 38(22Q13.1) MUTATED    43   2  42
  DEL PEAK 38(22Q13.1) WILD-TYPE 230   7 170
D94V6, multiclass
    clus
vv   DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE
  M0                           43                            230
  M1                            2                              7
  MX                           42                            170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V7, binary
                                cls
clus                               0   1
  DEL PEAK 38(22Q13.1) MUTATED    61  26
  DEL PEAK 38(22Q13.1) WILD-TYPE 303 105
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(22Q13.1) MUTATED     61   26
  DEL PEAK 38(22Q13.1) WILD-TYPE  303  105
        clus
vv       DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE
  FEMALE                           61                            303
  MALE                             26                            105
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 38(22Q13.1) MUTATED                1
  DEL PEAK 38(22Q13.1) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 38(22Q13.1) MUTATED                                              60
  DEL PEAK 38(22Q13.1) WILD-TYPE                                           293
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 38(22Q13.1) MUTATED                                                                       23
  DEL PEAK 38(22Q13.1) WILD-TYPE                                                                     75
                                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                                                                  32
D94V8, multiclass
                                                                        clus
vv                                                                       DEL PEAK 38(22Q13.1) MUTATED
  OTHER  SPECIFY                                                                                    1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    60
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           23
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               3
                                                                        clus
vv                                                                       DEL PEAK 38(22Q13.1) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     293
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             75
  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"
D94V9, binary
                                cls
clus                               0   1
  DEL PEAK 38(22Q13.1) MUTATED     1  86
  DEL PEAK 38(22Q13.1) WILD-TYPE  13 395
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(22Q13.1) MUTATED      1   86
  DEL PEAK 38(22Q13.1) WILD-TYPE   13  395
     clus
vv    DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE
  NO                             1                             13
  YES                           86                            395
[1] 2 2
[1] FALSE
D94V10, binary
                                cls
clus                               0   1
  DEL PEAK 38(22Q13.1) MUTATED    78   1
  DEL PEAK 38(22Q13.1) WILD-TYPE 339  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(22Q13.1) MUTATED     78    1
  DEL PEAK 38(22Q13.1) WILD-TYPE  339   16
     clus
vv    DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE
  NO                            78                            339
  YES                            1                             16
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 38(22Q13.1) MUTATED             18                       1   63
  DEL PEAK 38(22Q13.1) WILD-TYPE          112                      15  265
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 38(22Q13.1) MUTATED                     0
  DEL PEAK 38(22Q13.1) WILD-TYPE                   1
D94V11, multiclass
                         clus
vv                        DEL PEAK 38(22Q13.1) MUTATED
  MINIMAL (T3)                                      18
  MODERATE/ADVANCED (T4A)                            1
  NONE                                              63
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK 38(22Q13.1) WILD-TYPE
  MINIMAL (T3)                                       112
  MODERATE/ADVANCED (T4A)                             15
  NONE                                               265
  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    66   6   1   8
  DEL PEAK 38(22Q13.1) WILD-TYPE 312  45   3  22
D94V12, multiclass
    clus
vv   DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE
  R0                           66                            312
  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 38(22Q13.1) MUTATED    45  40
  DEL PEAK 38(22Q13.1) WILD-TYPE 179 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(22Q13.1) MUTATED     45   40
  DEL PEAK 38(22Q13.1) WILD-TYPE  179  221
            clus
vv           DEL PEAK 38(22Q13.1) MUTATED DEL PEAK 38(22Q13.1) WILD-TYPE
  MULTIFOCAL                           45                            179
  UNIFOCAL                             40                            221
[1] 2 2
[1] FALSE
D94V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 38(22Q13.1) MUTATED                                  0    10
  DEL PEAK 38(22Q13.1) WILD-TYPE                                1    39
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 38(22Q13.1) MUTATED                           6    51
  DEL PEAK 38(22Q13.1) WILD-TYPE                        20   270
D94V16, multiclass
                                  clus
vv                                 DEL PEAK 38(22Q13.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      10
  BLACK OR AFRICAN AMERICAN                                   6
  WHITE                                                      51
                                  clus
vv                                 DEL PEAK 38(22Q13.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        39
  BLACK OR AFRICAN AMERICAN                                    20
  WHITE                                                       270
[1] 4 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 38(22Q13.1) MUTATED     6  60
  DEL PEAK 38(22Q13.1) WILD-TYPE  32 290
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(22Q13.1) MUTATED      6   60
  DEL PEAK 38(22Q13.1) WILD-TYPE   32  290
                        clus
vv                       DEL PEAK 38(22Q13.1) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           60
                        clus
vv                       DEL PEAK 38(22Q13.1) WILD-TYPE
  HISPANIC OR LATINO                                 32
  NOT HISPANIC OR LATINO                            290
[1] 2 2
[1] FALSE

Clustering(95) Variable = DEL PEAK 39(22Q13.2) MUTATION ANALYSIS
D95V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 39(22Q13.2) MUTATED    86   1
  DEL PEAK 39(22Q13.2) WILD-TYPE 391  13
  DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE 
                            87                            404 
  DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE 
                             1                             13 
$`DEL PEAK 39(22Q13.2) MUTATED`
TCGA-BJ-A0Z2 TCGA-BJ-A0Z5 TCGA-BJ-A0ZH TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A2P4 
       18.21        14.73        15.12        23.34        20.58         7.04 
TCGA-BJ-A3PT TCGA-BJ-A45D TCGA-BJ-A45F TCGA-CE-A484 TCGA-DE-A0XZ TCGA-DE-A4M8 
       23.31         6.48         3.45         0.39        20.22        18.54 
TCGA-DJ-A13M TCGA-DJ-A13T TCGA-DJ-A1QG TCGA-DJ-A1QN TCGA-DJ-A2PS TCGA-DJ-A2Q0 
       17.26        25.35        13.12         8.88         1.51         8.12 
TCGA-DJ-A2Q7 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A3UK TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.09        12.43        10.85        15.09        12.49        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-E3-A3DZ TCGA-E3-A3E5 TCGA-E8-A432 
       16.41        27.62        10.98        12.07        14.04        14.43 
TCGA-E8-A434 TCGA-EL-A3CL TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3GP 
       14.10        31.66         1.45        74.30        45.40         1.41 
TCGA-EL-A3GW TCGA-EL-A3T2 TCGA-EL-A3ZL TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4JZ 
       37.25        32.48        50.33        48.16        45.80        37.94 
TCGA-EL-A4K6 TCGA-EL-A4K9 TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A22K TCGA-EM-A22L 
       28.73        37.78         8.71        26.86        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22P TCGA-EM-A2CJ TCGA-EM-A2OY TCGA-EM-A3AP TCGA-EM-A3FO 
       14.53        11.15        16.44        17.59         8.35        17.49 
TCGA-EM-A3O9 TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FO TCGA-EM-A4FR TCGA-EM-A4FU 
        9.24        15.62        12.79         8.38         5.03        37.87 
TCGA-ET-A25L TCGA-ET-A25O TCGA-ET-A2N4 TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
       14.79        27.09         2.66        65.36        84.89        98.56 
TCGA-ET-A3BP TCGA-ET-A3DS TCGA-ET-A40P TCGA-ET-A40T TCGA-FE-A237 TCGA-FE-A3PB 
        4.18         0.30         3.22         2.14        81.34        85.15 
TCGA-FY-A3R7 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-IM-A3U3 
        0.03         0.76        17.06         1.15        12.53        16.90 
TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3YD TCGA-J8-A3YH TCGA-KS-A41I TCGA-KS-A4I7 
        9.63        43.17        31.82         5.75        15.98        32.45 
TCGA-KS-A4IB TCGA-MK-A84Z TCGA-QD-A8IV 
       84.72        10.98         5.19 

$`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         8.25        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         7.56        17.69        20.71         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
        8.09         4.87        21.04         2.79         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        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        15.48        18.64 
TCGA-BJ-A45C TCGA-BJ-A45E TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J 
        5.75         0.03         6.35         7.82         6.18         5.06 
TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD 
        8.98         4.93         5.98         0.53         0.10         0.20 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A485 TCGA-DE-A0Y2 
        0.23        11.38        10.68         0.10         0.10        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       36.46         5.98        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-A13O 
       30.02        25.12         4.27         3.22         2.76        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
      137.88         3.39         8.71        13.41        11.90        14.60 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QH TCGA-DJ-A1QI 
        7.99        11.01       100.01        18.51         7.99        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        7.20         1.45         1.02         5.95        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
        5.33         8.48        10.45         9.60        12.56         8.28 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        7.69         5.52         8.78         8.42         9.34         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.21         9.44         9.90         8.61         7.07        10.36 
TCGA-DJ-A2QC TCGA-DJ-A3UM TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       15.88        31.04        19.56        36.33        32.81        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UT 
        8.32        17.36        17.23        18.21        10.78        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
       21.53         2.33        31.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       30.31         1.15        22.29        19.59        13.61        14.27 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A433 TCGA-E8-A436 
       13.81        14.07        14.27         3.02        14.70        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CM TCGA-EL-A3CN 
        7.69        20.68        13.78        13.58        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-A3D5 
       37.94        57.01        80.91         4.18        58.82        33.47 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
      108.36        39.32        30.18       102.84        65.39       124.04 
TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.37       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        38.66        52.73       139.00       131.15       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        12.16       147.42       130.72 
TCGA-EL-A3T1 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
      129.57       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZN 
       66.90        82.82        77.36        78.97        31.50        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JW 
       47.38        52.50        45.53         7.07        44.65        19.30 
TCGA-EL-A4JX TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K7 
       45.96        31.04        19.59        30.51        33.60        41.13 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       29.95        13.32        11.87        18.18        20.91        12.36 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
       18.05        19.79        19.46        54.21        57.01        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22Q TCGA-EM-A2CK 
       14.73        14.50        10.65        11.74        14.24        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ 
       10.49        13.15        22.16        13.84        19.73        12.07 
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        17.46        18.97 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AQ TCGA-EM-A3AR 
       15.68        14.14        19.63        13.38        16.44        16.77 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FP 
       27.95        23.77        16.80        21.01        12.07        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        11.15         7.33        12.53 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SY TCGA-EM-A4FF 
       13.91         7.82        11.51        16.41        13.51        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FV 
       16.90         9.01         4.83         8.61         9.80        12.72 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25M 
        0.95        47.47        48.20        29.69        32.35        12.33 
TCGA-ET-A25N TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       14.79        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       16.08        29.19        19.76        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       80.02        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
       28.24         5.85         2.43         5.56        24.72        38.30 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       42.25         2.37         4.50        80.81        69.24        59.87 
TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40Q 
       43.50        17.98        25.32       132.36        24.72         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        4.80         5.03         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        24.69        68.22       102.90        66.77 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FE-A3PD 
       39.95        33.63        81.83       106.36        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       46.06         4.08         0.89        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
       91.17         1.25         1.15        17.82         1.64         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        1.51         0.76         4.67        16.57        18.08         0.30 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A76V TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
        1.68        17.00        21.67        12.46         2.99        20.05 
TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A41Y TCGA-IM-A420 
       18.61        48.92        47.41        10.26         9.80         2.96 
TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YE TCGA-J8-A3YF 
        8.65        17.23        27.19        11.24        27.85        24.69 
TCGA-J8-A3YG TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41J 
       22.29         2.47         2.60         0.20       143.57        15.68 
TCGA-KS-A41L TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IC 
       86.70         6.02        12.43         6.74        87.39        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         0.72        16.64 
TCGA-MK-A4N7 TCGA-MK-A4N9 
       32.45         8.71 

  DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE 
                          0.03                           0.03 
  DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE 
                         98.56                         158.83 
  DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE 
                        15.090                         17.115 
[1] "0.0 - 98.6 (15.1)"  "0.0 - 158.8 (17.1)"
[1] "hr=" "1.9"
D95V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 39(22Q13.2) MUTATED        49       11        16        1         9
  DEL PEAK 39(22Q13.2) WILD-TYPE     231       40        93        1        36
                                vv
clus                             STAGE IVC
  DEL PEAK 39(22Q13.2) MUTATED           1
  DEL PEAK 39(22Q13.2) WILD-TYPE         5
D95V3, multiclass
           clus
vv          DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE
  STAGE I                             49                            231
  STAGE II                            11                             40
  STAGE III                           16                             93
  STAGE IV                             1                              1
  STAGE IVA                            9                             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    25  34  25   3
  DEL PEAK 39(22Q13.2) WILD-TYPE 115 132 140  18
D95V4, multiclass
    clus
vv   DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE
  T1                           25                            115
  T2                           34                            132
  T3                           25                            140
  T4                            3                             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"
D95V5, binary
                                cls
clus                               0   1
  DEL PEAK 39(22Q13.2) MUTATED    44  35
  DEL PEAK 39(22Q13.2) WILD-TYPE 179 187
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(22Q13.2) MUTATED     44   35
  DEL PEAK 39(22Q13.2) WILD-TYPE  179  187
   clus
vv  DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE
  0                           44                            179
  1                           35                            187
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 39(22Q13.2) MUTATED    43   2  42
  DEL PEAK 39(22Q13.2) WILD-TYPE 230   7 170
D95V6, multiclass
    clus
vv   DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE
  M0                           43                            230
  M1                            2                              7
  MX                           42                            170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V7, binary
                                cls
clus                               0   1
  DEL PEAK 39(22Q13.2) MUTATED    61  26
  DEL PEAK 39(22Q13.2) WILD-TYPE 303 105
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(22Q13.2) MUTATED     61   26
  DEL PEAK 39(22Q13.2) WILD-TYPE  303  105
        clus
vv       DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE
  FEMALE                           61                            303
  MALE                             26                            105
[1] 2 2
[1] FALSE
                                vv
clus                             OTHER  SPECIFY
  DEL PEAK 39(22Q13.2) MUTATED                1
  DEL PEAK 39(22Q13.2) WILD-TYPE              8
                                vv
clus                             THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 39(22Q13.2) MUTATED                                              60
  DEL PEAK 39(22Q13.2) WILD-TYPE                                           293
                                vv
clus                             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 39(22Q13.2) MUTATED                                                                       23
  DEL PEAK 39(22Q13.2) WILD-TYPE                                                                     75
                                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                                                                  32
D95V8, multiclass
                                                                        clus
vv                                                                       DEL PEAK 39(22Q13.2) MUTATED
  OTHER  SPECIFY                                                                                    1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    60
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                           23
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                               3
                                                                        clus
vv                                                                       DEL PEAK 39(22Q13.2) WILD-TYPE
  OTHER  SPECIFY                                                                                      8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     293
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                             75
  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"
D95V9, binary
                                cls
clus                               0   1
  DEL PEAK 39(22Q13.2) MUTATED     1  86
  DEL PEAK 39(22Q13.2) WILD-TYPE  13 395
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(22Q13.2) MUTATED      1   86
  DEL PEAK 39(22Q13.2) WILD-TYPE   13  395
     clus
vv    DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE
  NO                             1                             13
  YES                           86                            395
[1] 2 2
[1] FALSE
D95V10, binary
                                cls
clus                               0   1
  DEL PEAK 39(22Q13.2) MUTATED    78   1
  DEL PEAK 39(22Q13.2) WILD-TYPE 339  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(22Q13.2) MUTATED     78    1
  DEL PEAK 39(22Q13.2) WILD-TYPE  339   16
     clus
vv    DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE
  NO                            78                            339
  YES                            1                             16
[1] 2 2
[1] FALSE
                                vv
clus                             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 39(22Q13.2) MUTATED             18                       1   63
  DEL PEAK 39(22Q13.2) WILD-TYPE          112                      15  265
                                vv
clus                             VERY ADVANCED (T4B)
  DEL PEAK 39(22Q13.2) MUTATED                     0
  DEL PEAK 39(22Q13.2) WILD-TYPE                   1
D95V11, multiclass
                         clus
vv                        DEL PEAK 39(22Q13.2) MUTATED
  MINIMAL (T3)                                      18
  MODERATE/ADVANCED (T4A)                            1
  NONE                                              63
  VERY ADVANCED (T4B)                                0
                         clus
vv                        DEL PEAK 39(22Q13.2) WILD-TYPE
  MINIMAL (T3)                                       112
  MODERATE/ADVANCED (T4A)                             15
  NONE                                               265
  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    66   6   1   8
  DEL PEAK 39(22Q13.2) WILD-TYPE 312  45   3  22
D95V12, multiclass
    clus
vv   DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE
  R0                           66                            312
  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"
D95V13, continuous
D95V14, binary
                                cls
clus                               0   1
  DEL PEAK 39(22Q13.2) MUTATED    45  40
  DEL PEAK 39(22Q13.2) WILD-TYPE 179 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(22Q13.2) MUTATED     45   40
  DEL PEAK 39(22Q13.2) WILD-TYPE  179  221
            clus
vv           DEL PEAK 39(22Q13.2) MUTATED DEL PEAK 39(22Q13.2) WILD-TYPE
  MULTIFOCAL                           45                            179
  UNIFOCAL                             40                            221
[1] 2 2
[1] FALSE
D95V15, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 39(22Q13.2) MUTATED                                  0    10
  DEL PEAK 39(22Q13.2) WILD-TYPE                                1    39
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 39(22Q13.2) MUTATED                           6    51
  DEL PEAK 39(22Q13.2) WILD-TYPE                        20   270
D95V16, multiclass
                                  clus
vv                                 DEL PEAK 39(22Q13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                      10
  BLACK OR AFRICAN AMERICAN                                   6
  WHITE                                                      51
                                  clus
vv                                 DEL PEAK 39(22Q13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        39
  BLACK OR AFRICAN AMERICAN                                    20
  WHITE                                                       270
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V17, binary
                                cls
clus                               0   1
  DEL PEAK 39(22Q13.2) MUTATED     6  60
  DEL PEAK 39(22Q13.2) WILD-TYPE  32 290
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(22Q13.2) MUTATED      6   60
  DEL PEAK 39(22Q13.2) WILD-TYPE   32  290
                        clus
vv                       DEL PEAK 39(22Q13.2) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           60
                        clus
vv                       DEL PEAK 39(22Q13.2) WILD-TYPE
  HISPANIC OR LATINO                                 32
  NOT HISPANIC OR LATINO                            290
[1] 2 2
[1] FALSE

Clustering(96) Variable = DEL PEAK 40(22Q13.32) MUTATION ANALYSIS
D96V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 40(22Q13.32) MUTATED    87   1
  DEL PEAK 40(22Q13.32) WILD-TYPE 390  13
  DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE 
                             88                             403 
  DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE 
                              1                              13 
$`DEL PEAK 40(22Q13.32) MUTATED`
TCGA-BJ-A0Z2 TCGA-BJ-A0Z5 TCGA-BJ-A0ZH TCGA-BJ-A18Y TCGA-BJ-A190 TCGA-BJ-A2P4 
       18.21        14.73        15.12        23.34        20.58         7.04 
TCGA-BJ-A3PT TCGA-BJ-A45D TCGA-BJ-A45F TCGA-CE-A484 TCGA-DE-A0XZ TCGA-DE-A4M8 
       23.31         6.48         3.45         0.39        20.22        18.54 
TCGA-DJ-A13M TCGA-DJ-A13T TCGA-DJ-A1QG TCGA-DJ-A1QN TCGA-DJ-A2PS TCGA-DJ-A2Q0 
       17.26        25.35        13.12         8.88         1.51         8.12 
TCGA-DJ-A2Q7 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A3UK TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.09        12.43        10.85        15.09        12.49        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3VM TCGA-DJ-A4UR TCGA-E3-A3DZ TCGA-E3-A3E5 TCGA-E8-A432 
       16.41        27.62        10.98        12.07        14.04        14.43 
TCGA-E8-A434 TCGA-EL-A3CL TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3GP 
       14.10        31.66         1.45        74.30        45.40         1.41 
TCGA-EL-A3GW TCGA-EL-A3T2 TCGA-EL-A3ZL TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4JZ 
       37.25        32.48        50.33        48.16        45.80        37.94 
TCGA-EL-A4K6 TCGA-EL-A4K9 TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A22K TCGA-EM-A22L 
       28.73        37.78         8.71        26.86        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22P TCGA-EM-A2CJ TCGA-EM-A2OY TCGA-EM-A3AP TCGA-EM-A3FO 
       14.53        11.15        16.44        17.59         8.35        17.49 
TCGA-EM-A3O9 TCGA-EM-A3SX TCGA-EM-A3SZ TCGA-EM-A4FO TCGA-EM-A4FR TCGA-EM-A4FU 
        9.24        15.62        12.79         8.38         5.03        37.87 
TCGA-ET-A25L TCGA-ET-A25O TCGA-ET-A2N4 TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
       14.79        27.09         2.66        65.36        84.89        98.56 
TCGA-ET-A3BP TCGA-ET-A3DS TCGA-ET-A40P TCGA-ET-A40T TCGA-FE-A237 TCGA-FE-A3PB 
        4.18         0.30         3.22         2.14        81.34        85.15 
TCGA-FY-A3R7 TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A3RH 
        0.03         0.76        17.06         1.15        12.53        12.46 
TCGA-IM-A3U3 TCGA-IM-A41Z TCGA-J8-A3O0 TCGA-J8-A3YD TCGA-J8-A3YH TCGA-KS-A41I 
       16.90         9.63        43.17        31.82         5.75        15.98 
TCGA-KS-A4I7 TCGA-KS-A4IB TCGA-MK-A84Z TCGA-QD-A8IV 
       32.45        84.72        10.98         5.19 

$`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         8.25        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         7.56        17.69        20.71         4.83 
TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W 
        8.09         4.87        21.04         2.79         5.10        11.31 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A291 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       17.52         1.22        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        15.48        18.64 
TCGA-BJ-A45C TCGA-BJ-A45E TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A45J 
        5.75         0.03         6.35         7.82         6.18         5.06 
TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD 
        8.98         4.93         5.98         0.53         0.10         0.20 
TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A485 TCGA-DE-A0Y2 
        0.23        11.38        10.68         0.10         0.10        15.42 
TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB 
       36.46         5.98        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-A13O 
       30.02        25.12         4.27         3.22         2.76        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
      137.88         3.39         8.71        13.41        11.90        14.60 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QH TCGA-DJ-A1QI 
        7.99        11.01       100.01        18.51         7.99        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        7.20         1.45         1.02         5.95        10.09         7.99 
TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
        5.33         8.48        10.45         9.60        12.56         8.28 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
        7.69         5.52         8.78         8.42         9.34         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
        9.21         9.44         9.90         8.61         7.07        10.36 
TCGA-DJ-A2QC TCGA-DJ-A3UM TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT 
       15.88        31.04        19.56        36.33        32.81        24.23 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 
       17.69        43.00        11.34        21.37        12.76        25.02 
TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       20.22        30.61        14.56        19.20         9.83        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        11.93        22.92        21.01        18.97         7.76 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UT 
        8.32        17.36        17.23        18.21        10.78        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
       21.53         2.33        31.07        66.38        40.21        63.19 
TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 
       30.31         1.15        22.29        19.59        13.61        14.27 
TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-E8-A433 TCGA-E8-A436 
       13.81        14.07        14.27         3.02        14.70        14.96 
TCGA-E8-A437 TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CM TCGA-EL-A3CN 
        7.69        20.68        13.78        13.58        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-A3D5 
       37.94        57.01        80.91         4.18        58.82        33.47 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
      108.36        39.32        30.18       102.84        65.39       124.04 
TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.37       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        38.66        52.73       139.00       131.15       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        12.16       147.42       130.72 
TCGA-EL-A3T1 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
      129.57       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZN 
       66.90        82.82        77.36        78.97        31.50        53.06 
TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZS TCGA-EL-A3ZT TCGA-EL-A4JW 
       47.38        52.50        45.53         7.07        44.65        19.30 
TCGA-EL-A4JX TCGA-EL-A4K0 TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K7 
       45.96        31.04        19.59        30.51        33.60        41.13 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       29.95        13.32        11.87        18.18        20.91        12.36 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
       18.05        19.79        19.46        54.21        57.01        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22Q TCGA-EM-A2CK 
       14.73        14.50        10.65        11.74        14.24        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OZ 
       10.49        13.15        22.16        13.84        19.73        12.07 
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        17.46        18.97 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AQ TCGA-EM-A3AR 
       15.68        14.14        19.63        13.38        16.44        16.77 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FP 
       27.95        23.77        16.80        21.01        12.07        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        11.15         7.33        12.53 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SY TCGA-EM-A4FF 
       13.91         7.82        11.51        16.41        13.51        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FQ TCGA-EM-A4FV 
       16.90         9.01         4.83         8.61         9.80        12.72 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25M 
        0.95        47.47        48.20        29.69        32.35        12.33 
TCGA-ET-A25N TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ 
       14.79        18.38        29.49        54.05        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       16.08        29.19        19.76        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       80.02        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
       28.24         5.85         2.43         5.56        24.72        38.30 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       42.25         2.37         4.50        80.81        69.24        59.87 
TCGA-ET-A3DR TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40Q 
       43.50        17.98        25.32       132.36        24.72         7.17 
TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        4.80         5.03         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        24.69        68.22       102.90        66.77 
TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PC TCGA-FE-A3PD 
       39.95        33.63        81.83       106.36        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       46.06         4.08         0.89        22.03         0.92        48.10 
TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
       91.17         1.25         1.15        17.82         1.64         0.99 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY 
        1.51         0.76         4.67        16.57        18.08         0.30 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 
        6.87         4.14         6.58         4.54         0.89         1.35 
TCGA-FY-A76V TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 
        1.68        17.00        21.67         2.99        20.05        18.61 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A41Y TCGA-IM-A420 TCGA-IM-A4EB 
       48.92        47.41        10.26         9.80         2.96         8.65 
TCGA-J8-A3NZ TCGA-J8-A3O1 TCGA-J8-A3O2 TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG 
       17.23        27.19        11.24        27.85        24.69        22.29 
TCGA-J8-A42S TCGA-J8-A4HW TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41J TCGA-KS-A41L 
        2.47         2.60         0.20       143.57        15.68        86.70 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IC TCGA-KS-A4ID 
        6.02        12.43         6.74        87.39        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         0.72        16.64        32.45 
TCGA-MK-A4N9 
        8.71 

  DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE 
                           0.03                            0.03 
  DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE 
                          98.56                          158.83 
  DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE 
                          14.94                           17.23 
[1] "0.0 - 98.6 (14.9)"  "0.0 - 158.8 (17.2)"
[1] "hr=" "1.9"
D96V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 40(22Q13.32) MUTATED        50       11        16        1         9
  DEL PEAK 40(22Q13.32) WILD-TYPE     230       40        93        1        36
                                 vv
clus                              STAGE IVC
  DEL PEAK 40(22Q13.32) MUTATED           1
  DEL PEAK 40(22Q13.32) WILD-TYPE         5
D96V3, multiclass
           clus
vv          DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE
  STAGE I                              50                             230
  STAGE II                             11                              40
  STAGE III                            16                              93
  STAGE IV                              1                               1
  STAGE IVA                             9                              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    26  34  25   3
  DEL PEAK 40(22Q13.32) WILD-TYPE 114 132 140  18
D96V4, multiclass
    clus
vv   DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE
  T1                            26                             114
  T2                            34                             132
  T3                            25                             140
  T4                             3                              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"
D96V5, binary
                                 cls
clus                                0   1
  DEL PEAK 40(22Q13.32) MUTATED    45  35
  DEL PEAK 40(22Q13.32) WILD-TYPE 178 187
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(22Q13.32) MUTATED     45   35
  DEL PEAK 40(22Q13.32) WILD-TYPE  178  187
   clus
vv  DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE
  0                            45                             178
  1                            35                             187
[1] 2 2
[1] FALSE
                                 vv
clus                               M0  M1  MX
  DEL PEAK 40(22Q13.32) MUTATED    44   2  42
  DEL PEAK 40(22Q13.32) WILD-TYPE 229   7 170
D96V6, multiclass
    clus
vv   DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE
  M0                            44                             229
  M1                             2                               7
  MX                            42                             170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V7, binary
                                 cls
clus                                0   1
  DEL PEAK 40(22Q13.32) MUTATED    62  26
  DEL PEAK 40(22Q13.32) WILD-TYPE 302 105
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(22Q13.32) MUTATED     62   26
  DEL PEAK 40(22Q13.32) WILD-TYPE  302  105
        clus
vv       DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE
  FEMALE                            62                             302
  MALE                              26                             105
[1] 2 2
[1] FALSE
                                 vv
clus                              OTHER  SPECIFY
  DEL PEAK 40(22Q13.32) MUTATED                1
  DEL PEAK 40(22Q13.32) WILD-TYPE              8
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 40(22Q13.32) MUTATED                                              60
  DEL PEAK 40(22Q13.32) WILD-TYPE                                           293
                                 vv
clus                              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 40(22Q13.32) MUTATED                                                                       24
  DEL PEAK 40(22Q13.32) WILD-TYPE                                                                     74
                                 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                                                                  32
D96V8, multiclass
                                                                        clus
vv                                                                       DEL PEAK 40(22Q13.32) MUTATED
  OTHER  SPECIFY                                                                                     1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                     60
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                            24
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                                3
                                                                        clus
vv                                                                       DEL PEAK 40(22Q13.32) WILD-TYPE
  OTHER  SPECIFY                                                                                       8
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                      293
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)                              74
  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"
D96V9, binary
                                 cls
clus                                0   1
  DEL PEAK 40(22Q13.32) MUTATED     1  87
  DEL PEAK 40(22Q13.32) WILD-TYPE  13 394
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(22Q13.32) MUTATED      1   87
  DEL PEAK 40(22Q13.32) WILD-TYPE   13  394
     clus
vv    DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE
  NO                              1                              13
  YES                            87                             394
[1] 2 2
[1] FALSE
D96V10, binary
                                 cls
clus                                0   1
  DEL PEAK 40(22Q13.32) MUTATED    79   1
  DEL PEAK 40(22Q13.32) WILD-TYPE 338  16
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(22Q13.32) MUTATED     79    1
  DEL PEAK 40(22Q13.32) WILD-TYPE  338   16
     clus
vv    DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE
  NO                             79                             338
  YES                             1                              16
[1] 2 2
[1] FALSE
                                 vv
clus                              MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DEL PEAK 40(22Q13.32) MUTATED             18                       1   64
  DEL PEAK 40(22Q13.32) WILD-TYPE          112                      15  264
                                 vv
clus                              VERY ADVANCED (T4B)
  DEL PEAK 40(22Q13.32) MUTATED                     0
  DEL PEAK 40(22Q13.32) WILD-TYPE                   1
D96V11, multiclass
                         clus
vv                        DEL PEAK 40(22Q13.32) MUTATED
  MINIMAL (T3)                                       18
  MODERATE/ADVANCED (T4A)                             1
  NONE                                               64
  VERY ADVANCED (T4B)                                 0
                         clus
vv                        DEL PEAK 40(22Q13.32) WILD-TYPE
  MINIMAL (T3)                                        112
  MODERATE/ADVANCED (T4A)                              15
  NONE                                                264
  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    66   6   1   8
  DEL PEAK 40(22Q13.32) WILD-TYPE 312  45   3  22
D96V12, multiclass
    clus
vv   DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE
  R0                            66                             312
  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"
D96V13, continuous
D96V14, binary
                                 cls
clus                                0   1
  DEL PEAK 40(22Q13.32) MUTATED    46  40
  DEL PEAK 40(22Q13.32) WILD-TYPE 178 221
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(22Q13.32) MUTATED     46   40
  DEL PEAK 40(22Q13.32) WILD-TYPE  178  221
            clus
vv           DEL PEAK 40(22Q13.32) MUTATED DEL PEAK 40(22Q13.32) WILD-TYPE
  MULTIFOCAL                            46                             178
  UNIFOCAL                              40                             221
[1] 2 2
[1] FALSE
D96V15, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 40(22Q13.32) MUTATED                                  0    10
  DEL PEAK 40(22Q13.32) WILD-TYPE                                1    39
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 40(22Q13.32) MUTATED                           6    52
  DEL PEAK 40(22Q13.32) WILD-TYPE                        20   269
D96V16, multiclass
                                  clus
vv                                 DEL PEAK 40(22Q13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                    6
  WHITE                                                       52
                                  clus
vv                                 DEL PEAK 40(22Q13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         39
  BLACK OR AFRICAN AMERICAN                                     20
  WHITE                                                        269
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V17, binary
                                 cls
clus                                0   1
  DEL PEAK 40(22Q13.32) MUTATED     6  61
  DEL PEAK 40(22Q13.32) WILD-TYPE  32 289
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(22Q13.32) MUTATED      6   61
  DEL PEAK 40(22Q13.32) WILD-TYPE   32  289
                        clus
vv                       DEL PEAK 40(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            61
                        clus
vv                       DEL PEAK 40(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                  32
  NOT HISPANIC OR LATINO                             289
[1] 2 2
[1] FALSE

Clustering(97) Variable = DEL PEAK 41(XQ23) MUTATION ANALYSIS
D97V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 41(XQ23) MUTATED     4   0
  DEL PEAK 41(XQ23) WILD-TYPE 473  14
  DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE 
                          4                         487 
  DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE 
                          0                          14 
$`DEL PEAK 41(XQ23) MUTATED`
TCGA-BJ-A0Z0 TCGA-BJ-A190 TCGA-EM-A1YE TCGA-ET-A40S 
       13.78        20.58        54.08         5.03 

$`DEL PEAK 41(XQ23) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       24.79        18.21        16.34        14.73         8.25        18.87 
TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ 
        4.01        11.57        16.73         7.56        15.12        17.69 
TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S 
       23.34        20.71         4.83         8.09         4.87        21.04 
TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 
        2.79         5.10        11.31        17.52         1.22        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        15.48        23.31        18.64         5.75 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
        6.48         0.03         3.45         6.35         7.82         6.18 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
        5.06         8.98         4.93         5.98         0.53         0.10 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
        0.20         0.23        11.38        10.68         0.10         0.39 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.10        20.22        15.42        36.46         5.98        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-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
        4.27         3.22         2.76        17.26        14.07       137.88 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
        3.39         8.71        25.35        13.41        11.90        14.60 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        7.99        11.01       100.01        18.51        13.12         7.99 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96         7.20         1.45         8.88         1.02         5.95 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS 
       10.09         7.99         5.33         8.48        10.45         1.51 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY 
        9.60        12.56         8.28         7.69         5.52         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.42         8.12         9.34         6.77         9.21         9.44 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
        9.90         8.61        10.09         7.07        10.36        12.43 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        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        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04         1.15        22.29 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        12.36        18.05        19.79        19.46        54.21 
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        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       10.49        13.15        22.16        13.84        19.73        17.59 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       12.07        17.59        17.46        17.29        14.60        17.46 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       18.97        15.68        14.14        19.63        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       16.44        16.77        27.95        23.77        16.80        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 
       11.15         7.33        12.53         9.24        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        16.41        15.62        13.51        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
       80.02        65.36        84.89        98.56        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        2.43         5.56        24.72        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        4.80         2.14         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        24.69        68.22       102.90        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       81.34        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        46.06         4.08         0.89        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10        91.17         1.25         1.15        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        1.64         0.99         1.51         0.76         0.03         4.67 
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         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74        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         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE 
                       5.03                        0.03 
  DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE 
                      54.08                      158.83 
  DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE 
                      17.18                       16.57 
[1] "5.0 - 54.1 (17.2)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "3300000"
D97V2, 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     280       47       109        2        45
                             vv
clus                          STAGE IVC
  DEL PEAK 41(XQ23) MUTATED           0
  DEL PEAK 41(XQ23) WILD-TYPE         6
D97V3, multiclass
           clus
vv          DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE
  STAGE I                           0                         280
  STAGE II                          4                          47
  STAGE III                         0                         109
  STAGE IV                          0                           2
  STAGE IVA                         0                          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 41(XQ23) MUTATED     0   4   0   0
  DEL PEAK 41(XQ23) WILD-TYPE 140 162 165  21
D97V4, multiclass
    clus
vv   DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE
  T1                         0                         140
  T2                         4                         162
  T3                         0                         165
  T4                         0                          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"
D97V5, binary
                             cls
clus                            0   1
  DEL PEAK 41(XQ23) MUTATED     4   0
  DEL PEAK 41(XQ23) WILD-TYPE 219 222
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 41(XQ23) MUTATED      4    0
  DEL PEAK 41(XQ23) WILD-TYPE  219  222
   clus
vv  DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE
  0                         4                         219
  1                         0                         222
[1] 2 2
[1] FALSE
                             vv
clus                           M0  M1  MX
  DEL PEAK 41(XQ23) MUTATED     0   0   4
  DEL PEAK 41(XQ23) WILD-TYPE 273   9 208
D97V6, multiclass
    clus
vv   DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE
  M0                         0                         273
  M1                         0                           9
  MX                         4                         208
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V7, binary
                             cls
clus                            0   1
  DEL PEAK 41(XQ23) MUTATED     1   3
  DEL PEAK 41(XQ23) WILD-TYPE 363 128
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 41(XQ23) MUTATED      1    3
  DEL PEAK 41(XQ23) WILD-TYPE  363  128
        clus
vv       DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE
  FEMALE                         1                         363
  MALE                           3                         128
[1] 2 2
[1] FALSE
                             vv
clus                          OTHER  SPECIFY
  DEL PEAK 41(XQ23) MUTATED                0
  DEL PEAK 41(XQ23) WILD-TYPE              9
                             vv
clus                          THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 41(XQ23) MUTATED                                               3
  DEL PEAK 41(XQ23) WILD-TYPE                                           350
                             vv
clus                          THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 41(XQ23) MUTATED                                                                        1
  DEL PEAK 41(XQ23) WILD-TYPE                                                                     97
                             vv
clus                          THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DEL PEAK 41(XQ23) MUTATED                                                                     0
  DEL PEAK 41(XQ23) WILD-TYPE                                                                  35
D97V8, 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                                                                                   9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                  350
  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"
D97V9, binary
                             cls
clus                            0   1
  DEL PEAK 41(XQ23) MUTATED     0   4
  DEL PEAK 41(XQ23) WILD-TYPE  14 477
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 41(XQ23) MUTATED      0    4
  DEL PEAK 41(XQ23) WILD-TYPE   14  477
     clus
vv    DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE
  NO                          0                          14
  YES                         4                         477
[1] 2 2
[1] FALSE
D97V10, binary
                             cls
clus                            0   1
  DEL PEAK 41(XQ23) MUTATED     2   1
  DEL PEAK 41(XQ23) WILD-TYPE 415  16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 41(XQ23) MUTATED      2    1
  DEL PEAK 41(XQ23) WILD-TYPE  415   16
     clus
vv    DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE
  NO                          2                         415
  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          130                      16  324
                             vv
clus                          VERY ADVANCED (T4B)
  DEL PEAK 41(XQ23) MUTATED                     0
  DEL PEAK 41(XQ23) WILD-TYPE                   1
D97V11, multiclass
                         clus
vv                        DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE
  MINIMAL (T3)                                    0                         130
  MODERATE/ADVANCED (T4A)                         0                          16
  NONE                                            4                         324
  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 375  51   4  29
D97V12, multiclass
    clus
vv   DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE
  R0                         3                         375
  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"
D97V13, continuous
D97V14, binary
                             cls
clus                            0   1
  DEL PEAK 41(XQ23) MUTATED     2   2
  DEL PEAK 41(XQ23) WILD-TYPE 222 259
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 41(XQ23) MUTATED      2    2
  DEL PEAK 41(XQ23) WILD-TYPE  222  259
            clus
vv           DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE
  MULTIFOCAL                         2                         222
  UNIFOCAL                           2                         259
[1] 2 2
[1] FALSE
D97V15, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 41(XQ23) MUTATED                                  0     0
  DEL PEAK 41(XQ23) WILD-TYPE                                1    49
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 41(XQ23) MUTATED                           0     2
  DEL PEAK 41(XQ23) WILD-TYPE                        26   319
D97V16, multiclass
[1] "Remove cluster labels:"    "DEL PEAK 41(XQ23) MUTATED"
clus
  DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE 
                          2                         395 
                 TCGA-BJ-A0YZ                  TCGA-BJ-A0Z2 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A0Z3                  TCGA-BJ-A0Z5 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A0Z9                  TCGA-BJ-A0ZA 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A0ZB                  TCGA-BJ-A0ZC 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A0ZE                  TCGA-BJ-A0ZG 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A0ZH                  TCGA-BJ-A0ZJ 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A18Y                  TCGA-BJ-A18Z 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A191                  TCGA-BJ-A192 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A28R                  TCGA-BJ-A28S 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A28T                  TCGA-BJ-A28V 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A28W                  TCGA-BJ-A28X 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A28Z                  TCGA-BJ-A290 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A291                  TCGA-BJ-A2N7 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A2N8                  TCGA-BJ-A2N9 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A2NA                  TCGA-BJ-A2P4 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A3EZ                  TCGA-BJ-A3F0 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A3PR                  TCGA-BJ-A3PT 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A3PU                  TCGA-BJ-A45C 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A45D                  TCGA-BJ-A45E 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A45F                  TCGA-BJ-A45G 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A45H                  TCGA-BJ-A45I 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A45J                  TCGA-BJ-A45K 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-BJ-A4O8                  TCGA-BJ-A4O9 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-CE-A13K                  TCGA-CE-A27D 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-CE-A3MD                  TCGA-CE-A3ME 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-CE-A481                  TCGA-CE-A482 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-CE-A483                  TCGA-CE-A484 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-CE-A485                  TCGA-DE-A0XZ 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DE-A0Y2                  TCGA-DE-A0Y3 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DE-A2OL                  TCGA-DE-A3KN 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DE-A4M8                  TCGA-DE-A4M9 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DE-A4MA                  TCGA-DE-A4MB 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DE-A4MC                  TCGA-DE-A4MD 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DE-A69J                  TCGA-DE-A69K 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DE-A7U5                  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-A2PT                  TCGA-DJ-A2PU 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A2PV                  TCGA-DJ-A2PW 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A2PX                  TCGA-DJ-A2PY 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A2PZ                  TCGA-DJ-A2Q0 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A2Q1                  TCGA-DJ-A2Q2 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A2Q3                  TCGA-DJ-A2Q4 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A2Q5                  TCGA-DJ-A2Q6 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A2Q7                  TCGA-DJ-A2Q9 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A2QA                  TCGA-DJ-A2QB 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A3UK                  TCGA-DJ-A3UM 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A3UN                  TCGA-DJ-A3UO 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A3UQ                  TCGA-DJ-A3UR 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A3US                  TCGA-DJ-A3UT 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A3UU                  TCGA-DJ-A3UW 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A3UX                  TCGA-DJ-A3UY 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A3UZ                  TCGA-DJ-A3V2 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A3V3                  TCGA-DJ-A3V4 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A3V5                  TCGA-DJ-A3V7 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A3V8                  TCGA-DJ-A3V9 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A3VD                  TCGA-DJ-A3VE 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A3VF                  TCGA-DJ-A3VG 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A3VJ                  TCGA-DJ-A3VL 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-DJ-A3VM                  TCGA-DJ-A4UL 
"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-A2JQ 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-E8-A3X7                  TCGA-E8-A413 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-E8-A414                  TCGA-E8-A415 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-E8-A416                  TCGA-E8-A417 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-E8-A418                  TCGA-E8-A419 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-E8-A432                  TCGA-E8-A433 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-E8-A434                  TCGA-E8-A436 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-E8-A437                  TCGA-E8-A438 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-E8-A44K                  TCGA-E8-A44M 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3CL                  TCGA-EL-A3CM 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3CN                  TCGA-EL-A3CO 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3CP                  TCGA-EL-A3CR 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3CS                  TCGA-EL-A3CT 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3CU                  TCGA-EL-A3CV 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3CW                  TCGA-EL-A3CX 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3CY                  TCGA-EL-A3CZ 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3D0                  TCGA-EL-A3D1 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3D4                  TCGA-EL-A3D5 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3D6                  TCGA-EL-A3GO 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3GP                  TCGA-EL-A3GQ 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3GR                  TCGA-EL-A3GS 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3GU                  TCGA-EL-A3GV 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3GW                  TCGA-EL-A3GX 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3GY                  TCGA-EL-A3GZ 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3H1                  TCGA-EL-A3H2 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3H3                  TCGA-EL-A3H4 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3H5                  TCGA-EL-A3H7 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3H8                  TCGA-EL-A3MW 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3MX                  TCGA-EL-A3MY 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3MZ                  TCGA-EL-A3N2 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3N3                  TCGA-EL-A3T0 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3T1                  TCGA-EL-A3T2 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3T3                  TCGA-EL-A3T6 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3T7                  TCGA-EL-A3T8 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3T9                  TCGA-EL-A3TA 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3TB                  TCGA-EL-A3ZG 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3ZH                  TCGA-EL-A3ZK 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3ZL                  TCGA-EL-A3ZN 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3ZO                  TCGA-EL-A3ZP 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3ZQ                  TCGA-EL-A3ZR 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A3ZS                  TCGA-EL-A3ZT 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A4JV                  TCGA-EL-A4JW 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A4JX                  TCGA-EL-A4JZ 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A4K0                  TCGA-EL-A4K1 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A4K2                  TCGA-EL-A4K4 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A4K6                  TCGA-EL-A4K7 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A4K9                  TCGA-EL-A4KD 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A4KG                  TCGA-EL-A4KH 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-EL-A4KI                  TCGA-ET-A25G 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A25I                  TCGA-ET-A25J 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A25K                  TCGA-ET-A25L 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A25M                  TCGA-ET-A25N 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A25O                  TCGA-ET-A25P 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A25R                  TCGA-ET-A2MX 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A2MY                  TCGA-ET-A2MZ 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A2N0                  TCGA-ET-A2N1 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A2N3                  TCGA-ET-A2N4 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A2N5                  TCGA-ET-A39I 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A39J                  TCGA-ET-A39K 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A39M                  TCGA-ET-A39N 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A39O                  TCGA-ET-A39P 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A39R                  TCGA-ET-A39S 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A39T                  TCGA-ET-A3BN 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A3BO                  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-A3DO 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A3DP                  TCGA-ET-A3DQ 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A3DR                  TCGA-ET-A3DS 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A3DT                  TCGA-ET-A3DU 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A3DV                  TCGA-ET-A3DW 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A40P                  TCGA-ET-A40Q 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A40R                  TCGA-ET-A40T 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-ET-A4KN                  TCGA-ET-A4KQ 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FE-A22Z                  TCGA-FE-A230 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FE-A231                  TCGA-FE-A232 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FE-A233                  TCGA-FE-A234 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FE-A235                  TCGA-FE-A236 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FE-A237                  TCGA-FE-A238 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FE-A239                  TCGA-FE-A23A 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FE-A3PA                  TCGA-FE-A3PB 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FE-A3PC                  TCGA-FE-A3PD 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FK-A3S3                  TCGA-FK-A3SB 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FK-A3SD                  TCGA-FK-A3SE 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FK-A3SG                  TCGA-FK-A3SH 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FK-A4UB                  TCGA-FY-A2QD 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FY-A3BL                  TCGA-FY-A3I4 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FY-A3I5                  TCGA-FY-A3NM 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FY-A3ON                  TCGA-FY-A3R6 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FY-A3R7                  TCGA-FY-A3R8 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FY-A3R9                  TCGA-FY-A3RA 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FY-A3W9                  TCGA-FY-A3WA 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FY-A3YR                  TCGA-FY-A40K 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FY-A40L                  TCGA-FY-A40M 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FY-A40N                  TCGA-FY-A4B0 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FY-A4B3                  TCGA-FY-A4B4 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-FY-A76V                  TCGA-GE-A2C6 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-H2-A26U                  TCGA-H2-A2K9 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-H2-A3RH                  TCGA-H2-A3RI 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-H2-A421                  TCGA-H2-A422 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-IM-A3EB                  TCGA-IM-A3ED 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-IM-A3U2                  TCGA-IM-A3U3 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-IM-A41Y                  TCGA-IM-A41Z 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-IM-A420                  TCGA-IM-A4EB 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-J8-A3NZ                  TCGA-J8-A3O0 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-J8-A3O1                  TCGA-J8-A3O2 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-J8-A3YD                  TCGA-J8-A3YE 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-J8-A3YF                  TCGA-J8-A3YG 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-J8-A3YH                  TCGA-J8-A42S 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-J8-A4HW                  TCGA-J8-A4HY 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-KS-A41F                  TCGA-KS-A41I 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-KS-A41J                  TCGA-KS-A41L 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-KS-A4I1                  TCGA-KS-A4I3 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-KS-A4I5                  TCGA-KS-A4I7 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-KS-A4I9                  TCGA-KS-A4IB 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-KS-A4IC                  TCGA-KS-A4ID 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-L6-A4EP                  TCGA-L6-A4EQ 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-L6-A4ET                  TCGA-L6-A4EU 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-MK-A4N6                  TCGA-MK-A4N7 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-MK-A4N9                  TCGA-MK-A84Z 
"DEL PEAK 41(XQ23) WILD-TYPE" "DEL PEAK 41(XQ23) WILD-TYPE" 
                 TCGA-QD-A8IV 
"DEL PEAK 41(XQ23) WILD-TYPE" 
D97V17, binary
                             cls
clus                            0   1
  DEL PEAK 41(XQ23) MUTATED     0   3
  DEL PEAK 41(XQ23) WILD-TYPE  38 347
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 41(XQ23) MUTATED      0    3
  DEL PEAK 41(XQ23) WILD-TYPE   38  347
                        clus
vv                       DEL PEAK 41(XQ23) MUTATED DEL PEAK 41(XQ23) WILD-TYPE
  HISPANIC OR LATINO                             0                          38
  NOT HISPANIC OR LATINO                         3                         347
[1] 2 2
[1] FALSE

Clustering(98) Variable = DEL PEAK 42(XQ22.3) MUTATION ANALYSIS
D98V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 42(XQ22.3) MUTATED     4   0
  DEL PEAK 42(XQ22.3) WILD-TYPE 473  14
  DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE 
                            4                           487 
  DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE 
                            0                            14 
$`DEL PEAK 42(XQ22.3) MUTATED`
TCGA-BJ-A0Z0 TCGA-BJ-A190 TCGA-EM-A1YE TCGA-ET-A40S 
       13.78        20.58        54.08         5.03 

$`DEL PEAK 42(XQ22.3) WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       24.79        18.21        16.34        14.73         8.25        18.87 
TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ 
        4.01        11.57        16.73         7.56        15.12        17.69 
TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S 
       23.34        20.71         4.83         8.09         4.87        21.04 
TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28W TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 
        2.79         5.10        11.31        17.52         1.22        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        15.48        23.31        18.64         5.75 
TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I 
        6.48         0.03         3.45         6.35         7.82         6.18 
TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D 
        5.06         8.98         4.93         5.98         0.53         0.10 
TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 TCGA-CE-A484 
        0.20         0.23        11.38        10.68         0.10         0.39 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.10        20.22        15.42        36.46         5.98        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-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
        4.27         3.22         2.76        17.26        14.07       137.88 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
        3.39         8.71        25.35        13.41        11.90        14.60 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        7.99        11.01       100.01        18.51        13.12         7.99 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96         7.20         1.45         8.88         1.02         5.95 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS 
       10.09         7.99         5.33         8.48        10.45         1.51 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY 
        9.60        12.56         8.28         7.69         5.52         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.42         8.12         9.34         6.77         9.21         9.44 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
        9.90         8.61        10.09         7.07        10.36        12.43 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       10.85        15.88        15.09        31.04        12.49        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        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ TCGA-DJ-A3V0 TCGA-DJ-A3V2 
       43.00        11.34        21.37        12.76        25.02        20.22 
TCGA-DJ-A3V3 TCGA-DJ-A3V4 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 TCGA-DJ-A3V9 
       30.61        14.56        19.20         9.83        21.27        20.48 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VG 
       11.93        22.92        21.01        18.97         7.76         8.32 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UQ TCGA-DJ-A4UR 
       17.36        17.23        27.62        18.21        10.78        10.98 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04         1.15        22.29 
TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 
       19.59        13.61        14.27        13.81        14.07        14.27 
TCGA-E8-A418 TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 
        3.02        14.43        14.70        14.10        14.96         7.69 
TCGA-E8-A438 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       20.68        13.78        13.58        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        80.91         4.18        58.82         1.45 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       74.30        45.40        33.47       108.36        39.32         1.41 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       30.18       102.84        65.39       124.04        50.37        37.25 
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 
       38.66        52.73       139.00       131.15       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        12.16       147.42       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       116.91        98.24        41.29        95.38         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        77.36        78.97        31.50        50.33 
TCGA-EL-A3ZN TCGA-EL-A3ZO TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       53.06        47.38        52.50        45.53        48.16         7.07 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       44.65        45.80        19.30        45.96        37.94        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       19.59        30.51        33.60        28.73        41.13        37.78 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       29.95        13.32        11.87         8.71        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        12.36        18.05        19.79        19.46        54.21 
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        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS 
       13.18        23.51         6.05         2.99        12.30        15.19 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       10.49        13.15        22.16        13.84        19.73        17.59 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       12.07        17.59        17.46        17.29        14.60        17.46 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       18.97        15.68        14.14        19.63        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       16.44        16.77        27.95        23.77        16.80        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 
       11.15         7.33        12.53         9.24        13.91         7.82 
TCGA-EM-A3ST TCGA-EM-A3SU TCGA-EM-A3SX TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF 
       11.51        16.41        15.62        13.51        12.79        70.65 
TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ 
       16.90         9.01         4.83         8.61         8.38         9.80 
TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
        5.03        37.87        12.72         0.95        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
       29.69        32.35        14.79        12.33        14.79        27.09 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       18.38        29.49        54.05        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N3 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       29.19        19.76         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
       80.02        65.36        84.89        98.56        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        2.43         5.56        24.72        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40P TCGA-ET-A40Q 
       17.98        25.32       132.36        24.72         3.22         7.17 
TCGA-ET-A40R TCGA-ET-A40T TCGA-ET-A4KN TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 
        4.80         2.14         4.01         1.94        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        24.69        68.22       102.90        66.77 
TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA TCGA-FE-A3PB 
       81.34        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        46.06         4.08         0.89        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10        91.17         1.25         1.15        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        1.64         0.99         1.51         0.76         0.03         4.67 
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         6.87 
TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B3 TCGA-FY-A4B4 
        4.14         6.58         4.54         0.89         1.35         1.15 
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        10.26        16.90 
TCGA-IM-A41Y TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3NZ TCGA-J8-A3O0 
        9.80         9.63         2.96         8.65        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        86.70         6.02        12.43         6.74        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         0.72        16.64        32.45         8.71        10.98 
TCGA-QD-A8IV 
        5.19 

  DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE 
                         5.03                          0.03 
  DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE 
                        54.08                        158.83 
  DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE 
                        17.18                         16.57 
[1] "5.0 - 54.1 (17.2)"  "0.0 - 158.8 (16.6)"
[1] "hr="     "3300000"
D98V2, 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     280       47       109        2        45
                               vv
clus                            STAGE IVC
  DEL PEAK 42(XQ22.3) MUTATED           0
  DEL PEAK 42(XQ22.3) WILD-TYPE         6
D98V3, multiclass
           clus
vv          DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE
  STAGE I                             0                           280
  STAGE II                            4                            47
  STAGE III                           0                           109
  STAGE IV                            0                             2
  STAGE IVA                           0                            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 42(XQ22.3) MUTATED     0   4   0   0
  DEL PEAK 42(XQ22.3) WILD-TYPE 140 162 165  21
D98V4, multiclass
    clus
vv   DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE
  T1                           0                           140
  T2                           4                           162
  T3                           0                           165
  T4                           0                            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"
D98V5, binary
                               cls
clus                              0   1
  DEL PEAK 42(XQ22.3) MUTATED     4   0
  DEL PEAK 42(XQ22.3) WILD-TYPE 219 222
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 42(XQ22.3) MUTATED      4    0
  DEL PEAK 42(XQ22.3) WILD-TYPE  219  222
   clus
vv  DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE
  0                           4                           219
  1                           0                           222
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  DEL PEAK 42(XQ22.3) MUTATED     0   0   4
  DEL PEAK 42(XQ22.3) WILD-TYPE 273   9 208
D98V6, multiclass
    clus
vv   DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE
  M0                           0                           273
  M1                           0                             9
  MX                           4                           208
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V7, binary
                               cls
clus                              0   1
  DEL PEAK 42(XQ22.3) MUTATED     1   3
  DEL PEAK 42(XQ22.3) WILD-TYPE 363 128
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 42(XQ22.3) MUTATED      1    3
  DEL PEAK 42(XQ22.3) WILD-TYPE  363  128
        clus
vv       DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE
  FEMALE                           1                           363
  MALE                             3                           128
[1] 2 2
[1] FALSE
                               vv
clus                            OTHER  SPECIFY
  DEL PEAK 42(XQ22.3) MUTATED                0
  DEL PEAK 42(XQ22.3) WILD-TYPE              9
                               vv
clus                            THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DEL PEAK 42(XQ22.3) MUTATED                                               3
  DEL PEAK 42(XQ22.3) WILD-TYPE                                           350
                               vv
clus                            THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DEL PEAK 42(XQ22.3) MUTATED                                                                        1
  DEL PEAK 42(XQ22.3) WILD-TYPE                                                                     97
                               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                                                                  35
D98V8, 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                                                                                     9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                                    350
  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"
D98V9, binary
                               cls
clus                              0   1
  DEL PEAK 42(XQ22.3) MUTATED     0   4
  DEL PEAK 42(XQ22.3) WILD-TYPE  14 477
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 42(XQ22.3) MUTATED      0    4
  DEL PEAK 42(XQ22.3) WILD-TYPE   14  477
     clus
vv    DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE
  NO                            0                            14
  YES                           4                           477
[1] 2 2
[1] FALSE
D98V10, binary
                               cls
clus                              0   1
  DEL PEAK 42(XQ22.3) MUTATED     2   1
  DEL PEAK 42(XQ22.3) WILD-TYPE 415  16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 42(XQ22.3) MUTATED      2    1
  DEL PEAK 42(XQ22.3) WILD-TYPE  415   16
     clus
vv    DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE
  NO                            2                           415
  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          130                      16  324
                               vv
clus                            VERY ADVANCED (T4B)
  DEL PEAK 42(XQ22.3) MUTATED                     0
  DEL PEAK 42(XQ22.3) WILD-TYPE                   1
D98V11, 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)                                      130
  MODERATE/ADVANCED (T4A)                            16
  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 42(XQ22.3) MUTATED     3   0   0   1
  DEL PEAK 42(XQ22.3) WILD-TYPE 375  51   4  29
D98V12, multiclass
    clus
vv   DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE
  R0                           3                           375
  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"
D98V13, continuous
D98V14, binary
                               cls
clus                              0   1
  DEL PEAK 42(XQ22.3) MUTATED     2   2
  DEL PEAK 42(XQ22.3) WILD-TYPE 222 259
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 42(XQ22.3) MUTATED      2    2
  DEL PEAK 42(XQ22.3) WILD-TYPE  222  259
            clus
vv           DEL PEAK 42(XQ22.3) MUTATED DEL PEAK 42(XQ22.3) WILD-TYPE
  MULTIFOCAL                           2                           222
  UNIFOCAL                             2                           259
[1] 2 2
[1] FALSE
D98V15, 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    49
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 42(XQ22.3) MUTATED                           0     2
  DEL PEAK 42(XQ22.3) WILD-TYPE                        26   319
D98V16, 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                           395 
                   TCGA-BJ-A0YZ                    TCGA-BJ-A0Z2 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A0Z3                    TCGA-BJ-A0Z5 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A0Z9                    TCGA-BJ-A0ZA 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A0ZB                    TCGA-BJ-A0ZC 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A0ZE                    TCGA-BJ-A0ZG 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A0ZH                    TCGA-BJ-A0ZJ 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A18Y                    TCGA-BJ-A18Z 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A191                    TCGA-BJ-A192 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A28R                    TCGA-BJ-A28S 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A28T                    TCGA-BJ-A28V 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A28W                    TCGA-BJ-A28X 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A28Z                    TCGA-BJ-A290 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A291                    TCGA-BJ-A2N7 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A2N8                    TCGA-BJ-A2N9 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A2NA                    TCGA-BJ-A2P4 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A3EZ                    TCGA-BJ-A3F0 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A3PR                    TCGA-BJ-A3PT 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A3PU                    TCGA-BJ-A45C 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A45D                    TCGA-BJ-A45E 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A45F                    TCGA-BJ-A45G 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A45H                    TCGA-BJ-A45I 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A45J                    TCGA-BJ-A45K 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-BJ-A4O8                    TCGA-BJ-A4O9 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-CE-A13K                    TCGA-CE-A27D 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-CE-A3MD                    TCGA-CE-A3ME 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-CE-A481                    TCGA-CE-A482 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-CE-A483                    TCGA-CE-A484 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-CE-A485                    TCGA-DE-A0XZ 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DE-A0Y2                    TCGA-DE-A0Y3 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DE-A2OL                    TCGA-DE-A3KN 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DE-A4M8                    TCGA-DE-A4M9 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DE-A4MA                    TCGA-DE-A4MB 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DE-A4MC                    TCGA-DE-A4MD 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DE-A69J                    TCGA-DE-A69K 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DE-A7U5                    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-A2PT                    TCGA-DJ-A2PU 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A2PV                    TCGA-DJ-A2PW 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A2PX                    TCGA-DJ-A2PY 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A2PZ                    TCGA-DJ-A2Q0 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q1                    TCGA-DJ-A2Q2 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q3                    TCGA-DJ-A2Q4 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q5                    TCGA-DJ-A2Q6 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A2Q7                    TCGA-DJ-A2Q9 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A2QA                    TCGA-DJ-A2QB 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A3UK                    TCGA-DJ-A3UM 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A3UN                    TCGA-DJ-A3UO 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A3UQ                    TCGA-DJ-A3UR 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A3US                    TCGA-DJ-A3UT 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A3UU                    TCGA-DJ-A3UW 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A3UX                    TCGA-DJ-A3UY 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A3UZ                    TCGA-DJ-A3V2 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A3V3                    TCGA-DJ-A3V4 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A3V5                    TCGA-DJ-A3V7 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A3V8                    TCGA-DJ-A3V9 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A3VD                    TCGA-DJ-A3VE 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A3VF                    TCGA-DJ-A3VG 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A3VJ                    TCGA-DJ-A3VL 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-DJ-A3VM                    TCGA-DJ-A4UL 
"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-A2JQ 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-E8-A3X7                    TCGA-E8-A413 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-E8-A414                    TCGA-E8-A415 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-E8-A416                    TCGA-E8-A417 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-E8-A418                    TCGA-E8-A419 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-E8-A432                    TCGA-E8-A433 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-E8-A434                    TCGA-E8-A436 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-E8-A437                    TCGA-E8-A438 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-E8-A44K                    TCGA-E8-A44M 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3CL                    TCGA-EL-A3CM 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3CN                    TCGA-EL-A3CO 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3CP                    TCGA-EL-A3CR 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3CS                    TCGA-EL-A3CT 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3CU                    TCGA-EL-A3CV 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3CW                    TCGA-EL-A3CX 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3CY                    TCGA-EL-A3CZ 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3D0                    TCGA-EL-A3D1 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3D4                    TCGA-EL-A3D5 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3D6                    TCGA-EL-A3GO 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3GP                    TCGA-EL-A3GQ 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3GR                    TCGA-EL-A3GS 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3GU                    TCGA-EL-A3GV 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3GW                    TCGA-EL-A3GX 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3GY                    TCGA-EL-A3GZ 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3H1                    TCGA-EL-A3H2 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3H3                    TCGA-EL-A3H4 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3H5                    TCGA-EL-A3H7 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3H8                    TCGA-EL-A3MW 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3MX                    TCGA-EL-A3MY 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3MZ                    TCGA-EL-A3N2 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3N3                    TCGA-EL-A3T0 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3T1                    TCGA-EL-A3T2 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3T3                    TCGA-EL-A3T6 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3T7                    TCGA-EL-A3T8 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3T9                    TCGA-EL-A3TA 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3TB                    TCGA-EL-A3ZG 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3ZH                    TCGA-EL-A3ZK 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3ZL                    TCGA-EL-A3ZN 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3ZO                    TCGA-EL-A3ZP 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3ZQ                    TCGA-EL-A3ZR 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A3ZS                    TCGA-EL-A3ZT 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A4JV                    TCGA-EL-A4JW 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A4JX                    TCGA-EL-A4JZ 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A4K0                    TCGA-EL-A4K1 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A4K2                    TCGA-EL-A4K4 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A4K6                    TCGA-EL-A4K7 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A4K9                    TCGA-EL-A4KD 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A4KG                    TCGA-EL-A4KH 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-EL-A4KI                    TCGA-ET-A25G 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A25I                    TCGA-ET-A25J 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A25K                    TCGA-ET-A25L 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A25M                    TCGA-ET-A25N 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A25O                    TCGA-ET-A25P 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A25R                    TCGA-ET-A2MX 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A2MY                    TCGA-ET-A2MZ 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A2N0                    TCGA-ET-A2N1 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A2N3                    TCGA-ET-A2N4 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A2N5                    TCGA-ET-A39I 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A39J                    TCGA-ET-A39K 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A39M                    TCGA-ET-A39N 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A39O                    TCGA-ET-A39P 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A39R                    TCGA-ET-A39S 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A39T                    TCGA-ET-A3BN 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A3BO                    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-A3DO 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A3DP                    TCGA-ET-A3DQ 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A3DR                    TCGA-ET-A3DS 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A3DT                    TCGA-ET-A3DU 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A3DV                    TCGA-ET-A3DW 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A40P                    TCGA-ET-A40Q 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A40R                    TCGA-ET-A40T 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-ET-A4KN                    TCGA-ET-A4KQ 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FE-A22Z                    TCGA-FE-A230 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FE-A231                    TCGA-FE-A232 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FE-A233                    TCGA-FE-A234 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FE-A235                    TCGA-FE-A236 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FE-A237                    TCGA-FE-A238 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FE-A239                    TCGA-FE-A23A 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FE-A3PA                    TCGA-FE-A3PB 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FE-A3PC                    TCGA-FE-A3PD 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FK-A3S3                    TCGA-FK-A3SB 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FK-A3SD                    TCGA-FK-A3SE 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FK-A3SG                    TCGA-FK-A3SH 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FK-A4UB                    TCGA-FY-A2QD 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FY-A3BL                    TCGA-FY-A3I4 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FY-A3I5                    TCGA-FY-A3NM 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FY-A3ON                    TCGA-FY-A3R6 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FY-A3R7                    TCGA-FY-A3R8 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FY-A3R9                    TCGA-FY-A3RA 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FY-A3W9                    TCGA-FY-A3WA 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FY-A3YR                    TCGA-FY-A40K 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FY-A40L                    TCGA-FY-A40M 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FY-A40N                    TCGA-FY-A4B0 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FY-A4B3                    TCGA-FY-A4B4 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-FY-A76V                    TCGA-GE-A2C6 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-H2-A26U                    TCGA-H2-A2K9 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-H2-A3RH                    TCGA-H2-A3RI 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-H2-A421                    TCGA-H2-A422 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-IM-A3EB                    TCGA-IM-A3ED 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-IM-A3U2                    TCGA-IM-A3U3 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-IM-A41Y                    TCGA-IM-A41Z 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-IM-A420                    TCGA-IM-A4EB 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-J8-A3NZ                    TCGA-J8-A3O0 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-J8-A3O1                    TCGA-J8-A3O2 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-J8-A3YD                    TCGA-J8-A3YE 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-J8-A3YF                    TCGA-J8-A3YG 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-J8-A3YH                    TCGA-J8-A42S 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-J8-A4HW                    TCGA-J8-A4HY 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-KS-A41F                    TCGA-KS-A41I 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-KS-A41J                    TCGA-KS-A41L 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-KS-A4I1                    TCGA-KS-A4I3 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-KS-A4I5                    TCGA-KS-A4I7 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-KS-A4I9                    TCGA-KS-A4IB 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-KS-A4IC                    TCGA-KS-A4ID 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-L6-A4EP                    TCGA-L6-A4EQ 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-L6-A4ET                    TCGA-L6-A4EU 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-MK-A4N6                    TCGA-MK-A4N7 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-MK-A4N9                    TCGA-MK-A84Z 
"DEL PEAK 42(XQ22.3) WILD-TYPE" "DEL PEAK 42(XQ22.3) WILD-TYPE" 
                   TCGA-QD-A8IV 
"DEL PEAK 42(XQ22.3) WILD-TYPE" 
D98V17, binary
                               cls
clus                              0   1
  DEL PEAK 42(XQ22.3) MUTATED     0   3
  DEL PEAK 42(XQ22.3) WILD-TYPE  38 347
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 42(XQ22.3) MUTATED      0    3
  DEL PEAK 42(XQ22.3) WILD-TYPE   38  347
                        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                           347
[1] 2 2
[1] FALSE
