[1] "ofn"        "-oTESCA-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/ESCA-TP/15078602/ESCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ESCA-TP/15084414/transformed.cor.cli.txt"

nPatients in clinical file=174, in cluster file=184, common to both=173
[1]  85 173
[1] "AMP PEAK  1(1P34.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                           37                           136 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                           37                           136 
[1] "AMP PEAK  2(1Q23.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE 
                           84                            89 
  AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE 
                           84                            89 
[1] "AMP PEAK  3(1Q42.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                           87                            86 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                           87                            86 
[1] "AMP PEAK  4(2Q14.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE 
                           55                           118 
  AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE 
                           55                           118 
[1] "AMP PEAK  5(2Q31.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE 
                           55                           118 
  AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE 
                           55                           118 
[1] "AMP PEAK  6(3Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                          118                            55 
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                          118                            55 
[1] "AMP PEAK  7(4Q21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(4Q21.1) MUTATED AMP PEAK  7(4Q21.1) WILD-TYPE 
                           31                           142 
  AMP PEAK  7(4Q21.1) MUTATED AMP PEAK  7(4Q21.1) WILD-TYPE 
                           31                           142 
[1] "AMP PEAK  8(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                            89                             84 
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                            89                             84 
[1] "AMP PEAK  9(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                           65                           108 
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                           65                           108 
[1] "AMP PEAK 10(6Q23.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE 
                           40                           133 
  AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE 
                           40                           133 
[1] "AMP PEAK 11(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                          117                            56 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                          117                            56 
[1] "AMP PEAK 12(7Q21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                          107                            66 
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                          107                            66 
[1] "AMP PEAK 13(8P23.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE 
                           50                           123 
  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE 
                           50                           123 
[1] "AMP PEAK 14(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE 
                            81                             92 
  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE 
                            81                             92 
[1] "AMP PEAK 15(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                           136                             37 
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                           136                             37 
[1] "AMP PEAK 16(9P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE 
                           34                           139 
  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE 
                           34                           139 
[1] "AMP PEAK 17(9Q34.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE 
                           59                           114 
  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE 
                           59                           114 
[1] "AMP PEAK 18(11P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE 
                          49                          124 
  AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE 
                          49                          124 
[1] "AMP PEAK 19(11P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE 
                          46                          127 
  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE 
                          46                          127 
[1] "AMP PEAK 20(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                            95                             78 
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                            95                             78 
[1] "AMP PEAK 21(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE 
                            74                             99 
  AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE 
                            74                             99 
[1] "AMP PEAK 22(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE 
                          49                          124 
  AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE 
                          49                          124 
[1] "AMP PEAK 23(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE 
                            62                            111 
  AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE 
                            62                            111 
[1] "AMP PEAK 24(14Q21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE 
                            55                            118 
  AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE 
                            55                            118 
[1] "AMP PEAK 25(15Q26.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE 
                            54                            119 
  AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE 
                            54                            119 
[1] "AMP PEAK 26(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE 
                          71                          102 
  AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE 
                          71                          102 
[1] "AMP PEAK 27(18P11.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE 
                             64                             109 
  AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE 
                             64                             109 
[1] "AMP PEAK 28(18Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE 
                            56                            117 
  AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE 
                            56                            117 
[1] "AMP PEAK 29(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(19P13.2) MUTATED AMP PEAK 29(19P13.2) WILD-TYPE 
                            30                            143 
  AMP PEAK 29(19P13.2) MUTATED AMP PEAK 29(19P13.2) WILD-TYPE 
                            30                            143 
[1] "AMP PEAK 30(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE 
                          51                          122 
  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE 
                          51                          122 
[1] "AMP PEAK 31(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 31(XQ28) MUTATED AMP PEAK 31(XQ28) WILD-TYPE 
                         64                         109 
  AMP PEAK 31(XQ28) MUTATED AMP PEAK 31(XQ28) WILD-TYPE 
                         64                         109 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            70                            103 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            70                            103 
[1] "DEL PEAK  2(1P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           58                           115 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           58                           115 
[1] "DEL PEAK  3(1Q44) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         17                         156 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         17                         156 
[1] "DEL PEAK  4(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           52                           121 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           52                           121 
[1] "DEL PEAK  5(2Q33.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                           32                           141 
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                           32                           141 
[1] "DEL PEAK  6(3P26.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                          101                            72 
  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                          101                            72 
[1] "DEL PEAK  7(3P14.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                          116                            57 
  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                          116                            57 
[1] "DEL PEAK  8(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                          114                            59 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                          114                            59 
[1] "DEL PEAK  9(3Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE 
                           32                           141 
  DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE 
                           32                           141 
[1] "DEL PEAK 10(3Q26.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                            15                            158 
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                            15                            158 
[1] "DEL PEAK 11(4P15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                          100                            73 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                          100                            73 
[1] "DEL PEAK 12(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                          100                            73 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                          100                            73 
[1] "DEL PEAK 13(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                           94                            79 
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                           94                            79 
[1] "DEL PEAK 14(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                          105                            68 
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                          105                            68 
[1] "DEL PEAK 15(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           70                           103 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           70                           103 
[1] "DEL PEAK 16(6Q16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE 
                           51                           122 
  DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE 
                           51                           122 
[1] "DEL PEAK 17(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         48                         125 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         48                         125 
[1] "DEL PEAK 18(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                           55                           118 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                           55                           118 
[1] "DEL PEAK 19(7Q36.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE 
                           66                           107 
  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE 
                           66                           107 
[1] "DEL PEAK 20(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE 
                           81                            92 
  DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE 
                           81                            92 
[1] "DEL PEAK 21(8P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE 
                         68                         105 
  DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE 
                         68                         105 
[1] "DEL PEAK 22(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                        102                          71 
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                        102                          71 
[1] "DEL PEAK 23(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                          131                            42 
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                          131                            42 
[1] "DEL PEAK 24(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                            48                            125 
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                            48                            125 
[1] "DEL PEAK 25(10P11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE 
                             45                             128 
  DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE 
                             45                             128 
[1] "DEL PEAK 26(10Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE 
                            40                            133 
  DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE 
                            40                            133 
[1] "DEL PEAK 27(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE 
                             59                             114 
  DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE 
                             59                             114 
[1] "DEL PEAK 28(11P15.4) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE 
                            74                             99 
  DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE 
                            74                             99 
[1] "DEL PEAK 29(11Q25) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE 
                          73                          100 
  DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE 
                          73                          100 
[1] "DEL PEAK 30(12Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE 
                            47                            126 
  DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE 
                            47                            126 
[1] "DEL PEAK 31(13Q12.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE 
                             71                             102 
  DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE 
                             71                             102 
[1] "DEL PEAK 32(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                            69                            104 
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                            69                            104 
[1] "DEL PEAK 33(13Q21.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE 
                             64                             109 
  DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE 
                             64                             109 
[1] "DEL PEAK 34(14Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                            49                            124 
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                            49                            124 
[1] "DEL PEAK 35(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE 
                            59                            114 
  DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE 
                            59                            114 
[1] "DEL PEAK 36(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                            63                            110 
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                            63                            110 
[1] "DEL PEAK 37(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            80                             93 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            80                             93 
[1] "DEL PEAK 38(17P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                          81                           92 
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                          81                           92 
[1] "DEL PEAK 39(17Q25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE 
                            40                            133 
  DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE 
                            40                            133 
[1] "DEL PEAK 40(18P11.23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE 
                             56                             117 
  DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE 
                             56                             117 
[1] "DEL PEAK 41(18Q12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                           103                             70 
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                           103                             70 
[1] "DEL PEAK 42(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                           110                             63 
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                           110                             63 
[1] "DEL PEAK 43(18Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE 
                           103                             70 
  DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE 
                           103                             70 
[1] "DEL PEAK 44(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                            88                             85 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                            88                             85 
[1] "DEL PEAK 45(19Q11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(19Q11) MUTATED DEL PEAK 45(19Q11) WILD-TYPE 
                          46                          127 
  DEL PEAK 45(19Q11) MUTATED DEL PEAK 45(19Q11) WILD-TYPE 
                          46                          127 
[1] "DEL PEAK 46(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE 
                            32                            141 
  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE 
                            32                            141 
[1] "DEL PEAK 47(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE 
                            99                             74 
  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE 
                            99                             74 
[1] "DEL PEAK 48(21Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 48(21Q21.1) MUTATED DEL PEAK 48(21Q21.1) WILD-TYPE 
                           101                             72 
  DEL PEAK 48(21Q21.1) MUTATED DEL PEAK 48(21Q21.1) WILD-TYPE 
                           101                             72 
[1] "DEL PEAK 49(21Q22.12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 49(21Q22.12) MUTATED DEL PEAK 49(21Q22.12) WILD-TYPE 
                            101                              72 
  DEL PEAK 49(21Q22.12) MUTATED DEL PEAK 49(21Q22.12) WILD-TYPE 
                            101                              72 
[1] "DEL PEAK 50(22Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE 
                            76                             97 
  DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE 
                            76                             97 
[1] "DEL PEAK 51(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                           65                           108 
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                           65                           108 
[1] "DEL PEAK 52(XP11.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                           69                           104 
  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                           69                           104 
[1] "DEL PEAK 53(XQ11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 53(XQ11.2) MUTATED DEL PEAK 53(XQ11.2) WILD-TYPE 
                           40                           133 
  DEL PEAK 53(XQ11.2) MUTATED DEL PEAK 53(XQ11.2) WILD-TYPE 
                           40                           133 
[1] "DEL PEAK 54(XQ21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 54(XQ21.33) MUTATED DEL PEAK 54(XQ21.33) WILD-TYPE 
                            39                            134 
  DEL PEAK 54(XQ21.33) MUTATED DEL PEAK 54(XQ21.33) WILD-TYPE 
                            39                            134 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "NEOPLASM_DISEASESTAGE"                 
 [6] "PATHOLOGY_T_STAGE"                     
 [7] "PATHOLOGY_N_STAGE"                     
 [8] "PATHOLOGY_M_STAGE"                     
 [9] "DCC_UPLOAD_DATE"                       
[10] "GENDER"                                
[11] "RADIATIONS_RADIATION_REGIMENINDICATION"
[12] "NUMBER_PACK_YEARS_SMOKED"              
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCH_NUMBER"                          

Input Data has 15 rows and 173 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=69,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=105,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'NEOPLASM_DISEASESTAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY_T_STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DCC_UPLOAD_DATE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE excluded in the analysis because there is no case of (both >= 3) in the table below"
              12-3-2015 26-3-2015
freq.values   "1"       "172"    
freq.contrast "172"     "1"      
both >= 3     "FALSE"   "FALSE"  
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 12:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'BATCH_NUMBER':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 173 columns, 1 survival variables, and 9 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"           "NEOPLASM_DISEASESTAGE"   
[3] "PATHOLOGY_T_STAGE"        "PATHOLOGY_N_STAGE"       
[5] "PATHOLOGY_M_STAGE"        "GENDER"                  
[7] "NUMBER_PACK_YEARS_SMOKED" "RACE"                    
[9] "ETHNICITY"               
YEARS_TO_BIRTH, nv=46, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=12, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T0 T1 T2 T3 T4 
 1 30 36 85  5 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   31    36    85     5 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T0 T1 T2 T3 T4 
 1 30 36 85  5 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   31    36    85     5 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
71 64 12  8 
[1] "table(vv)"
vv
N0 N1 N2 N3 
71 64 12  8 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 N3 
71 64 12  8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


N0 N1 N2 N3 
71 64 12  8 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=45, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1P34.2) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  1(1P34.2) MUTATED   21 16
  AMP PEAK  1(1P34.2) WILD-TYPE 79 55
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                           37                           134 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                           16                            55 
$`AMP PEAK  1(1P34.2) MUTATED`
TCGA-2H-A9GN TCGA-IG-A3YA TCGA-IG-A51D TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FH 
        8.94        20.78        17.03         4.67       122.10        42.77 
TCGA-JY-A93E TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OW TCGA-L5-A88Y 
       25.22        47.93        18.35         1.38         7.13         0.36 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NL TCGA-L5-A8NS 
        3.95         3.02        55.50         2.66        13.22        13.41 
TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A9 TCGA-LN-A7HY 
       10.45        13.15        13.25         0.10        11.54        12.03 
TCGA-LN-A9FO TCGA-R6-A6DN TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8WG 
        0.13         8.02        29.59         6.35        53.95        12.69 
TCGA-V5-A7RC TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8EX TCGA-VR-AA7B TCGA-Z6-A8JE 
        3.42        19.96        22.82        28.11        11.24         2.10 
TCGA-ZR-A9CJ 
       19.73 

$`AMP PEAK  1(1P34.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
       13.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        20.09         0.85         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         9.30         0.53         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB 
        9.96        14.86        14.50        12.16        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        25.41        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       31.56        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        4.31         8.94        24.00         3.68         4.70        32.61 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS 
       19.99        21.01         3.32         7.17         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
        4.90        29.00         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
       25.12         7.40        35.97        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT 
       13.55         7.76         5.49        21.37         8.71        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M 
       83.24        52.57        46.09        10.36         5.92        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49Y 
       12.43        13.41         0.10        15.35         0.10        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39         0.10 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       15.52        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU 
       10.52        12.00        12.23        13.18        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y2 
        7.82         7.59         5.06        14.70         7.04         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
       15.78         2.89         1.45         7.00        20.02        20.38 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        5.29         4.80        15.35         9.27         4.44        18.81 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43         1.55        18.31         8.12        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       42.87        46.19        15.06         9.17        15.91        10.16 
TCGA-Z6-A8JD TCGA-Z6-AAPN 
        3.42         2.66 

  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                          0.1                           0.1 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                       122.10                         83.24 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                        12.69                         12.54 
[1] "0.1 - 122.1 (12.7)" "0.1 - 83.2 (12.5)" 
[1] "hr=" "1"  
D1V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  1(1P34.2) MUTATED         2        1        0        0         5
  AMP PEAK  1(1P34.2) WILD-TYPE       6        4        7        1        34
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  1(1P34.2) MUTATED           6         5          4          2
  AMP PEAK  1(1P34.2) WILD-TYPE        23        20          8          8
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  1(1P34.2) MUTATED            1        1         2
  AMP PEAK  1(1P34.2) WILD-TYPE          6        4         2
D1V3, multiclass
            clus
vv           AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  STAGE I                              2                             6
  STAGE IA                             1                             4
  STAGE IB                             0                             7
  STAGE II                             0                             1
  STAGE IIA                            5                            34
  STAGE IIB                            6                            23
  STAGE III                            5                            20
  STAGE IIIA                           4                             8
  STAGE IIIB                           2                             8
  STAGE IIIC                           1                             6
  STAGE IV                             1                             4
  STAGE IVA                            2                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  1(1P34.2) MUTATED       8  7 15  1
  AMP PEAK  1(1P34.2) WILD-TYPE    23 29 70  4
D1V4, multiclass
       clus
vv      AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  T0+T1                           8                            23
  T2                              7                            29
  T3                             15                            70
  T4                              1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  1(1P34.2) MUTATED   12 14  3  2
  AMP PEAK  1(1P34.2) WILD-TYPE 59 50  9  6
D1V5, multiclass
    clus
vv   AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  N0                          12                            59
  N1                          14                            50
  N2                           3                             9
  N3                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P34.2) MUTATED    23   3
  AMP PEAK  1(1P34.2) WILD-TYPE 103   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.2) MUTATED     23    3
  AMP PEAK  1(1P34.2) WILD-TYPE  103    6
   clus
vv  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  0                          23                           103
  1                           3                             6
[1] 2 2
[1] FALSE
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P34.2) MUTATED     4  33
  AMP PEAK  1(1P34.2) WILD-TYPE  20 116
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.2) MUTATED      4   33
  AMP PEAK  1(1P34.2) WILD-TYPE   20  116
        clus
vv       AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  FEMALE                           4                            20
  MALE                            33                           116
[1] 2 2
[1] FALSE
D1V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1P34.2) MUTATED       8                         1    25
  AMP PEAK  1(1P34.2) WILD-TYPE    33                         1    86
D1V9, multiclass
                           clus
vv                          AMP PEAK  1(1P34.2) MUTATED
  ASIAN                                               8
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              25
                           clus
vv                          AMP PEAK  1(1P34.2) WILD-TYPE
  ASIAN                                                33
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P34.2) MUTATED    1 16
  AMP PEAK  1(1P34.2) WILD-TYPE  2 65
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.2) MUTATED      1   16
  AMP PEAK  1(1P34.2) WILD-TYPE    2   65
                        clus
vv                       AMP PEAK  1(1P34.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          16
                        clus
vv                       AMP PEAK  1(1P34.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            65
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(1Q23.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  2(1Q23.3) MUTATED   46 37
  AMP PEAK  2(1Q23.3) WILD-TYPE 54 34
  AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE 
                           83                            88 
  AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE 
                           37                            34 
$`AMP PEAK  2(1Q23.3) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       31.27        58.55        13.94         8.94        16.24         4.21 
TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        7.69        20.09         0.85        20.12        18.64         3.88 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A8O2 
        0.53        17.03         0.79        23.41        12.82         4.67 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A93D 
       14.50       122.10        44.75        60.39         3.68        31.56 
TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
       25.22         0.30        32.61        19.99        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A88V 
       18.35         7.17         1.38         4.90         7.43         2.60 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        0.36         7.40         3.95         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NS TCGA-L5-A8NV 
       12.92        16.47        13.22         5.49        13.41        52.57 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
        5.92        10.45        12.66        13.15        15.35         0.10 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.49        12.76        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-R6-A6DN TCGA-R6-A6L4 
       12.33        12.00        13.18         0.13         8.02        14.70 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-S8-A6BV 
       29.59         6.35        53.95        15.78        12.69        20.02 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8EW 
       20.38         3.42         4.80        18.81        22.82         8.12 
TCGA-VR-A8EX TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       28.11        10.16         2.10         2.66        19.73 

$`AMP PEAK  2(1Q23.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IC-A6RF 
       25.78        14.30         7.63         5.92        32.45         6.21 
TCGA-IG-A3I8 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A6QS TCGA-IG-A7DP 
       33.27        20.78         2.63         9.30         9.96        14.86 
TCGA-IG-A97I TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       12.16        68.02        41.52        42.77        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J 
       23.18        24.03         6.28         3.16        30.25         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OO TCGA-L5-A4OR 
        8.94        24.00         3.68         4.70         3.32         3.16 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W 
       58.59        29.00         7.13         6.94         8.71        25.12 
TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR 
       35.97        13.48        13.55         7.76        21.37         8.71 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49N TCGA-LN-A49O 
       27.12        83.24        46.09        10.36        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A4 
        0.10        13.25         0.10        12.46        12.59        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX 
       22.39         0.10        15.52        25.25        10.52        12.23 
TCGA-LN-A7HY TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.03        33.11         5.16         7.82         7.59         5.06 
TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB 
        7.04         9.30         2.89         1.45         7.00         5.29 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET 
       15.35         9.27         4.44        19.96        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       18.31        30.71        18.18        42.87        46.19        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD 
       11.24         9.17        15.91         3.42 

  AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE 
                          0.1                           0.1 
  AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE 
                       122.10                         83.24 
  AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE 
                        12.76                         12.43 
[1] "0.1 - 122.1 (12.8)" "0.1 - 83.2 (12.4)" 
[1] "hr=" "1.2"
D2V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  2(1Q23.3) MUTATED         6        2        3        0        16
  AMP PEAK  2(1Q23.3) WILD-TYPE       2        3        4        1        23
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  2(1Q23.3) MUTATED          14        11          7          5
  AMP PEAK  2(1Q23.3) WILD-TYPE        15        14          5          5
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  2(1Q23.3) MUTATED            3        3         4
  AMP PEAK  2(1Q23.3) WILD-TYPE          4        2         0
D2V3, multiclass
            clus
vv           AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE
  STAGE I                              6                             2
  STAGE IA                             2                             3
  STAGE IB                             3                             4
  STAGE II                             0                             1
  STAGE IIA                           16                            23
  STAGE IIB                           14                            15
  STAGE III                           11                            14
  STAGE IIIA                           7                             5
  STAGE IIIB                           5                             5
  STAGE IIIC                           3                             4
  STAGE IV                             3                             2
  STAGE IVA                            4                             0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  2(1Q23.3) MUTATED      20 16 40  1
  AMP PEAK  2(1Q23.3) WILD-TYPE    11 20 45  4
D2V4, multiclass
       clus
vv      AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE
  T0+T1                          20                            11
  T2                             16                            20
  T3                             40                            45
  T4                              1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  2(1Q23.3) MUTATED   33 35  5  3
  AMP PEAK  2(1Q23.3) WILD-TYPE 38 29  7  5
D2V5, multiclass
    clus
vv   AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE
  N0                          33                            38
  N1                          35                            29
  N2                           5                             7
  N3                           3                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q23.3) MUTATED   59  7
  AMP PEAK  2(1Q23.3) WILD-TYPE 67  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q23.3) MUTATED     59    7
  AMP PEAK  2(1Q23.3) WILD-TYPE   67    2
   clus
vv  AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE
  0                          59                            67
  1                           7                             2
[1] 2 2
[1] FALSE
D2V7, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q23.3) MUTATED    6 78
  AMP PEAK  2(1Q23.3) WILD-TYPE 18 71
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q23.3) MUTATED      6   78
  AMP PEAK  2(1Q23.3) WILD-TYPE   18   71
        clus
vv       AMP PEAK  2(1Q23.3) MUTATED AMP PEAK  2(1Q23.3) WILD-TYPE
  FEMALE                           6                            18
  MALE                            78                            71
[1] 2 2
[1] FALSE
D2V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1Q23.3) MUTATED      23                         1    53
  AMP PEAK  2(1Q23.3) WILD-TYPE    18                         1    58
D2V9, multiclass
                           clus
vv                          AMP PEAK  2(1Q23.3) MUTATED
  ASIAN                                              23
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              53
                           clus
vv                          AMP PEAK  2(1Q23.3) WILD-TYPE
  ASIAN                                                18
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q23.3) MUTATED    1 44
  AMP PEAK  2(1Q23.3) WILD-TYPE  2 37
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q23.3) MUTATED      1   44
  AMP PEAK  2(1Q23.3) WILD-TYPE    2   37
                        clus
vv                       AMP PEAK  2(1Q23.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          44
                        clus
vv                       AMP PEAK  2(1Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            37
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(1Q42.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  3(1Q42.3) MUTATED   48 38
  AMP PEAK  3(1Q42.3) WILD-TYPE 52 33
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                           86                            85 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                           38                            33 
$`AMP PEAK  3(1Q42.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IC-A6RE 
       25.78        31.27        13.94         8.94        16.24         7.69 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L 
       20.09         0.85         2.63        20.12        18.64         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97H 
       17.03         0.79        23.41        12.82         4.67        14.50 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A93D TCGA-JY-A93E 
      122.10        60.39         3.68        42.77        31.56        25.22 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
        0.30         3.68        32.61        47.93        18.35         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z 
        1.38         4.90         7.43         2.60         0.36         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.95         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
       13.22         5.49        52.57        46.09        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A2 
       10.45        13.15        15.35         0.10        13.25        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.76        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-R6-A6KZ 
       12.33        12.00        12.23        13.18         0.13         5.06 
TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8WG 
       14.70        29.59         6.35        53.95        15.78        12.69 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EW TCGA-VR-A8EX 
       20.38         3.42         4.80         9.27         8.12        28.11 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JE 
       18.18        42.87        46.19        15.91        10.16         2.10 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

$`AMP PEAK  3(1Q42.3) WILD-TYPE`
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-2H-A9GR 
       14.30        58.55         7.63         5.92         4.21        32.45 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A6QS 
        6.21        33.27        20.78         3.88         9.30         9.96 
TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A938 
       14.86        12.16        44.75        68.02        41.52        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       21.70        23.18        24.03         6.28         3.16        30.25 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ 
        4.31         8.94        24.00         4.70        19.99        21.01 
TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S 
        3.32         3.16        58.59        29.00         7.13         6.94 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A8NG TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM 
        8.71        25.12        35.97        16.47        13.55         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-LN-A49M 
       21.37         8.71        13.41        27.12        83.24        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       12.43        13.41         0.10         0.10        12.46        12.59 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HY 
       12.59        22.39         0.10        25.25        10.52        12.03 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 
       33.11         5.16         7.82         8.02         7.59         7.04 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        9.30         2.89         1.45         7.00        20.02         5.29 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         4.44        18.81        19.96        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
        1.55        18.31        30.71        15.06        11.24         9.17 
TCGA-Z6-A8JD 
        3.42 

  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                          0.1                           0.1 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                       122.10                         83.24 
  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE 
                       12.725                        12.460 
[1] "0.1 - 122.1 (12.7)" "0.1 - 83.2 (12.5)" 
[1] "hr=" "1.2"
D3V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  3(1Q42.3) MUTATED         4        2        5        0        17
  AMP PEAK  3(1Q42.3) WILD-TYPE       4        3        2        1        22
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  3(1Q42.3) MUTATED          14        12          8          3
  AMP PEAK  3(1Q42.3) WILD-TYPE        15        13          4          7
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  3(1Q42.3) MUTATED            4        3         4
  AMP PEAK  3(1Q42.3) WILD-TYPE          3        2         0
D3V3, multiclass
            clus
vv           AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  STAGE I                              4                             4
  STAGE IA                             2                             3
  STAGE IB                             5                             2
  STAGE II                             0                             1
  STAGE IIA                           17                            22
  STAGE IIB                           14                            15
  STAGE III                           12                            13
  STAGE IIIA                           8                             4
  STAGE IIIB                           3                             7
  STAGE IIIC                           4                             3
  STAGE IV                             3                             2
  STAGE IVA                            4                             0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  3(1Q42.3) MUTATED      20 18 39  2
  AMP PEAK  3(1Q42.3) WILD-TYPE    11 18 46  3
D3V4, multiclass
       clus
vv      AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  T0+T1                          20                            11
  T2                             18                            18
  T3                             39                            46
  T4                              2                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  3(1Q42.3) MUTATED   31 39  4  4
  AMP PEAK  3(1Q42.3) WILD-TYPE 40 25  8  4
D3V5, multiclass
    clus
vv   AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  N0                          31                            40
  N1                          39                            25
  N2                           4                             8
  N3                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                               cls
clus                             0  1
  AMP PEAK  3(1Q42.3) MUTATED   61  7
  AMP PEAK  3(1Q42.3) WILD-TYPE 65  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED     61    7
  AMP PEAK  3(1Q42.3) WILD-TYPE   65    2
   clus
vv  AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  0                          61                            65
  1                           7                             2
[1] 2 2
[1] FALSE
D3V7, binary
                               cls
clus                             0  1
  AMP PEAK  3(1Q42.3) MUTATED    5 82
  AMP PEAK  3(1Q42.3) WILD-TYPE 19 67
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED      5   82
  AMP PEAK  3(1Q42.3) WILD-TYPE   19   67
        clus
vv       AMP PEAK  3(1Q42.3) MUTATED AMP PEAK  3(1Q42.3) WILD-TYPE
  FEMALE                           5                            19
  MALE                            82                            67
[1] 2 2
[1] FALSE
D3V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(1Q42.3) MUTATED      24                         1    56
  AMP PEAK  3(1Q42.3) WILD-TYPE    17                         1    55
D3V9, multiclass
                           clus
vv                          AMP PEAK  3(1Q42.3) MUTATED
  ASIAN                                              24
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              56
                           clus
vv                          AMP PEAK  3(1Q42.3) WILD-TYPE
  ASIAN                                                17
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, binary
                               cls
clus                             0  1
  AMP PEAK  3(1Q42.3) MUTATED    1 46
  AMP PEAK  3(1Q42.3) WILD-TYPE  2 35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.3) MUTATED      1   46
  AMP PEAK  3(1Q42.3) WILD-TYPE    2   35
                        clus
vv                       AMP PEAK  3(1Q42.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          46
                        clus
vv                       AMP PEAK  3(1Q42.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            35
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(2Q14.2) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  4(2Q14.2) MUTATED   35 18
  AMP PEAK  4(2Q14.2) WILD-TYPE 65 53
  AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE 
                           53                           118 
  AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE 
                           18                            53 
$`AMP PEAK  4(2Q14.2) MUTATED`
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A5S3 
       13.94         8.94         6.21        20.09         2.63        23.41 
TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43J TCGA-L5-A43M 
       14.50        44.75        31.56        25.22         4.31         8.94 
TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OX TCGA-L5-A88V 
       32.61        47.93         3.32         1.38         7.43         2.60 
TCGA-L5-A88Y TCGA-L5-A8NE TCGA-L5-A8NR TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49R 
        0.36        55.50         8.71        52.57         5.92         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A5U6 
       13.25         0.10        12.49         0.10        12.33        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A9FO TCGA-Q9-A6FW TCGA-R6-A6DQ 
       25.25        12.00        12.03         0.13         7.82         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A8WG TCGA-S8-A6BW 
        5.06        14.70         7.04         6.35        12.69        20.38 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EX 
        3.42         4.80        15.35        18.81        19.96        28.11 
TCGA-VR-A8EY TCGA-VR-AA4D TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN 
       30.71        46.19        10.16         3.42         2.66 

$`AMP PEAK  4(2Q14.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 
       16.24         4.21        32.45         7.69        33.27         0.85 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
       20.78        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03         0.79        12.82         9.96        14.86         4.67 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        60.39        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC 
       42.77        25.41        21.70        23.18        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        3.16        30.25         0.30        24.00         3.68         4.70 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS 
       19.99        21.01        18.35         7.17         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W 
        4.90        29.00         7.13         6.94         8.71        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        7.40         3.95         3.02         2.66        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ 
       21.37        13.41        27.12        83.24        46.09        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U 
       10.45        12.66        12.43        13.41        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10        12.46        12.59        12.76        12.59        22.39 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX 
       15.52        11.54        13.22         4.47        10.52        12.23 
TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6XG TCGA-R6-A6Y0 
       13.18        33.11         5.16         8.02        29.59        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV 
        9.30        15.78         2.89         1.45         7.00        20.02 
TCGA-V5-A7RB TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        5.29         9.27         4.44        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B 
       18.31         8.12        18.18        42.87        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JE TCGA-ZR-A9CJ 
        9.17        15.91         2.10        19.73 

  AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE 
                          0.1                           0.1 
  AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE 
                         55.5                         122.1 
  AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE 
                        12.00                         12.87 
[1] "0.1 - 55.5 (12.0)"  "0.1 - 122.1 (12.9)"
[1] "hr=" "1.1"
D4V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  4(2Q14.2) MUTATED         1        2        3        1        11
  AMP PEAK  4(2Q14.2) WILD-TYPE       7        3        4        0        28
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  4(2Q14.2) MUTATED          11         7          3          3
  AMP PEAK  4(2Q14.2) WILD-TYPE        18        18          9          7
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  4(2Q14.2) MUTATED            2        0         1
  AMP PEAK  4(2Q14.2) WILD-TYPE          5        5         3
D4V3, multiclass
            clus
vv           AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE
  STAGE I                              1                             7
  STAGE IA                             2                             3
  STAGE IB                             3                             4
  STAGE II                             1                             0
  STAGE IIA                           11                            28
  STAGE IIB                           11                            18
  STAGE III                            7                            18
  STAGE IIIA                           3                             9
  STAGE IIIB                           3                             7
  STAGE IIIC                           2                             5
  STAGE IV                             0                             5
  STAGE IVA                            1                             3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  4(2Q14.2) MUTATED       9 12 27  0
  AMP PEAK  4(2Q14.2) WILD-TYPE    22 24 58  5
D4V4, multiclass
       clus
vv      AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE
  T0+T1                           9                            22
  T2                             12                            24
  T3                             27                            58
  T4                              0                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  4(2Q14.2) MUTATED   23 18  4  2
  AMP PEAK  4(2Q14.2) WILD-TYPE 48 46  8  6
D4V5, multiclass
    clus
vv   AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE
  N0                          23                            48
  N1                          18                            46
  N2                           4                             8
  N3                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                               cls
clus                             0  1
  AMP PEAK  4(2Q14.2) MUTATED   38  1
  AMP PEAK  4(2Q14.2) WILD-TYPE 88  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q14.2) MUTATED     38    1
  AMP PEAK  4(2Q14.2) WILD-TYPE   88    8
   clus
vv  AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE
  0                          38                            88
  1                           1                             8
[1] 2 2
[1] FALSE
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(2Q14.2) MUTATED     7  48
  AMP PEAK  4(2Q14.2) WILD-TYPE  17 101
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q14.2) MUTATED      7   48
  AMP PEAK  4(2Q14.2) WILD-TYPE   17  101
        clus
vv       AMP PEAK  4(2Q14.2) MUTATED AMP PEAK  4(2Q14.2) WILD-TYPE
  FEMALE                           7                            17
  MALE                            48                           101
[1] 2 2
[1] FALSE
D4V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(2Q14.2) MUTATED      16                         2    32
  AMP PEAK  4(2Q14.2) WILD-TYPE    25                         0    79
D4V9, multiclass
                           clus
vv                          AMP PEAK  4(2Q14.2) MUTATED
  ASIAN                                              16
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              32
                           clus
vv                          AMP PEAK  4(2Q14.2) WILD-TYPE
  ASIAN                                                25
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, binary
                               cls
clus                             0  1
  AMP PEAK  4(2Q14.2) MUTATED    1 31
  AMP PEAK  4(2Q14.2) WILD-TYPE  2 50
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2Q14.2) MUTATED      1   31
  AMP PEAK  4(2Q14.2) WILD-TYPE    2   50
                        clus
vv                       AMP PEAK  4(2Q14.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          31
                        clus
vv                       AMP PEAK  4(2Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            50
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(2Q31.1) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  5(2Q31.1) MUTATED   31 22
  AMP PEAK  5(2Q31.1) WILD-TYPE 69 49
  AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE 
                           53                           118 
  AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE 
                           22                            49 
$`AMP PEAK  5(2Q31.1) MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IC-A6RF TCGA-IG-A3YB TCGA-IG-A4QS 
       58.55        13.94         8.94         6.21         2.63         3.88 
TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A93E TCGA-L5-A43J TCGA-L5-A4OH 
       23.41         4.67        14.50        25.22         4.31        32.61 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y 
       47.93         3.32         1.38         6.94         2.60         0.36 
TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49R TCGA-LN-A49U 
       55.50        13.48        52.57         5.92         0.10        15.35 
TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-LN-A5U7 
       13.25        12.59        12.49         0.10        12.33        25.25 
TCGA-LN-A7HW TCGA-LN-A9FO TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.00         0.13         7.82         7.59         5.06        14.70 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC 
       29.59         6.35        53.95        12.69        20.38         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EU 
        4.80        15.35        18.81        19.96        12.43        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-X8-AAAR 
        8.12        28.11        18.18        46.19        10.16 

$`AMP PEAK  5(2Q31.1) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GO 
       25.78        31.27        14.30         7.63         5.92        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.78        20.12        18.64         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6F8 
        0.79        12.82         9.96        14.86        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       44.75        60.39        68.02         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       25.41        21.70        23.18        31.56        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
        3.16        30.25         0.30         8.94        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR 
        4.70        19.99        21.01        18.35         7.17         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T 
       58.59         4.90        29.00         7.13         7.43         8.71 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG 
       25.12         7.40         3.95         3.02         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW 
       21.37         8.71        13.41        27.12        83.24        46.09 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S 
       10.36        10.45        12.66        12.43        13.41        13.15 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10         0.10        12.46        12.76        12.59        22.39 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV 
       15.52        11.54        12.33        13.22         4.47        10.52 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN 
       12.23        12.03        13.18        33.11         5.16         8.02 
TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
        7.04         9.30        15.78         2.89         1.45         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ET 
       20.02         5.29         9.27         4.44        22.82         1.55 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       30.71        42.87        15.06        11.24         9.17        15.91 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        3.42         2.10         2.66        19.73 

  AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE 
                          0.1                           0.1 
  AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE 
                        58.55                        122.10 
  AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE 
                       12.490                        12.625 
[1] "0.1 - 58.5 (12.5)"  "0.1 - 122.1 (12.6)"
[1] "hr=" "1"  
D5V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  5(2Q31.1) MUTATED         2        2        4        1        10
  AMP PEAK  5(2Q31.1) WILD-TYPE       6        3        3        0        29
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  5(2Q31.1) MUTATED           7         6          3          6
  AMP PEAK  5(2Q31.1) WILD-TYPE        22        19          9          4
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  5(2Q31.1) MUTATED            2        1         1
  AMP PEAK  5(2Q31.1) WILD-TYPE          5        4         3
D5V3, multiclass
            clus
vv           AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE
  STAGE I                              2                             6
  STAGE IA                             2                             3
  STAGE IB                             4                             3
  STAGE II                             1                             0
  STAGE IIA                           10                            29
  STAGE IIB                            7                            22
  STAGE III                            6                            19
  STAGE IIIA                           3                             9
  STAGE IIIB                           6                             4
  STAGE IIIC                           2                             5
  STAGE IV                             1                             4
  STAGE IVA                            1                             3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  5(2Q31.1) MUTATED      11  9 26  1
  AMP PEAK  5(2Q31.1) WILD-TYPE    20 27 59  4
D5V4, multiclass
       clus
vv      AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE
  T0+T1                          11                            20
  T2                              9                            27
  T3                             26                            59
  T4                              1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  5(2Q31.1) MUTATED   22 16  6  2
  AMP PEAK  5(2Q31.1) WILD-TYPE 49 48  6  6
D5V5, multiclass
    clus
vv   AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE
  N0                          22                            49
  N1                          16                            48
  N2                           6                             6
  N3                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                               cls
clus                             0  1
  AMP PEAK  5(2Q31.1) MUTATED   36  2
  AMP PEAK  5(2Q31.1) WILD-TYPE 90  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q31.1) MUTATED     36    2
  AMP PEAK  5(2Q31.1) WILD-TYPE   90    7
   clus
vv  AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE
  0                          36                            90
  1                           2                             7
[1] 2 2
[1] FALSE
D5V7, binary
                               cls
clus                             0  1
  AMP PEAK  5(2Q31.1) MUTATED    4 51
  AMP PEAK  5(2Q31.1) WILD-TYPE 20 98
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q31.1) MUTATED      4   51
  AMP PEAK  5(2Q31.1) WILD-TYPE   20   98
        clus
vv       AMP PEAK  5(2Q31.1) MUTATED AMP PEAK  5(2Q31.1) WILD-TYPE
  FEMALE                           4                            20
  MALE                            51                            98
[1] 2 2
[1] FALSE
D5V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(2Q31.1) MUTATED      16                         2    32
  AMP PEAK  5(2Q31.1) WILD-TYPE    25                         0    79
D5V9, multiclass
                           clus
vv                          AMP PEAK  5(2Q31.1) MUTATED
  ASIAN                                              16
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              32
                           clus
vv                          AMP PEAK  5(2Q31.1) WILD-TYPE
  ASIAN                                                25
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, binary
                               cls
clus                             0  1
  AMP PEAK  5(2Q31.1) MUTATED    1 30
  AMP PEAK  5(2Q31.1) WILD-TYPE  2 51
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q31.1) MUTATED      1   30
  AMP PEAK  5(2Q31.1) WILD-TYPE    2   51
                        clus
vv                       AMP PEAK  5(2Q31.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          30
                        clus
vv                       AMP PEAK  5(2Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            51
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(3Q26.2) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  6(3Q26.2) MUTATED   67 49
  AMP PEAK  6(3Q26.2) WILD-TYPE 33 22
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                          116                            55 
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                           49                            22 
$`AMP PEAK  6(3Q26.2) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GO 
       31.27        14.30        58.55         7.63         5.92        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
        4.21        32.45         7.69         6.21        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE 
        4.67        14.50        12.16        44.75        60.39         3.68 
TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       42.77        23.18        25.22        30.25         0.30         4.31 
TCGA-L5-A4OE TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       24.00        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z 
        3.16        29.00         7.13         6.94         2.60         7.40 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN 
       55.50         2.66        35.97        16.47        13.22         5.49 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K 
        8.71        13.41        27.12        52.57        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.45        12.66        12.43        13.41         0.10        13.15 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.10        13.25        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39         0.10        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-R6-A6DN 
       12.23        12.03        13.18         0.13         5.16         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WG 
        7.59         5.06         6.35        53.95         2.89        12.69 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       20.38         3.42         9.27         4.44        18.81        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       22.82        12.43        18.31         8.12        28.11        30.71 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        42.87        15.06        11.24         9.17        15.91 
TCGA-Z6-A8JD TCGA-ZR-A9CJ 
        3.42        19.73 

$`AMP PEAK  6(3Q26.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IG-A4QT TCGA-IG-A7DP TCGA-JY-A6F8 
       25.78        13.94         8.94         9.30        14.86       122.10 
TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F 
       68.02        41.52        25.41        21.70        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        6.28         3.16         8.94         3.68         4.70        32.61 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A88T 
       19.99        21.01        58.59         4.90         7.43         8.71 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI 
       25.12         0.36         3.95         3.02        12.92        13.48 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49U 
       13.55         7.76        21.37        83.24        46.09        15.35 
TCGA-LN-A49X TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        0.10        33.11         7.82        14.70         7.04        29.59 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        9.30        15.78         1.45         7.00        20.02         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8ET TCGA-VR-AA4D TCGA-X8-AAAR TCGA-Z6-A8JE 
        4.80        15.35         1.55        46.19        10.16         2.10 
TCGA-Z6-AAPN 
        2.66 

  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                          0.1                           0.1 
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                        60.39                        122.10 
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                       12.475                        13.480 
[1] "0.1 - 60.4 (12.5)"  "0.1 - 122.1 (13.5)"
[1] "hr=" "1.3"
D6V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  6(3Q26.2) MUTATED         3        4        3        1        28
  AMP PEAK  6(3Q26.2) WILD-TYPE       5        1        4        0        11
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  6(3Q26.2) MUTATED          19        21          9          9
  AMP PEAK  6(3Q26.2) WILD-TYPE        10         4          3          1
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  6(3Q26.2) MUTATED            5        3         3
  AMP PEAK  6(3Q26.2) WILD-TYPE          2        2         1
D6V3, multiclass
            clus
vv           AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  STAGE I                              3                             5
  STAGE IA                             4                             1
  STAGE IB                             3                             4
  STAGE II                             1                             0
  STAGE IIA                           28                            11
  STAGE IIB                           19                            10
  STAGE III                           21                             4
  STAGE IIIA                           9                             3
  STAGE IIIB                           9                             1
  STAGE IIIC                           5                             2
  STAGE IV                             3                             2
  STAGE IVA                            3                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  6(3Q26.2) MUTATED      15 26 63  4
  AMP PEAK  6(3Q26.2) WILD-TYPE    16 10 22  1
D6V4, multiclass
       clus
vv      AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  T0+T1                          15                            16
  T2                             26                            10
  T3                             63                            22
  T4                              4                             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                            N0 N1 N2 N3
  AMP PEAK  6(3Q26.2) MUTATED   48 43 10  6
  AMP PEAK  6(3Q26.2) WILD-TYPE 23 21  2  2
D6V5, multiclass
    clus
vv   AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  N0                          48                            23
  N1                          43                            21
  N2                          10                             2
  N3                           6                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                               cls
clus                             0  1
  AMP PEAK  6(3Q26.2) MUTATED   90  6
  AMP PEAK  6(3Q26.2) WILD-TYPE 36  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(3Q26.2) MUTATED     90    6
  AMP PEAK  6(3Q26.2) WILD-TYPE   36    3
   clus
vv  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  0                          90                            36
  1                           6                             3
[1] 2 2
[1] FALSE
D6V7, binary
                               cls
clus                              0   1
  AMP PEAK  6(3Q26.2) MUTATED    13 105
  AMP PEAK  6(3Q26.2) WILD-TYPE  11  44
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(3Q26.2) MUTATED     13  105
  AMP PEAK  6(3Q26.2) WILD-TYPE   11   44
        clus
vv       AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  FEMALE                          13                            11
  MALE                           105                            44
[1] 2 2
[1] FALSE
D6V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(3Q26.2) MUTATED      38                         1    66
  AMP PEAK  6(3Q26.2) WILD-TYPE     3                         1    45
D6V9, multiclass
                           clus
vv                          AMP PEAK  6(3Q26.2) MUTATED
  ASIAN                                              38
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              66
                           clus
vv                          AMP PEAK  6(3Q26.2) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, binary
                               cls
clus                             0  1
  AMP PEAK  6(3Q26.2) MUTATED    1 63
  AMP PEAK  6(3Q26.2) WILD-TYPE  2 18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(3Q26.2) MUTATED      1   63
  AMP PEAK  6(3Q26.2) WILD-TYPE    2   18
                        clus
vv                       AMP PEAK  6(3Q26.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          63
                        clus
vv                       AMP PEAK  6(3Q26.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            18
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(4Q21.1) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  7(4Q21.1) MUTATED   23  8
  AMP PEAK  7(4Q21.1) WILD-TYPE 77 63
  AMP PEAK  7(4Q21.1) MUTATED AMP PEAK  7(4Q21.1) WILD-TYPE 
                           31                           140 
  AMP PEAK  7(4Q21.1) MUTATED AMP PEAK  7(4Q21.1) WILD-TYPE 
                            8                            63 
$`AMP PEAK  7(4Q21.1) MUTATED`
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A50L TCGA-IG-A5S3 TCGA-JY-A6F8 TCGA-JY-A6FA 
       20.78         2.63         0.53        23.41       122.10        44.75 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OS TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NN 
       18.35         3.32        58.59        55.50        13.48         5.49 
TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU TCGA-LN-A49R TCGA-LN-A49X TCGA-LN-A4A8 
        8.71        27.12        83.24         0.10         0.10        15.52 
TCGA-LN-A4A9 TCGA-LN-A7HX TCGA-LN-A7HY TCGA-Q9-A6FW TCGA-R6-A8W5 TCGA-S8-A6BV 
       11.54        12.23        12.03         7.82        15.78        20.02 
TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8EW TCGA-VR-AA4G TCGA-VR-AA7B TCGA-X8-AAAR 
        3.42        18.81         8.12        15.06        11.24        10.16 
TCGA-Z6-A8JE 
        2.10 

$`AMP PEAK  7(4Q21.1) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4P3 
        6.21        33.27        20.09         0.85        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        3.88         9.30        17.03         0.79        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FB TCGA-JY-A6FD 
       14.86         4.67        14.50        12.16        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
        3.68        41.52        42.77        25.41        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        0.30         4.31         8.94        24.00         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OQ 
       32.61        19.99        21.01        47.93         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16         4.90        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 
        8.71         2.60        25.12         0.36         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.02         2.66        35.97        12.92        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW 
       13.22         7.76        21.37        13.41        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        15.35         0.10        13.25        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ 
       12.49        12.76        12.59        22.39         0.10        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6DQ 
       13.18         0.13        33.11         5.16         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        14.70         7.04        29.59         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
        9.30         2.89         1.45        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP 
        5.29         4.80        15.35         9.27         4.44        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY 
       22.82        12.43         1.55        18.31        28.11        30.71 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD 
       18.18        42.87        46.19         9.17        15.91         3.42 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

  AMP PEAK  7(4Q21.1) MUTATED AMP PEAK  7(4Q21.1) WILD-TYPE 
                          0.1                           0.1 
  AMP PEAK  7(4Q21.1) MUTATED AMP PEAK  7(4Q21.1) WILD-TYPE 
                       122.10                         68.02 
  AMP PEAK  7(4Q21.1) MUTATED AMP PEAK  7(4Q21.1) WILD-TYPE 
                        12.23                         12.59 
[1] "0.1 - 122.1 (12.2)" "0.1 - 68.0 (12.6)" 
[1] "hr=" "2.4"
D7V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  7(4Q21.1) MUTATED         1        0        0        0         5
  AMP PEAK  7(4Q21.1) WILD-TYPE       7        5        7        1        34
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  7(4Q21.1) MUTATED           6         5          6          3
  AMP PEAK  7(4Q21.1) WILD-TYPE        23        20          6          7
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  7(4Q21.1) MUTATED            1        1         1
  AMP PEAK  7(4Q21.1) WILD-TYPE          6        4         3
D7V3, multiclass
            clus
vv           AMP PEAK  7(4Q21.1) MUTATED AMP PEAK  7(4Q21.1) WILD-TYPE
  STAGE I                              1                             7
  STAGE IA                             0                             5
  STAGE IB                             0                             7
  STAGE II                             0                             1
  STAGE IIA                            5                            34
  STAGE IIB                            6                            23
  STAGE III                            5                            20
  STAGE IIIA                           6                             6
  STAGE IIIB                           3                             7
  STAGE IIIC                           1                             6
  STAGE IV                             1                             4
  STAGE IVA                            1                             3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  7(4Q21.1) MUTATED       3  8 18  1
  AMP PEAK  7(4Q21.1) WILD-TYPE    28 28 67  4
D7V4, multiclass
       clus
vv      AMP PEAK  7(4Q21.1) MUTATED AMP PEAK  7(4Q21.1) WILD-TYPE
  T0+T1                           3                            28
  T2                              8                            28
  T3                             18                            67
  T4                              1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  7(4Q21.1) MUTATED   10 15  3  2
  AMP PEAK  7(4Q21.1) WILD-TYPE 61 49  9  6
D7V5, multiclass
    clus
vv   AMP PEAK  7(4Q21.1) MUTATED AMP PEAK  7(4Q21.1) WILD-TYPE
  N0                          10                            61
  N1                          15                            49
  N2                           3                             9
  N3                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                               cls
clus                              0   1
  AMP PEAK  7(4Q21.1) MUTATED    25   2
  AMP PEAK  7(4Q21.1) WILD-TYPE 101   7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4Q21.1) MUTATED     25    2
  AMP PEAK  7(4Q21.1) WILD-TYPE  101    7
   clus
vv  AMP PEAK  7(4Q21.1) MUTATED AMP PEAK  7(4Q21.1) WILD-TYPE
  0                          25                           101
  1                           2                             7
[1] 2 2
[1] FALSE
D7V7, binary
                               cls
clus                              0   1
  AMP PEAK  7(4Q21.1) MUTATED     5  26
  AMP PEAK  7(4Q21.1) WILD-TYPE  19 123
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4Q21.1) MUTATED      5   26
  AMP PEAK  7(4Q21.1) WILD-TYPE   19  123
        clus
vv       AMP PEAK  7(4Q21.1) MUTATED AMP PEAK  7(4Q21.1) WILD-TYPE
  FEMALE                           5                            19
  MALE                            26                           123
[1] 2 2
[1] FALSE
D7V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(4Q21.1) MUTATED       9                         1    20
  AMP PEAK  7(4Q21.1) WILD-TYPE    32                         1    91
D7V9, multiclass
                           clus
vv                          AMP PEAK  7(4Q21.1) MUTATED
  ASIAN                                               9
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              20
                           clus
vv                          AMP PEAK  7(4Q21.1) WILD-TYPE
  ASIAN                                                32
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, binary
                               cls
clus                             0  1
  AMP PEAK  7(4Q21.1) MUTATED    0 16
  AMP PEAK  7(4Q21.1) WILD-TYPE  3 65
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4Q21.1) MUTATED      0   16
  AMP PEAK  7(4Q21.1) WILD-TYPE    3   65
                        clus
vv                       AMP PEAK  7(4Q21.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          16
                        clus
vv                       AMP PEAK  7(4Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            65
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(5P15.33) MUTATION ANALYSIS
D8V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  8(5P15.33) MUTATED   59 29
  AMP PEAK  8(5P15.33) WILD-TYPE 41 42
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                            88                             83 
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                            29                             42 
$`AMP PEAK  8(5P15.33) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3YB TCGA-IG-A3YC 
       14.30         5.92        32.45        33.27         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H 
       18.64         0.53         0.79        23.41         4.67        14.50 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A93D TCGA-JY-A93E 
       44.75        68.02         3.68        42.77        31.56        25.22 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OH TCGA-L5-A4OI 
        3.16         0.30         4.31         8.94        32.61        19.99 
TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
       47.93         7.17         3.16         4.90        29.00         7.13 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NG 
        6.94         2.60         0.36         3.95        55.50        35.97 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV 
       12.92        16.47        13.55        13.41        27.12        52.57 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       10.36         5.92        13.41         0.10        13.15        15.35 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A5 
       13.25         0.10        12.46        12.59        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
        0.10        15.52        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W5 
        5.16         5.06        14.70        29.59        53.95        15.78 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EO TCGA-VR-A8EP 
        7.00        20.38         3.42         4.80        18.81        19.96 
TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7I 
       18.31        30.71        18.18        42.87        15.06        15.91 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        3.42         2.10         2.66        19.73 

$`AMP PEAK  8(5P15.33) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        31.27        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21         7.69         6.21        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS 
       20.78         3.88         9.30        17.03        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FG TCGA-JY-A938 
       14.86        12.16       122.10        60.39        41.52        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A4OE 
       21.70        23.18        24.03         6.28        30.25        24.00 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        3.68         4.70        21.01        18.35         3.32         1.38 
TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 
       58.59         7.43         8.71        25.12         7.40         3.02 
TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
        2.66        13.48        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
        8.71        83.24        46.09        10.45        12.66        12.43 
TCGA-LN-A49V TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A9 TCGA-LN-A9FO TCGA-M9-A5M8 
        0.10        12.49        12.76        11.54         0.13        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 
        7.82         8.02         7.59         7.04         6.35         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASV 
        2.89         1.45        12.69        20.02         5.29        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW 
        9.27         4.44        22.82        12.43         1.55         8.12 
TCGA-VR-A8EX TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR 
       28.11        46.19        11.24         9.17        10.16 

  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                           0.1                            0.1 
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                         68.02                         122.10 
  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE 
                         13.20                          11.54 
[1] "0.1 - 68.0 (13.2)"  "0.1 - 122.1 (11.5)"
[1] "hr=" "1.5"
D8V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  8(5P15.33) MUTATED         1        3        4        1        24
  AMP PEAK  8(5P15.33) WILD-TYPE       7        2        3        0        15
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  8(5P15.33) MUTATED          13        13          7          4
  AMP PEAK  8(5P15.33) WILD-TYPE        16        12          5          6
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  8(5P15.33) MUTATED            5        4         1
  AMP PEAK  8(5P15.33) WILD-TYPE          2        1         3
D8V3, multiclass
            clus
vv           AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  STAGE I                               1                              7
  STAGE IA                              3                              2
  STAGE IB                              4                              3
  STAGE II                              1                              0
  STAGE IIA                            24                             15
  STAGE IIB                            13                             16
  STAGE III                            13                             12
  STAGE IIIA                            7                              5
  STAGE IIIB                            4                              6
  STAGE IIIC                            5                              2
  STAGE IV                              4                              1
  STAGE IVA                             1                              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK  8(5P15.33) MUTATED       9 19 54  1
  AMP PEAK  8(5P15.33) WILD-TYPE    22 17 31  4
D8V4, multiclass
       clus
vv      AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  T0+T1                            9                             22
  T2                              19                             17
  T3                              54                             31
  T4                               1                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK  8(5P15.33) MUTATED   41 31  5  5
  AMP PEAK  8(5P15.33) WILD-TYPE 30 33  7  3
D8V5, multiclass
    clus
vv   AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  N0                           41                             30
  N1                           31                             33
  N2                            5                              7
  N3                            5                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                                cls
clus                              0  1
  AMP PEAK  8(5P15.33) MUTATED   66  5
  AMP PEAK  8(5P15.33) WILD-TYPE 60  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED     66    5
  AMP PEAK  8(5P15.33) WILD-TYPE   60    4
   clus
vv  AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  0                           66                             60
  1                            5                              4
[1] 2 2
[1] FALSE
D8V7, binary
                                cls
clus                              0  1
  AMP PEAK  8(5P15.33) MUTATED   12 77
  AMP PEAK  8(5P15.33) WILD-TYPE 12 72
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED     12   77
  AMP PEAK  8(5P15.33) WILD-TYPE   12   72
        clus
vv       AMP PEAK  8(5P15.33) MUTATED AMP PEAK  8(5P15.33) WILD-TYPE
  FEMALE                           12                             12
  MALE                             77                             72
[1] 2 2
[1] FALSE
D8V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(5P15.33) MUTATED      29                         1    54
  AMP PEAK  8(5P15.33) WILD-TYPE    12                         1    57
D8V9, multiclass
                           clus
vv                          AMP PEAK  8(5P15.33) MUTATED
  ASIAN                                               29
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               54
                           clus
vv                          AMP PEAK  8(5P15.33) WILD-TYPE
  ASIAN                                                 12
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, binary
                                cls
clus                              0  1
  AMP PEAK  8(5P15.33) MUTATED    0 47
  AMP PEAK  8(5P15.33) WILD-TYPE  3 34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(5P15.33) MUTATED      0   47
  AMP PEAK  8(5P15.33) WILD-TYPE    3   34
                        clus
vv                       AMP PEAK  8(5P15.33) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           47
                        clus
vv                       AMP PEAK  8(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                             34
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(6P21.1) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  9(6P21.1) MUTATED   33 31
  AMP PEAK  9(6P21.1) WILD-TYPE 67 40
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                           64                           107 
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                           31                            40 
$`AMP PEAK  9(6P21.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        14.30        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A4QS TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
       16.24         4.21         3.88         4.67        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A939 TCGA-L5-A43E TCGA-L5-A4OM 
       44.75        60.39        68.02        21.70        30.25        47.93 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88S 
       18.35         7.17         1.38        58.59         7.13         6.94 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60         0.36         3.95         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NT 
       35.97        12.92        13.48         5.49        21.37        27.12 
TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49S 
       52.57        10.36         5.92        10.45        13.41        13.15 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U6 
        0.10         0.10        12.49        11.54        12.33        12.33 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       12.00        12.23         8.02         7.59        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-S8-A6BV TCGA-V5-A7RC 
       29.59        53.95        15.78         2.89        20.02         3.42 
TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA7I TCGA-Z6-A8JE 
        4.44        22.82        15.91         2.10 

$`AMP PEAK  9(6P21.1) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 
       31.27         5.92        32.45         7.69         6.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       20.09         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
        9.96        14.86        14.50         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       25.41        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
        3.16         0.30         4.31         8.94        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OR 
        4.70        32.61        19.99        21.01         3.32         3.16 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z 
        4.90        29.00         7.43         8.71        25.12         7.40 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.55        13.22         7.76         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49U 
       83.24        46.09        12.66        12.43         0.10        15.35 
TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       13.25        12.46        12.59        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV 
        0.10        15.52        13.22         4.47        25.25        10.52 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.03        13.18         0.13        33.11         5.16         7.82 
TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        5.06         6.35         9.30         1.45        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO 
       20.38         5.29         4.80        15.35         9.27        18.81 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       19.96        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       30.71        18.18        42.87        46.19        15.06        11.24 
TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        9.17        10.16         3.42         2.66        19.73 

  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                          0.1                           0.1 
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                       122.10                         83.24 
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                        12.33                         12.66 
[1] "0.1 - 122.1 (12.3)" "0.1 - 83.2 (12.7)" 
[1] "hr=" "1.1"
D9V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  9(6P21.1) MUTATED         5        2        1        0        14
  AMP PEAK  9(6P21.1) WILD-TYPE       3        3        6        1        25
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  9(6P21.1) MUTATED          10        12          3          2
  AMP PEAK  9(6P21.1) WILD-TYPE        19        13          9          8
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  9(6P21.1) MUTATED            1        1         3
  AMP PEAK  9(6P21.1) WILD-TYPE          6        4         1
D9V3, multiclass
            clus
vv           AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  STAGE I                              5                             3
  STAGE IA                             2                             3
  STAGE IB                             1                             6
  STAGE II                             0                             1
  STAGE IIA                           14                            25
  STAGE IIB                           10                            19
  STAGE III                           12                            13
  STAGE IIIA                           3                             9
  STAGE IIIB                           2                             8
  STAGE IIIC                           1                             6
  STAGE IV                             1                             4
  STAGE IVA                            3                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  9(6P21.1) MUTATED      13 13 29  1
  AMP PEAK  9(6P21.1) WILD-TYPE    18 23 56  4
D9V4, multiclass
       clus
vv      AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  T0+T1                          13                            18
  T2                             13                            23
  T3                             29                            56
  T4                              1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  9(6P21.1) MUTATED   27 25  3  1
  AMP PEAK  9(6P21.1) WILD-TYPE 44 39  9  7
D9V5, multiclass
    clus
vv   AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  N0                          27                            44
  N1                          25                            39
  N2                           3                             9
  N3                           1                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                               cls
clus                             0  1
  AMP PEAK  9(6P21.1) MUTATED   43  4
  AMP PEAK  9(6P21.1) WILD-TYPE 83  5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6P21.1) MUTATED     43    4
  AMP PEAK  9(6P21.1) WILD-TYPE   83    5
   clus
vv  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  0                          43                            83
  1                           4                             5
[1] 2 2
[1] FALSE
D9V7, binary
                               cls
clus                             0  1
  AMP PEAK  9(6P21.1) MUTATED    7 58
  AMP PEAK  9(6P21.1) WILD-TYPE 17 91
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6P21.1) MUTATED      7   58
  AMP PEAK  9(6P21.1) WILD-TYPE   17   91
        clus
vv       AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  FEMALE                           7                            17
  MALE                            58                            91
[1] 2 2
[1] FALSE
D9V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(6P21.1) MUTATED      16                         1    39
  AMP PEAK  9(6P21.1) WILD-TYPE    25                         1    72
D9V9, multiclass
                           clus
vv                          AMP PEAK  9(6P21.1) MUTATED
  ASIAN                                              16
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              39
                           clus
vv                          AMP PEAK  9(6P21.1) WILD-TYPE
  ASIAN                                                25
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, binary
                               cls
clus                             0  1
  AMP PEAK  9(6P21.1) MUTATED    0 29
  AMP PEAK  9(6P21.1) WILD-TYPE  3 52
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6P21.1) MUTATED      0   29
  AMP PEAK  9(6P21.1) WILD-TYPE    3   52
                        clus
vv                       AMP PEAK  9(6P21.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          29
                        clus
vv                       AMP PEAK  9(6P21.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            52
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(6Q23.3) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 10(6Q23.3) MUTATED   20 20
  AMP PEAK 10(6Q23.3) WILD-TYPE 80 51
  AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE 
                           40                           131 
  AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE 
                           20                            51 
$`AMP PEAK 10(6Q23.3) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GM TCGA-2H-A9GO TCGA-IG-A4QS TCGA-JY-A6F8 
       31.27        14.30        13.94        16.24         3.88       122.10 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A938 TCGA-L5-A43E TCGA-L5-A4OG TCGA-L5-A4OW 
       60.39        68.02        25.41        30.25         4.70         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        7.43         6.94         3.95         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NQ TCGA-L5-A8NT TCGA-L7-A6VZ TCGA-LN-A49L 
       12.92        13.48        21.37        27.12        10.36        10.45 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-M9-A5M8 
       13.15         0.10         4.47        10.52        12.03        33.11 
TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-VR-A8EU TCGA-VR-A8EZ 
        8.02        14.70         7.04        15.78        18.31        18.18 
TCGA-VR-AA7B TCGA-VR-AA7I TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       11.24        15.91         2.10        19.73 

$`AMP PEAK 10(6Q23.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ 
       25.78        58.55         7.63         5.92         8.94         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       32.45         7.69         6.21        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L 
       20.78         2.63        20.12        18.64         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG 
        4.67        14.50        12.16        44.75         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       42.77        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
        6.28         3.16         0.30         4.31         8.94        24.00 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        3.68        32.61        19.99        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
       29.00         8.71         2.60        25.12         0.36         7.40 
TCGA-L5-A8NG TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       35.97        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K 
        8.71        13.41        83.24        52.57        46.09         5.92 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W 
       12.66        12.43        13.41         0.10        15.35        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39         0.10        15.52        11.54        12.33        13.22 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A9FO 
       12.33        25.25        12.00        12.23        13.18         0.13 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ 
        5.16         7.82         7.59         5.06        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95         9.30         2.89         1.45        12.69         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
       20.02        20.38         5.29         3.42         4.80        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         4.44        18.81        19.96        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D 
        1.55         8.12        28.11        30.71        42.87        46.19 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN 
       15.06         9.17        10.16         3.42         2.66 

  AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE 
                          0.1                           0.1 
  AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE 
                       122.10                         83.24 
  AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE 
                       13.315                        12.460 
[1] "0.1 - 122.1 (13.3)" "0.1 - 83.2 (12.5)" 
[1] "hr=" "1.1"
D10V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 10(6Q23.3) MUTATED         5        0        1        0         7
  AMP PEAK 10(6Q23.3) WILD-TYPE       3        5        6        1        32
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 10(6Q23.3) MUTATED           7         4          1          1
  AMP PEAK 10(6Q23.3) WILD-TYPE        22        21         11          9
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 10(6Q23.3) MUTATED            3        4         3
  AMP PEAK 10(6Q23.3) WILD-TYPE          4        1         1
D10V3, multiclass
            clus
vv           AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE
  STAGE I                              5                             3
  STAGE IA                             0                             5
  STAGE IB                             1                             6
  STAGE II                             0                             1
  STAGE IIA                            7                            32
  STAGE IIB                            7                            22
  STAGE III                            4                            21
  STAGE IIIA                           1                            11
  STAGE IIIB                           1                             9
  STAGE IIIC                           3                             4
  STAGE IV                             4                             1
  STAGE IVA                            3                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK 10(6Q23.3) MUTATED      10  6 20  1
  AMP PEAK 10(6Q23.3) WILD-TYPE    21 30 65  4
D10V4, multiclass
       clus
vv      AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE
  T0+T1                          10                            21
  T2                              6                            30
  T3                             20                            65
  T4                              1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK 10(6Q23.3) MUTATED   18 14  1  4
  AMP PEAK 10(6Q23.3) WILD-TYPE 53 50 11  4
D10V5, multiclass
    clus
vv   AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE
  N0                          18                            53
  N1                          14                            50
  N2                           1                            11
  N3                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                               cls
clus                             0  1
  AMP PEAK 10(6Q23.3) MUTATED   27  7
  AMP PEAK 10(6Q23.3) WILD-TYPE 99  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6Q23.3) MUTATED     27    7
  AMP PEAK 10(6Q23.3) WILD-TYPE   99    2
   clus
vv  AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE
  0                          27                            99
  1                           7                             2
[1] 2 2
[1] FALSE
D10V7, binary
                               cls
clus                              0   1
  AMP PEAK 10(6Q23.3) MUTATED     5  35
  AMP PEAK 10(6Q23.3) WILD-TYPE  19 114
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6Q23.3) MUTATED      5   35
  AMP PEAK 10(6Q23.3) WILD-TYPE   19  114
        clus
vv       AMP PEAK 10(6Q23.3) MUTATED AMP PEAK 10(6Q23.3) WILD-TYPE
  FEMALE                           5                            19
  MALE                            35                           114
[1] 2 2
[1] FALSE
D10V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(6Q23.3) MUTATED       7                         0    27
  AMP PEAK 10(6Q23.3) WILD-TYPE    34                         2    84
D10V9, multiclass
                           clus
vv                          AMP PEAK 10(6Q23.3) MUTATED
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              27
                           clus
vv                          AMP PEAK 10(6Q23.3) WILD-TYPE
  ASIAN                                                34
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, binary
                               cls
clus                             0  1
  AMP PEAK 10(6Q23.3) MUTATED    0 14
  AMP PEAK 10(6Q23.3) WILD-TYPE  3 67
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6Q23.3) MUTATED      0   14
  AMP PEAK 10(6Q23.3) WILD-TYPE    3   67
                        clus
vv                       AMP PEAK 10(6Q23.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          14
                        clus
vv                       AMP PEAK 10(6Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            67
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(7P11.2) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 11(7P11.2) MUTATED   72 44
  AMP PEAK 11(7P11.2) WILD-TYPE 28 27
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                          116                            55 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                           44                            27 
$`AMP PEAK 11(7P11.2) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4P3 
       32.45         7.69        20.09         0.85        20.12        18.64 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FA 
        0.53        17.03         0.79        23.41        14.50        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C 
       60.39        68.02        21.70        23.18        25.22         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
       30.25         0.30         4.31        24.00         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
       32.61        21.01        47.93        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S 
        3.16        58.59         4.90        29.00         7.13         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        8.71         2.60         0.36         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        35.97        12.92        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49         8.71        13.41        27.12        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V 
       10.36         5.92        13.41         0.10        15.35         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25         0.10        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
       12.59         0.10        15.52        12.33        13.22        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-Q9-A6FW 
       25.25        12.00        12.03         0.13         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ 
        8.02         7.59         5.06        14.70         7.04         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95         9.30         2.89         1.45        12.69         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW 
       20.02        20.38         5.29         3.42        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX 
        4.44        18.81        19.96         1.55         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7I TCGA-X8-AAAR 
       30.71        18.18        42.87        46.19        15.91        10.16 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

$`AMP PEAK 11(7P11.2) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GQ TCGA-IC-A6RF TCGA-IG-A3I8 
       31.27        14.30        58.55         4.21         6.21        33.27 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A6QS 
       20.78         2.63         3.88         9.30        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG 
       14.86         4.67        12.16       122.10         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43M 
       42.77        25.41        31.56        24.03         6.28         8.94 
TCGA-L5-A4OI TCGA-L5-A4OP TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NI 
       19.99         7.17         7.43        25.12         7.40        13.48 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
        7.76        21.37        83.24        10.45        12.66        12.43 
TCGA-LN-A49S TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX 
       13.15        22.39        11.54         4.47        10.52        12.23 
TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-R6-A6XG TCGA-R6-A8W5 TCGA-V5-A7RE TCGA-VR-A8EQ 
       13.18        33.11        29.59        15.78         4.80        22.82 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-Z6-A8JD 
       12.43        18.31        15.06        11.24         9.17         3.42 
TCGA-Z6-A8JE 
        2.10 

  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                          0.1                           2.1 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                        68.02                        122.10 
  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE 
                        12.54                         12.66 
[1] "0.1 - 68.0 (12.5)"  "2.1 - 122.1 (12.7)"
[1] "hr=" "1.1"
D11V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 11(7P11.2) MUTATED         6        2        5        1        22
  AMP PEAK 11(7P11.2) WILD-TYPE       2        3        2        0        17
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 11(7P11.2) MUTATED          21        18          7          7
  AMP PEAK 11(7P11.2) WILD-TYPE         8         7          5          3
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 11(7P11.2) MUTATED            4        2         3
  AMP PEAK 11(7P11.2) WILD-TYPE          3        3         1
D11V3, multiclass
            clus
vv           AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  STAGE I                              6                             2
  STAGE IA                             2                             3
  STAGE IB                             5                             2
  STAGE II                             1                             0
  STAGE IIA                           22                            17
  STAGE IIB                           21                             8
  STAGE III                           18                             7
  STAGE IIIA                           7                             5
  STAGE IIIB                           7                             3
  STAGE IIIC                           4                             3
  STAGE IV                             2                             3
  STAGE IVA                            3                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK 11(7P11.2) MUTATED      22 18 60  2
  AMP PEAK 11(7P11.2) WILD-TYPE     9 18 25  3
D11V4, multiclass
       clus
vv      AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  T0+T1                          22                             9
  T2                             18                            18
  T3                             60                            25
  T4                              2                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK 11(7P11.2) MUTATED   45 45  7  4
  AMP PEAK 11(7P11.2) WILD-TYPE 26 19  5  4
D11V5, multiclass
    clus
vv   AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  N0                          45                            26
  N1                          45                            19
  N2                           7                             5
  N3                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                               cls
clus                             0  1
  AMP PEAK 11(7P11.2) MUTATED   80  5
  AMP PEAK 11(7P11.2) WILD-TYPE 46  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED     80    5
  AMP PEAK 11(7P11.2) WILD-TYPE   46    4
   clus
vv  AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  0                          80                            46
  1                           5                             4
[1] 2 2
[1] FALSE
D11V7, binary
                               cls
clus                              0   1
  AMP PEAK 11(7P11.2) MUTATED    14 103
  AMP PEAK 11(7P11.2) WILD-TYPE  10  46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED     14  103
  AMP PEAK 11(7P11.2) WILD-TYPE   10   46
        clus
vv       AMP PEAK 11(7P11.2) MUTATED AMP PEAK 11(7P11.2) WILD-TYPE
  FEMALE                          14                            10
  MALE                           103                            46
[1] 2 2
[1] FALSE
D11V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(7P11.2) MUTATED      28                         2    76
  AMP PEAK 11(7P11.2) WILD-TYPE    13                         0    35
D11V9, multiclass
                           clus
vv                          AMP PEAK 11(7P11.2) MUTATED
  ASIAN                                              28
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              76
                           clus
vv                          AMP PEAK 11(7P11.2) WILD-TYPE
  ASIAN                                                13
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, binary
                               cls
clus                             0  1
  AMP PEAK 11(7P11.2) MUTATED    3 53
  AMP PEAK 11(7P11.2) WILD-TYPE  0 28
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7P11.2) MUTATED      3   53
  AMP PEAK 11(7P11.2) WILD-TYPE    0   28
                        clus
vv                       AMP PEAK 11(7P11.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          53
                        clus
vv                       AMP PEAK 11(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            28
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(7Q21.2) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 12(7Q21.2) MUTATED   64 42
  AMP PEAK 12(7Q21.2) WILD-TYPE 36 29
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                          106                            65 
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                           42                            29 
$`AMP PEAK 12(7Q21.2) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL 
       31.27         8.94        16.24        32.45         7.69        20.09 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
        2.63        20.12         3.88         0.53        17.03        23.41 
TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
        9.96        14.50        44.75        60.39        68.02         3.68 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C 
       42.77        21.70        23.18        31.56        25.22         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OM 
       30.25         0.30        24.00         4.70        32.61        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         3.32         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 
       29.00         7.13         6.94         2.60         0.36         3.95 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.02         2.66        35.97        12.92        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
       13.22        13.41        27.12        52.57        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
        5.92        10.45        13.41         0.10        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.10         0.10        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U6 
       12.59         0.10        15.52        11.54        12.33        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A9FO TCGA-Q9-A6FW TCGA-R6-A6DN 
       25.25        12.00        12.03         0.13         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 
        7.59         7.04        29.59         6.35         9.30         2.89 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV 
       12.69         7.00        20.38         5.29         3.42        15.35 
TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
        9.27        18.81        19.96         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        30.71        18.18        46.19        15.06        11.24 
TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-ZR-A9CJ 
        9.17        10.16         2.10        19.73 

$`AMP PEAK 12(7Q21.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GQ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4P3 
        4.21         6.21        33.27         0.85        20.78        18.64 
TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
        9.30         0.79        12.82        14.86         4.67        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43J 
      122.10        41.52        25.41        24.03         6.28         4.31 
TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OP TCGA-L5-A4OX 
        8.94         3.68        19.99        21.01         7.17         7.43 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NM 
        8.71        25.12         7.40        55.50        13.48         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49N 
        5.49        21.37         8.71        83.24        12.66        12.43 
TCGA-LN-A49W TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX 
       13.25        22.39        13.22         4.47        10.52        12.23 
TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6Y0 
       13.18        33.11         5.16         5.06        14.70        53.95 
TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-S8-A6BV TCGA-V5-A7RE TCGA-V5-AASX TCGA-VR-A8EQ 
       15.78         1.45        20.02         4.80         4.44        22.82 
TCGA-VR-A8ER TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-AAPN 
       12.43        42.87        15.91         3.42         2.66 

  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                         0.10                          0.79 
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                        68.02                        122.10 
  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE 
                        12.54                         12.66 
[1] "0.1 - 68.0 (12.5)"  "0.8 - 122.1 (12.7)"
[1] "hr=" "1"  
D12V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 12(7Q21.2) MUTATED         5        2        4        1        24
  AMP PEAK 12(7Q21.2) WILD-TYPE       3        3        3        0        15
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 12(7Q21.2) MUTATED          17        12          7          7
  AMP PEAK 12(7Q21.2) WILD-TYPE        12        13          5          3
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 12(7Q21.2) MUTATED            6        4         3
  AMP PEAK 12(7Q21.2) WILD-TYPE          1        1         1
D12V3, multiclass
            clus
vv           AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  STAGE I                              5                             3
  STAGE IA                             2                             3
  STAGE IB                             4                             3
  STAGE II                             1                             0
  STAGE IIA                           24                            15
  STAGE IIB                           17                            12
  STAGE III                           12                            13
  STAGE IIIA                           7                             5
  STAGE IIIB                           7                             3
  STAGE IIIC                           6                             1
  STAGE IV                             4                             1
  STAGE IVA                            3                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK 12(7Q21.2) MUTATED      21 19 56  0
  AMP PEAK 12(7Q21.2) WILD-TYPE    10 17 29  5
D12V4, multiclass
       clus
vv      AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  T0+T1                          21                            10
  T2                             19                            17
  T3                             56                            29
  T4                              0                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK 12(7Q21.2) MUTATED   42 38  8  7
  AMP PEAK 12(7Q21.2) WILD-TYPE 29 26  4  1
D12V5, multiclass
    clus
vv   AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  N0                          42                            29
  N1                          38                            26
  N2                           8                             4
  N3                           7                             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"
D12V6, binary
                               cls
clus                             0  1
  AMP PEAK 12(7Q21.2) MUTATED   75  7
  AMP PEAK 12(7Q21.2) WILD-TYPE 51  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7Q21.2) MUTATED     75    7
  AMP PEAK 12(7Q21.2) WILD-TYPE   51    2
   clus
vv  AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  0                          75                            51
  1                           7                             2
[1] 2 2
[1] FALSE
D12V7, binary
                               cls
clus                             0  1
  AMP PEAK 12(7Q21.2) MUTATED   13 94
  AMP PEAK 12(7Q21.2) WILD-TYPE 11 55
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7Q21.2) MUTATED     13   94
  AMP PEAK 12(7Q21.2) WILD-TYPE   11   55
        clus
vv       AMP PEAK 12(7Q21.2) MUTATED AMP PEAK 12(7Q21.2) WILD-TYPE
  FEMALE                          13                            11
  MALE                            94                            55
[1] 2 2
[1] FALSE
D12V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(7Q21.2) MUTATED      29                         2    68
  AMP PEAK 12(7Q21.2) WILD-TYPE    12                         0    43
D12V9, multiclass
                           clus
vv                          AMP PEAK 12(7Q21.2) MUTATED
  ASIAN                                              29
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              68
                           clus
vv                          AMP PEAK 12(7Q21.2) WILD-TYPE
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V10, binary
                               cls
clus                             0  1
  AMP PEAK 12(7Q21.2) MUTATED    3 49
  AMP PEAK 12(7Q21.2) WILD-TYPE  0 32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7Q21.2) MUTATED      3   49
  AMP PEAK 12(7Q21.2) WILD-TYPE    0   32
                        clus
vv                       AMP PEAK 12(7Q21.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          49
                        clus
vv                       AMP PEAK 12(7Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            32
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(8P23.1) MUTATION ANALYSIS
D13V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 13(8P23.1) MUTATED   26 24
  AMP PEAK 13(8P23.1) WILD-TYPE 74 47
  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE 
                           50                           121 
  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE 
                           24                            47 
$`AMP PEAK 13(8P23.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3I8 
       25.78        14.30         8.94        16.24        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A939 
       20.09        20.78         4.67       122.10        68.02        21.70 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       31.56        25.22        24.03         3.16        30.25         0.30 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OT 
       19.99        21.01        47.93        18.35         3.16         4.90 
TCGA-L5-A4OW TCGA-L5-A88Y TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NM 
        7.13         0.36        55.50        12.92        13.55         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49U 
        5.49        21.37         8.71        10.36         5.92        15.35 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A7HZ TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A8W5 
        0.10         0.10        13.18         7.59         5.06        15.78 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EQ 
       12.69         7.00         4.80        15.35        19.96        22.82 
TCGA-X8-AAAR TCGA-ZR-A9CJ 
       10.16        19.73 

$`AMP PEAK 13(8P23.1) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ 
       31.27        58.55         7.63         5.92        13.94         4.21 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
        7.69         6.21         0.85         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
       12.82         9.96        14.86        14.50        12.16        44.75 
TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C 
       60.39         3.68        41.52        42.77        25.41        23.18 
TCGA-KH-A6WC TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        6.28         4.31         8.94        24.00         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU 
       32.61         3.32         7.17         1.38        58.59        29.00 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.43         6.94         8.71         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.95         3.02         2.66        35.97        13.48        16.47 
TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       13.22        13.41        27.12        83.24        52.57        46.09 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.45        12.66        12.43        13.41         0.10        13.15 
TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39         0.10        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03         0.13        33.11         5.16         7.82         8.02 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       14.70         7.04        29.59         6.35        53.95         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89         1.45        20.02        20.38         5.29         3.42 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        9.27         4.44        18.81        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        30.71        18.18        42.87        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE 
       15.06        11.24         9.17        15.91         3.42         2.10 
TCGA-Z6-AAPN 
        2.66 

  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE 
                          0.1                           0.1 
  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE 
                       122.10                         83.24 
  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE 
                       14.825                        12.330 
[1] "0.1 - 122.1 (14.8)" "0.1 - 83.2 (12.3)" 
[1] "hr=" "1.1"
D13V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 13(8P23.1) MUTATED         3        2        2        0        10
  AMP PEAK 13(8P23.1) WILD-TYPE       5        3        5        1        29
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 13(8P23.1) MUTATED           8         7          2          2
  AMP PEAK 13(8P23.1) WILD-TYPE        21        18         10          8
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 13(8P23.1) MUTATED            4        2         2
  AMP PEAK 13(8P23.1) WILD-TYPE          3        3         2
D13V3, multiclass
            clus
vv           AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE
  STAGE I                              3                             5
  STAGE IA                             2                             3
  STAGE IB                             2                             5
  STAGE II                             0                             1
  STAGE IIA                           10                            29
  STAGE IIB                            8                            21
  STAGE III                            7                            18
  STAGE IIIA                           2                            10
  STAGE IIIB                           2                             8
  STAGE IIIC                           4                             3
  STAGE IV                             2                             3
  STAGE IVA                            2                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK 13(8P23.1) MUTATED      12  7 26  1
  AMP PEAK 13(8P23.1) WILD-TYPE    19 29 59  4
D13V4, multiclass
       clus
vv      AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE
  T0+T1                          12                            19
  T2                              7                            29
  T3                             26                            59
  T4                              1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK 13(8P23.1) MUTATED   22 18  2  4
  AMP PEAK 13(8P23.1) WILD-TYPE 49 46 10  4
D13V5, multiclass
    clus
vv   AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE
  N0                          22                            49
  N1                          18                            46
  N2                           2                            10
  N3                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                               cls
clus                             0  1
  AMP PEAK 13(8P23.1) MUTATED   33  4
  AMP PEAK 13(8P23.1) WILD-TYPE 93  5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(8P23.1) MUTATED     33    4
  AMP PEAK 13(8P23.1) WILD-TYPE   93    5
   clus
vv  AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE
  0                          33                            93
  1                           4                             5
[1] 2 2
[1] FALSE
D13V7, binary
                               cls
clus                              0   1
  AMP PEAK 13(8P23.1) MUTATED    11  39
  AMP PEAK 13(8P23.1) WILD-TYPE  13 110
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(8P23.1) MUTATED     11   39
  AMP PEAK 13(8P23.1) WILD-TYPE   13  110
        clus
vv       AMP PEAK 13(8P23.1) MUTATED AMP PEAK 13(8P23.1) WILD-TYPE
  FEMALE                          11                            13
  MALE                            39                           110
[1] 2 2
[1] FALSE
D13V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(8P23.1) MUTATED       7                         1    35
  AMP PEAK 13(8P23.1) WILD-TYPE    34                         1    76
D13V9, multiclass
                           clus
vv                          AMP PEAK 13(8P23.1) MUTATED
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              35
                           clus
vv                          AMP PEAK 13(8P23.1) WILD-TYPE
  ASIAN                                                34
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V10, binary
                               cls
clus                             0  1
  AMP PEAK 13(8P23.1) MUTATED    1 18
  AMP PEAK 13(8P23.1) WILD-TYPE  2 63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(8P23.1) MUTATED      1   18
  AMP PEAK 13(8P23.1) WILD-TYPE    2   63
                        clus
vv                       AMP PEAK 13(8P23.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          18
                        clus
vv                       AMP PEAK 13(8P23.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            63
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(8P11.21) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 14(8P11.21) MUTATED   44 35
  AMP PEAK 14(8P11.21) WILD-TYPE 56 36
  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE 
                            79                             92 
  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE 
                            35                             36 
$`AMP PEAK 14(8P11.21) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       14.30        58.55        13.94         8.94        16.24         4.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A51D 
       33.27        20.09        20.78        18.64         3.88        17.03 
TCGA-IG-A625 TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
       12.82         4.67       122.10        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E 
        3.68        23.18        31.56        24.03         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.30         3.68        19.99        47.93        18.35         3.32 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88Y TCGA-L5-A891 
        3.16         4.90         7.13         7.43         0.36         3.95 
TCGA-L5-A8NG TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       35.97        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
        8.71        13.41        27.12        10.36         5.92        10.45 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 
       13.15        15.35         0.10         0.10        12.46        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A7HV TCGA-LN-A7HY 
       12.59         0.10        11.54        12.33        10.52        12.03 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6Y0 TCGA-R6-A8W5 
       13.18         0.13         7.59         5.06        53.95        15.78 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-AASV TCGA-V5-AASX 
       12.69         7.00        20.02        20.38        15.35         4.44 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA7I 
       19.96        22.82         8.12        28.11        18.18        15.91 
TCGA-Z6-A8JE 
        2.10 

$`AMP PEAK 14(8P11.21) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IC-A6RE 
       25.78        31.27         7.63         5.92        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A50L 
        6.21         0.85         2.63        20.12         9.30         0.53 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I 
        0.79        23.41         9.96        14.86        14.50        12.16 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93E TCGA-KH-A6WC 
       41.52        42.77        25.41        21.70        25.22         6.28 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ 
        4.31         8.94        24.00         4.70        32.61        21.01 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88T 
        7.17         1.38        58.59        29.00         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60        25.12         7.40         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       12.92        13.48        16.47        83.24        52.57        46.09 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A4A1 
       12.66        12.43        13.41         0.10        13.25        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.49        22.39        15.52        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       25.25        12.00        12.23        33.11         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 
        8.02        14.70         7.04        29.59         6.35         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW 
        2.89         1.45         5.29         3.42         4.80         9.27 
TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8Q7 
       18.81        12.43         1.55        18.31        30.71        42.87 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD 
       46.19        15.06        11.24         9.17        10.16         3.42 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE 
                           0.1                            0.1 
  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE 
                        122.10                          83.24 
  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE 
                         12.82                          12.38 
[1] "0.1 - 122.1 (12.8)" "0.1 - 83.2 (12.4)" 
[1] "hr=" "1.1"
D14V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 14(8P11.21) MUTATED         4        2        2        1        16
  AMP PEAK 14(8P11.21) WILD-TYPE       4        3        5        0        23
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 14(8P11.21) MUTATED          15        15          3          6
  AMP PEAK 14(8P11.21) WILD-TYPE        14        10          9          4
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 14(8P11.21) MUTATED            5        1         3
  AMP PEAK 14(8P11.21) WILD-TYPE          2        4         1
D14V3, multiclass
            clus
vv           AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              2                              3
  STAGE IB                              2                              5
  STAGE II                              1                              0
  STAGE IIA                            16                             23
  STAGE IIB                            15                             14
  STAGE III                            15                             10
  STAGE IIIA                            3                              9
  STAGE IIIB                            6                              4
  STAGE IIIC                            5                              2
  STAGE IV                              1                              4
  STAGE IVA                             3                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 14(8P11.21) MUTATED      13 16 44  2
  AMP PEAK 14(8P11.21) WILD-TYPE    18 20 41  3
D14V4, multiclass
       clus
vv      AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE
  T0+T1                           13                             18
  T2                              16                             20
  T3                              44                             41
  T4                               2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 14(8P11.21) MUTATED   32 32  6  5
  AMP PEAK 14(8P11.21) WILD-TYPE 39 32  6  3
D14V5, multiclass
    clus
vv   AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE
  N0                           32                             39
  N1                           32                             32
  N2                            6                              6
  N3                            5                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                                cls
clus                              0  1
  AMP PEAK 14(8P11.21) MUTATED   61  4
  AMP PEAK 14(8P11.21) WILD-TYPE 65  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(8P11.21) MUTATED     61    4
  AMP PEAK 14(8P11.21) WILD-TYPE   65    5
   clus
vv  AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE
  0                           61                             65
  1                            4                              5
[1] 2 2
[1] FALSE
D14V7, binary
                                cls
clus                              0  1
  AMP PEAK 14(8P11.21) MUTATED   10 71
  AMP PEAK 14(8P11.21) WILD-TYPE 14 78
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(8P11.21) MUTATED     10   71
  AMP PEAK 14(8P11.21) WILD-TYPE   14   78
        clus
vv       AMP PEAK 14(8P11.21) MUTATED AMP PEAK 14(8P11.21) WILD-TYPE
  FEMALE                           10                             14
  MALE                             71                             78
[1] 2 2
[1] FALSE
D14V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(8P11.21) MUTATED      24                         1    47
  AMP PEAK 14(8P11.21) WILD-TYPE    17                         1    64
D14V9, multiclass
                           clus
vv                          AMP PEAK 14(8P11.21) MUTATED
  ASIAN                                               24
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               47
                           clus
vv                          AMP PEAK 14(8P11.21) WILD-TYPE
  ASIAN                                                 17
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V10, binary
                                cls
clus                              0  1
  AMP PEAK 14(8P11.21) MUTATED    1 37
  AMP PEAK 14(8P11.21) WILD-TYPE  2 44
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(8P11.21) MUTATED      1   37
  AMP PEAK 14(8P11.21) WILD-TYPE    2   44
                        clus
vv                       AMP PEAK 14(8P11.21) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           37
                        clus
vv                       AMP PEAK 14(8P11.21) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             44
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(8Q24.21) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 15(8Q24.21) MUTATED   76 58
  AMP PEAK 15(8Q24.21) WILD-TYPE 24 13
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                           134                             37 
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                            58                             13 
$`AMP PEAK 15(8Q24.21) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        3.88         0.53        17.03         0.79        12.82         9.96 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
        4.67        14.50        12.16       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        25.41        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       31.56        24.03         3.16        30.25         0.30         4.31 
TCGA-L5-A4OE TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
       24.00        32.61        19.99        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW 
        3.32         1.38         3.16        58.59         4.90         7.13 
TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NG 
        7.43         2.60         0.36         3.95        55.50        35.97 
TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       12.92        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
        8.71        13.41        27.12        46.09        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.45        12.66        12.43        13.41         0.10        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35         0.10        13.25         0.10        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 
       12.49        12.76        12.59        22.39         0.10        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.33        13.22        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.23        12.03        13.18         0.13         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W5 
        5.06        14.70         7.04        29.59        53.95        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89        12.69         7.00        20.02        20.38         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ 
        4.80        15.35         9.27         4.44        19.96        22.82 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43        18.31         8.12        28.11        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD 
       42.87        46.19        11.24         9.17        15.91         3.42 
TCGA-Z6-A8JE TCGA-ZR-A9CJ 
        2.10        19.73 

$`AMP PEAK 15(8Q24.21) WILD-TYPE`
TCGA-IC-A6RF TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5S3 TCGA-IG-A7DP TCGA-JY-A6FH 
        6.21        18.64         9.30        23.41        14.86        42.77 
TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OP 
       25.22         6.28         8.94         3.68         4.70         7.17 
TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 
       29.00         6.94         8.71        25.12         7.40         3.02 
TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A4A8 
        2.66        13.48        16.47        83.24        52.57        15.52 
TCGA-LN-A5U5 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6XQ TCGA-R6-A6Y2 
        4.47        33.11         5.16         7.82         6.35         9.30 
TCGA-R6-A8WC TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8ET TCGA-VR-AA4G TCGA-X8-AAAR 
        1.45         3.42        18.81         1.55        15.06        10.16 
TCGA-Z6-AAPN 
        2.66 

  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                          0.10                           1.45 
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                        122.10                          83.24 
  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE 
                        12.725                          8.940 
[1] "0.1 - 122.1 (12.7)" "1.4 - 83.2 (8.9)"  
[1] "hr=" "1.1"
D15V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 15(8Q24.21) MUTATED         6        2        6        1        29
  AMP PEAK 15(8Q24.21) WILD-TYPE       2        3        1        0        10
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 15(8Q24.21) MUTATED          24        23          9          7
  AMP PEAK 15(8Q24.21) WILD-TYPE         5         2          3          3
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 15(8Q24.21) MUTATED            7        4         3
  AMP PEAK 15(8Q24.21) WILD-TYPE          0        1         1
D15V3, multiclass
            clus
vv           AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  STAGE I                               6                              2
  STAGE IA                              2                              3
  STAGE IB                              6                              1
  STAGE II                              1                              0
  STAGE IIA                            29                             10
  STAGE IIB                            24                              5
  STAGE III                            23                              2
  STAGE IIIA                            9                              3
  STAGE IIIB                            7                              3
  STAGE IIIC                            7                              0
  STAGE IV                              4                              1
  STAGE IVA                             3                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 15(8Q24.21) MUTATED      22 29 69  4
  AMP PEAK 15(8Q24.21) WILD-TYPE     9  7 16  1
D15V4, multiclass
       clus
vv      AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  T0+T1                           22                              9
  T2                              29                              7
  T3                              69                             16
  T4                               4                              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                             N0 N1 N2 N3
  AMP PEAK 15(8Q24.21) MUTATED   53 54  8  8
  AMP PEAK 15(8Q24.21) WILD-TYPE 18 10  4  0
D15V5, multiclass
    clus
vv   AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  N0                           53                             18
  N1                           54                             10
  N2                            8                              4
  N3                            8                              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"
D15V6, binary
                                cls
clus                               0   1
  AMP PEAK 15(8Q24.21) MUTATED   102   7
  AMP PEAK 15(8Q24.21) WILD-TYPE  24   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8Q24.21) MUTATED    102    7
  AMP PEAK 15(8Q24.21) WILD-TYPE   24    2
   clus
vv  AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  0                          102                             24
  1                            7                              2
[1] 2 2
[1] FALSE
D15V7, binary
                                cls
clus                               0   1
  AMP PEAK 15(8Q24.21) MUTATED    14 122
  AMP PEAK 15(8Q24.21) WILD-TYPE  10  27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8Q24.21) MUTATED     14  122
  AMP PEAK 15(8Q24.21) WILD-TYPE   10   27
        clus
vv       AMP PEAK 15(8Q24.21) MUTATED AMP PEAK 15(8Q24.21) WILD-TYPE
  FEMALE                           14                             10
  MALE                            122                             27
[1] 2 2
[1] FALSE
D15V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(8Q24.21) MUTATED      39                         1    79
  AMP PEAK 15(8Q24.21) WILD-TYPE     2                         1    32
D15V9, multiclass
                           clus
vv                          AMP PEAK 15(8Q24.21) MUTATED
  ASIAN                                               39
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               79
                           clus
vv                          AMP PEAK 15(8Q24.21) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V10, binary
                                cls
clus                              0  1
  AMP PEAK 15(8Q24.21) MUTATED    2 66
  AMP PEAK 15(8Q24.21) WILD-TYPE  1 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8Q24.21) MUTATED      2   66
  AMP PEAK 15(8Q24.21) WILD-TYPE    1   15
                        clus
vv                       AMP PEAK 15(8Q24.21) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           66
                        clus
vv                       AMP PEAK 15(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                             15
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(9P13.3) MUTATION ANALYSIS
D16V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 16(9P13.3) MUTATED   18 15
  AMP PEAK 16(9P13.3) WILD-TYPE 82 56
  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE 
                           33                           138 
  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE 
                           15                            56 
$`AMP PEAK 16(9P13.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-IG-A625 TCGA-JY-A6F8 TCGA-JY-A6FD 
       25.78        14.30         5.92        12.82       122.10        68.02 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OU 
        0.30         4.31        32.61        18.35         3.16        29.00 
TCGA-L5-A88Y TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ 
        0.36        55.50        35.97        27.12        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A4MQ TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-Q9-A6FW 
        5.92        13.41        12.33        12.03        13.18         7.82 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A8W5 TCGA-S8-A6BW TCGA-V5-AASW TCGA-VR-A8EQ 
        5.06        14.70        15.78        20.38         9.27        22.82 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7D 
       18.18        42.87         9.17 

$`AMP PEAK 16(9P13.3) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
        4.21        32.45         7.69         6.21        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS 
        9.30         0.53        17.03         0.79        23.41         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB 
       14.86         4.67        14.50        12.16        44.75        60.39 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
        3.68        41.52        42.77        25.41        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ 
        8.94        24.00         3.68         4.70        19.99        21.01 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       47.93         3.32         7.17         1.38        58.59         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.95         3.02         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49L TCGA-LN-A49M 
        8.71        13.41        83.24        52.57        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.43         0.10        13.15        15.35         0.10        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 
       22.39         0.10        15.52        11.54        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A9FO 
       12.33        25.25        10.52        12.00        12.23         0.13 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG 
       33.11         5.16         8.02         7.59         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35        53.95         9.30         2.89         1.45        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.02         5.29         3.42         4.80        15.35 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        4.44        18.81        19.96        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
        8.12        28.11        30.71        46.19        15.06        11.24 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       15.91        10.16         3.42         2.10         2.66        19.73 

  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE 
                          0.3                           0.1 
  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE 
                       122.10                         83.24 
  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE 
                        14.30                         12.43 
[1] "0.3 - 122.1 (14.3)" "0.1 - 83.2 (12.4)" 
[1] "hr=" "1.2"
D16V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 16(9P13.3) MUTATED         2        1        2        0         6
  AMP PEAK 16(9P13.3) WILD-TYPE       6        4        5        1        33
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 16(9P13.3) MUTATED           4         8          1          2
  AMP PEAK 16(9P13.3) WILD-TYPE        25        17         11          8
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 16(9P13.3) MUTATED            3        0         1
  AMP PEAK 16(9P13.3) WILD-TYPE          4        5         3
D16V3, multiclass
            clus
vv           AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE
  STAGE I                              2                             6
  STAGE IA                             1                             4
  STAGE IB                             2                             5
  STAGE II                             0                             1
  STAGE IIA                            6                            33
  STAGE IIB                            4                            25
  STAGE III                            8                            17
  STAGE IIIA                           1                            11
  STAGE IIIB                           2                             8
  STAGE IIIC                           3                             4
  STAGE IV                             0                             5
  STAGE IVA                            1                             3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK 16(9P13.3) MUTATED       5  4 22  0
  AMP PEAK 16(9P13.3) WILD-TYPE    26 32 63  5
D16V4, multiclass
       clus
vv      AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE
  T0+T1                           5                            26
  T2                              4                            32
  T3                             22                            63
  T4                              0                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK 16(9P13.3) MUTATED   13 13  2  3
  AMP PEAK 16(9P13.3) WILD-TYPE 58 51 10  5
D16V5, multiclass
    clus
vv   AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE
  N0                          13                            58
  N1                          13                            51
  N2                           2                            10
  N3                           3                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                               cls
clus                              0   1
  AMP PEAK 16(9P13.3) MUTATED    24   1
  AMP PEAK 16(9P13.3) WILD-TYPE 102   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(9P13.3) MUTATED     24    1
  AMP PEAK 16(9P13.3) WILD-TYPE  102    8
   clus
vv  AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE
  0                          24                           102
  1                           1                             8
[1] 2 2
[1] FALSE
D16V7, binary
                               cls
clus                              0   1
  AMP PEAK 16(9P13.3) MUTATED     1  33
  AMP PEAK 16(9P13.3) WILD-TYPE  23 116
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(9P13.3) MUTATED      1   33
  AMP PEAK 16(9P13.3) WILD-TYPE   23  116
        clus
vv       AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE
  FEMALE                           1                            23
  MALE                            33                           116
[1] 2 2
[1] FALSE
D16V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(9P13.3) MUTATED       8                         0    22
  AMP PEAK 16(9P13.3) WILD-TYPE    33                         2    89
D16V9, multiclass
                           clus
vv                          AMP PEAK 16(9P13.3) MUTATED
  ASIAN                                               8
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              22
                           clus
vv                          AMP PEAK 16(9P13.3) WILD-TYPE
  ASIAN                                                33
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V10, binary
                               cls
clus                             0  1
  AMP PEAK 16(9P13.3) MUTATED    0 14
  AMP PEAK 16(9P13.3) WILD-TYPE  3 67
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(9P13.3) MUTATED      0   14
  AMP PEAK 16(9P13.3) WILD-TYPE    3   67
                        clus
vv                       AMP PEAK 16(9P13.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          14
                        clus
vv                       AMP PEAK 16(9P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            67
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(9Q34.3) MUTATION ANALYSIS
D17V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 17(9Q34.3) MUTATED   39 18
  AMP PEAK 17(9Q34.3) WILD-TYPE 61 53
  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE 
                           57                           114 
  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE 
                           18                            53 
$`AMP PEAK 17(9Q34.3) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A50L TCGA-IG-A625 
       31.27         5.92         4.21         7.69         0.53        12.82 
TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FH 
        9.96        14.50       122.10        60.39         3.68        42.77 
TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OU 
       23.18         3.16         4.31         3.32         1.38        29.00 
TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NL 
        7.13         2.60         0.36         3.95        55.50        13.22 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N 
       13.41        27.12        46.09        10.36         5.92        12.43 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A4 
       13.41         0.10         0.10         0.10        12.49        12.59 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW 
       11.54        12.33         4.47        12.33        10.52        12.00 
TCGA-LN-A7HZ TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8WC TCGA-S8-A6BV 
       13.18         8.02        14.70        53.95         1.45        20.02 
TCGA-S8-A6BW TCGA-VR-A8ER TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
       20.38        12.43        30.71        18.18        42.87        46.19 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-Z6-AAPN 
       15.06         9.17         2.66 

$`AMP PEAK 17(9Q34.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        14.30        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24        32.45         6.21        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
       17.03         0.79        23.41        14.86         4.67        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D 
       44.75        68.02        41.52        25.41        21.70        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M 
       25.22        24.03         6.28        30.25         0.30         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
       24.00         3.68         4.70        32.61        19.99        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       47.93        18.35         7.17         3.16        58.59         4.90 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 
        7.43         6.94         8.71        25.12         7.40         3.02 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        2.66        35.97        12.92        13.48        16.47        13.55 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49        21.37         8.71        83.24        52.57 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y 
       10.45        12.66        13.15        15.35        13.25        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MR 
       12.59        12.76        22.39         0.10        15.52        13.22 
TCGA-LN-A5U7 TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU 
       25.25        12.23        12.03         0.13        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.82         7.59         5.06         7.04        29.59         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB 
        9.30        15.78         2.89        12.69         7.00         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42         4.80        15.35         9.27         4.44        18.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       19.96        22.82         1.55        18.31         8.12        28.11 
TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       11.24        15.91        10.16         3.42         2.10        19.73 

  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE 
                          0.1                           0.1 
  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE 
                       122.10                         83.24 
  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE 
                        12.33                         12.84 
[1] "0.1 - 122.1 (12.3)" "0.1 - 83.2 (12.8)" 
[1] "hr=" "1.5"
D17V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 17(9Q34.3) MUTATED         2        0        3        0        14
  AMP PEAK 17(9Q34.3) WILD-TYPE       6        5        4        1        25
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 17(9Q34.3) MUTATED          12         9          5          2
  AMP PEAK 17(9Q34.3) WILD-TYPE        17        16          7          8
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 17(9Q34.3) MUTATED            4        1         0
  AMP PEAK 17(9Q34.3) WILD-TYPE          3        4         4
D17V3, multiclass
            clus
vv           AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE
  STAGE I                              2                             6
  STAGE IA                             0                             5
  STAGE IB                             3                             4
  STAGE II                             0                             1
  STAGE IIA                           14                            25
  STAGE IIB                           12                            17
  STAGE III                            9                            16
  STAGE IIIA                           5                             7
  STAGE IIIB                           2                             8
  STAGE IIIC                           4                             3
  STAGE IV                             1                             4
  STAGE IVA                            0                             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK 17(9Q34.3) MUTATED       6 15 32  1
  AMP PEAK 17(9Q34.3) WILD-TYPE    25 21 53  4
D17V4, multiclass
       clus
vv      AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE
  T0+T1                           6                            25
  T2                             15                            21
  T3                             32                            53
  T4                              1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK 17(9Q34.3) MUTATED   20 25  4  4
  AMP PEAK 17(9Q34.3) WILD-TYPE 51 39  8  4
D17V5, multiclass
    clus
vv   AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE
  N0                          20                            51
  N1                          25                            39
  N2                           4                             8
  N3                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                               cls
clus                             0  1
  AMP PEAK 17(9Q34.3) MUTATED   46  1
  AMP PEAK 17(9Q34.3) WILD-TYPE 80  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9Q34.3) MUTATED     46    1
  AMP PEAK 17(9Q34.3) WILD-TYPE   80    8
   clus
vv  AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE
  0                          46                            80
  1                           1                             8
[1] 2 2
[1] FALSE
D17V7, binary
                               cls
clus                             0  1
  AMP PEAK 17(9Q34.3) MUTATED    3 56
  AMP PEAK 17(9Q34.3) WILD-TYPE 21 93
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9Q34.3) MUTATED      3   56
  AMP PEAK 17(9Q34.3) WILD-TYPE   21   93
        clus
vv       AMP PEAK 17(9Q34.3) MUTATED AMP PEAK 17(9Q34.3) WILD-TYPE
  FEMALE                           3                            21
  MALE                            56                            93
[1] 2 2
[1] FALSE
D17V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(9Q34.3) MUTATED      21                         0    32
  AMP PEAK 17(9Q34.3) WILD-TYPE    20                         2    79
D17V9, multiclass
                           clus
vv                          AMP PEAK 17(9Q34.3) MUTATED
  ASIAN                                              21
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              32
                           clus
vv                          AMP PEAK 17(9Q34.3) WILD-TYPE
  ASIAN                                                20
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V10, binary
                               cls
clus                             0  1
  AMP PEAK 17(9Q34.3) MUTATED    0 30
  AMP PEAK 17(9Q34.3) WILD-TYPE  3 51
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9Q34.3) MUTATED      0   30
  AMP PEAK 17(9Q34.3) WILD-TYPE    3   51
                        clus
vv                       AMP PEAK 17(9Q34.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          30
                        clus
vv                       AMP PEAK 17(9Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            51
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(11P13) MUTATION ANALYSIS
D18V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 18(11P13) MUTATED   21 26
  AMP PEAK 18(11P13) WILD-TYPE 79 45
  AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE 
                          47                          124 
  AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE 
                          26                           45 
$`AMP PEAK 18(11P13) MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A50L TCGA-IG-A97H 
       58.55         7.63         8.94        16.24         0.53        14.50 
TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43M TCGA-L5-A4OE 
      122.10         3.68        25.22         6.28         8.94        24.00 
TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88S 
       32.61        47.93        18.35         4.90        29.00         6.94 
TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NN TCGA-L5-A8NT TCGA-L5-A8NV 
        3.95         2.66        13.48         5.49        27.12        52.57 
TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A4A1 TCGA-LN-A4MQ 
       46.09         5.92        13.15         0.10        12.59        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HW TCGA-LN-A7HY TCGA-Q9-A6FW TCGA-R6-A6DN 
       13.22         4.47        12.00        12.03         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-V5-A7RC 
        7.59         7.04         6.35        53.95         7.00         3.42 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EZ TCGA-ZR-A9CJ 
       22.82        12.43        18.31        18.18        19.73 

$`AMP PEAK 18(11P13) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ 
       25.78        31.27        14.30         5.92        13.94         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       32.45         7.69         6.21        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FG 
        4.67        12.16        44.75        60.39        68.02        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F 
       42.77        25.41        21.70        23.18        31.56        24.03 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OG 
        3.16        30.25         0.30         4.31         3.68         4.70 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       19.99        21.01         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
       58.59         7.13         7.43         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH 
        0.36         7.40         3.02        55.50        35.97        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         7.76        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       13.41        83.24        10.36        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.41         0.10        15.35        13.25         0.10        12.46 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39         0.10        15.52 
TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ 
       11.54        12.33        25.25        10.52        12.23        13.18 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG 
        0.13        33.11         5.16         5.06        14.70        29.59 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV 
        9.30        15.78         2.89         1.45        12.69        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
       20.38         5.29         4.80        15.35         9.27         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       18.81        19.96         1.55         8.12        28.11        30.71 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       42.87        46.19        15.06        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
       10.16         3.42         2.10         2.66 

  AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE 
                         0.1                          0.1 
  AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE 
                      122.10                        83.24 
  AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE 
                      12.330                       12.675 
[1] "0.1 - 122.1 (12.3)" "0.1 - 83.2 (12.7)" 
[1] "hr=" "1.4"
D18V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 18(11P13) MUTATED         3        2        2        0        10
  AMP PEAK 18(11P13) WILD-TYPE       5        3        5        1        29
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 18(11P13) MUTATED           4         9          2          2
  AMP PEAK 18(11P13) WILD-TYPE        25        16         10          8
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 18(11P13) MUTATED            2        3         2
  AMP PEAK 18(11P13) WILD-TYPE          5        2         2
D18V3, multiclass
            clus
vv           AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE
  STAGE I                             3                            5
  STAGE IA                            2                            3
  STAGE IB                            2                            5
  STAGE II                            0                            1
  STAGE IIA                          10                           29
  STAGE IIB                           4                           25
  STAGE III                           9                           16
  STAGE IIIA                          2                           10
  STAGE IIIB                          2                            8
  STAGE IIIC                          2                            5
  STAGE IV                            3                            2
  STAGE IVA                           2                            2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3 T4
  AMP PEAK 18(11P13) MUTATED       9  4 29  1
  AMP PEAK 18(11P13) WILD-TYPE    22 32 56  4
D18V4, multiclass
       clus
vv      AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE
  T0+T1                          9                           22
  T2                             4                           32
  T3                            29                           56
  T4                             1                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2 N3
  AMP PEAK 18(11P13) MUTATED   17 20  3  2
  AMP PEAK 18(11P13) WILD-TYPE 54 44  9  6
D18V5, multiclass
    clus
vv   AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE
  N0                         17                           54
  N1                         20                           44
  N2                          3                            9
  N3                          2                            6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                              cls
clus                            0  1
  AMP PEAK 18(11P13) MUTATED   32  5
  AMP PEAK 18(11P13) WILD-TYPE 94  4
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(11P13) MUTATED     32    5
  AMP PEAK 18(11P13) WILD-TYPE   94    4
   clus
vv  AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE
  0                         32                           94
  1                          5                            4
[1] 2 2
[1] FALSE
D18V7, binary
                              cls
clus                             0   1
  AMP PEAK 18(11P13) MUTATED     4  45
  AMP PEAK 18(11P13) WILD-TYPE  20 104
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(11P13) MUTATED      4   45
  AMP PEAK 18(11P13) WILD-TYPE   20  104
        clus
vv       AMP PEAK 18(11P13) MUTATED AMP PEAK 18(11P13) WILD-TYPE
  FEMALE                          4                           20
  MALE                           45                          104
[1] 2 2
[1] FALSE
D18V8, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(11P13) MUTATED      13                         1    29
  AMP PEAK 18(11P13) WILD-TYPE    28                         1    82
D18V9, multiclass
                           clus
vv                          AMP PEAK 18(11P13) MUTATED
  ASIAN                                             13
  BLACK OR AFRICAN AMERICAN                          1
  WHITE                                             29
                           clus
vv                          AMP PEAK 18(11P13) WILD-TYPE
  ASIAN                                               28
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V10, binary
                              cls
clus                            0  1
  AMP PEAK 18(11P13) MUTATED    0 23
  AMP PEAK 18(11P13) WILD-TYPE  3 58
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(11P13) MUTATED      0   23
  AMP PEAK 18(11P13) WILD-TYPE    3   58
                        clus
vv                       AMP PEAK 18(11P13) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                         23
                        clus
vv                       AMP PEAK 18(11P13) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           58
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(11P13) MUTATION ANALYSIS
D19V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 19(11P13) MUTATED   19 25
  AMP PEAK 19(11P13) WILD-TYPE 81 46
  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE 
                          44                          127 
  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE 
                          25                           46 
$`AMP PEAK 19(11P13) MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A50L TCGA-IG-A8O2 TCGA-IG-A97H 
        7.63         8.94        16.24         0.53         4.67        14.50 
TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A93E TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OH 
      122.10         3.68        25.22         8.94        24.00        32.61 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A8NF 
       47.93        18.35         4.90        29.00         6.94         2.66 
TCGA-L5-A8NN TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49S 
        5.49        27.12        52.57        46.09         5.92        13.15 
TCGA-LN-A49V TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
        0.10        12.59        22.39        12.33        13.22         4.47 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 
       10.52        12.00        12.03         7.82         7.59         7.04 
TCGA-RE-A7BO TCGA-V5-A7RC TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EX 
        7.00         3.42        22.82        12.43        18.31        28.11 
TCGA-VR-A8EZ TCGA-ZR-A9CJ 
       18.18        19.73 

$`AMP PEAK 19(11P13) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
        4.21        32.45         7.69         6.21        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FG 
       14.86        12.16        44.75        60.39        68.02        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F 
       42.77        25.41        21.70        23.18        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OF 
        6.28         3.16        30.25         0.30         4.31         3.68 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
        4.70        19.99        21.01         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V 
        3.16        58.59         7.13         7.43         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       25.12         0.36         7.40         3.95         3.02        55.50 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       35.97        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A6VZ 
        7.76        21.37         8.71        13.41        83.24        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U 
       10.45        12.66        12.43        13.41         0.10        15.35 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25         0.10        12.46        12.49        12.76        12.59 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HX 
        0.10        15.52        11.54        12.33        25.25        12.23 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6KZ 
       13.18         0.13        33.11         5.16         8.02         5.06 
TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
       14.70        29.59         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         1.45        12.69        20.02        20.38         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        4.80        15.35         9.27         4.44        18.81        19.96 
TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
        1.55         8.12        30.71        42.87        46.19        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE 
       11.24         9.17        15.91        10.16         3.42         2.10 
TCGA-Z6-AAPN 
        2.66 

  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE 
                         0.1                          0.1 
  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE 
                      122.10                        83.24 
  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE 
                       12.38                        12.66 
[1] "0.1 - 122.1 (12.4)" "0.1 - 83.2 (12.7)" 
[1] "hr=" "1.5"
D19V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 19(11P13) MUTATED         2        1        2        0        12
  AMP PEAK 19(11P13) WILD-TYPE       6        4        5        1        27
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 19(11P13) MUTATED           4         8          2          3
  AMP PEAK 19(11P13) WILD-TYPE        25        17         10          7
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 19(11P13) MUTATED            2        3         3
  AMP PEAK 19(11P13) WILD-TYPE          5        2         1
D19V3, multiclass
            clus
vv           AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE
  STAGE I                             2                            6
  STAGE IA                            1                            4
  STAGE IB                            2                            5
  STAGE II                            0                            1
  STAGE IIA                          12                           27
  STAGE IIB                           4                           25
  STAGE III                           8                           17
  STAGE IIIA                          2                           10
  STAGE IIIB                          3                            7
  STAGE IIIC                          2                            5
  STAGE IV                            3                            2
  STAGE IVA                           3                            1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3 T4
  AMP PEAK 19(11P13) MUTATED       8  6 28  1
  AMP PEAK 19(11P13) WILD-TYPE    23 30 57  4
D19V4, multiclass
       clus
vv      AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE
  T0+T1                          8                           23
  T2                             6                           30
  T3                            28                           57
  T4                             1                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2 N3
  AMP PEAK 19(11P13) MUTATED   17 19  4  2
  AMP PEAK 19(11P13) WILD-TYPE 54 45  8  6
D19V5, multiclass
    clus
vv   AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE
  N0                         17                           54
  N1                         19                           45
  N2                          4                            8
  N3                          2                            6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                              cls
clus                            0  1
  AMP PEAK 19(11P13) MUTATED   31  6
  AMP PEAK 19(11P13) WILD-TYPE 95  3
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(11P13) MUTATED     31    6
  AMP PEAK 19(11P13) WILD-TYPE   95    3
   clus
vv  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE
  0                         31                           95
  1                          6                            3
[1] 2 2
[1] FALSE
D19V7, binary
                              cls
clus                             0   1
  AMP PEAK 19(11P13) MUTATED     4  42
  AMP PEAK 19(11P13) WILD-TYPE  20 107
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(11P13) MUTATED      4   42
  AMP PEAK 19(11P13) WILD-TYPE   20  107
        clus
vv       AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE
  FEMALE                          4                           20
  MALE                           42                          107
[1] 2 2
[1] FALSE
D19V8, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(11P13) MUTATED      16                         1    23
  AMP PEAK 19(11P13) WILD-TYPE    25                         1    88
D19V9, multiclass
                           clus
vv                          AMP PEAK 19(11P13) MUTATED
  ASIAN                                             16
  BLACK OR AFRICAN AMERICAN                          1
  WHITE                                             23
                           clus
vv                          AMP PEAK 19(11P13) WILD-TYPE
  ASIAN                                               25
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V10, binary
                              cls
clus                            0  1
  AMP PEAK 19(11P13) MUTATED    0 22
  AMP PEAK 19(11P13) WILD-TYPE  3 59
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(11P13) MUTATED      0   22
  AMP PEAK 19(11P13) WILD-TYPE    3   59
                        clus
vv                       AMP PEAK 19(11P13) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                         22
                        clus
vv                       AMP PEAK 19(11P13) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           59
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(11Q13.3) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 20(11Q13.3) MUTATED   58 36
  AMP PEAK 20(11Q13.3) WILD-TYPE 42 35
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                            94                             77 
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                            36                             35 
$`AMP PEAK 20(11Q13.3) MUTATED`
TCGA-2H-A9GN TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 
        8.94        33.27         0.85        20.78        20.12        18.64 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       17.03        23.41         9.96         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A938 TCGA-JY-A93E TCGA-L5-A43H 
      122.10        60.39         3.68        25.41        25.22         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        4.31         8.94        24.00         3.68         4.70        32.61 
TCGA-L5-A4OM TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88V 
       47.93         1.38        58.59        29.00         6.94         2.60 
TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        0.36         3.95        55.50         2.66        12.92        13.48 
TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L5-A8NW 
       13.55         5.49        21.37         8.71        52.57        46.09 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V 
        5.92        12.66        12.43         0.10        13.15         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25         0.10        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        22.39         0.10        15.52        12.33        13.22 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       12.33        25.25        12.00        12.23        12.03        13.18 
TCGA-LN-A9FO TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ 
        0.13         7.82         8.02         7.59         7.04         6.35 
TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EO 
       53.95        15.78         7.00         3.42         9.27        18.81 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       22.82        12.43        18.31         8.12        28.11        30.71 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        46.19        15.06        11.24         9.17        15.91 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        3.42         2.10         2.66        19.73 

$`AMP PEAK 20(11Q13.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
       13.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 
       20.09         2.63         3.88         9.30         0.53         0.79 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH 
       12.82        14.86        44.75        68.02        41.52        42.77 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        31.56        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       30.25        19.99        21.01        18.35         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W 
        3.16         4.90         7.13         7.43         8.71        25.12 
TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NG TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
        7.40         3.02        35.97        16.47        13.22         7.76 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49O 
       13.41        27.12        83.24        10.36        10.45        13.41 
TCGA-LN-A49U TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-M9-A5M8 TCGA-Q9-A6FU 
       15.35        11.54         4.47        10.52        33.11         5.16 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC 
        5.06        14.70        29.59         9.30         2.89         1.45 
TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
       12.69        20.02        20.38         5.29         4.80        15.35 
TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8Q7 TCGA-X8-AAAR 
        4.44        19.96         1.55        42.87        10.16 

  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                          0.10                           0.53 
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                        122.10                          83.24 
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                        12.475                         12.820 
[1] "0.1 - 122.1 (12.5)" "0.5 - 83.2 (12.8)" 
[1] "hr=" "1.2"
D20V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 20(11Q13.3) MUTATED         4        1        3        1        25
  AMP PEAK 20(11Q13.3) WILD-TYPE       4        4        4        0        14
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 20(11Q13.3) MUTATED          14        16          7          5
  AMP PEAK 20(11Q13.3) WILD-TYPE        15         9          5          5
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 20(11Q13.3) MUTATED            3        3         3
  AMP PEAK 20(11Q13.3) WILD-TYPE          4        2         1
D20V3, multiclass
            clus
vv           AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              1                              4
  STAGE IB                              3                              4
  STAGE II                              1                              0
  STAGE IIA                            25                             14
  STAGE IIB                            14                             15
  STAGE III                            16                              9
  STAGE IIIA                            7                              5
  STAGE IIIB                            5                              5
  STAGE IIIC                            3                              4
  STAGE IV                              3                              2
  STAGE IVA                             3                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 20(11Q13.3) MUTATED      14 22 48  4
  AMP PEAK 20(11Q13.3) WILD-TYPE    17 14 37  1
D20V4, multiclass
       clus
vv      AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE
  T0+T1                           14                             17
  T2                              22                             14
  T3                              48                             37
  T4                               4                              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                             N0 N1 N2 N3
  AMP PEAK 20(11Q13.3) MUTATED   42 34  7  4
  AMP PEAK 20(11Q13.3) WILD-TYPE 29 30  5  4
D20V5, multiclass
    clus
vv   AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE
  N0                           42                             29
  N1                           34                             30
  N2                            7                              5
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                                cls
clus                              0  1
  AMP PEAK 20(11Q13.3) MUTATED   72  6
  AMP PEAK 20(11Q13.3) WILD-TYPE 54  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(11Q13.3) MUTATED     72    6
  AMP PEAK 20(11Q13.3) WILD-TYPE   54    3
   clus
vv  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE
  0                           72                             54
  1                            6                              3
[1] 2 2
[1] FALSE
D20V7, binary
                                cls
clus                              0  1
  AMP PEAK 20(11Q13.3) MUTATED   13 82
  AMP PEAK 20(11Q13.3) WILD-TYPE 11 67
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(11Q13.3) MUTATED     13   82
  AMP PEAK 20(11Q13.3) WILD-TYPE   11   67
        clus
vv       AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE
  FEMALE                           13                             11
  MALE                             82                             67
[1] 2 2
[1] FALSE
D20V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(11Q13.3) MUTATED      29                         1    59
  AMP PEAK 20(11Q13.3) WILD-TYPE    12                         1    52
D20V9, multiclass
                           clus
vv                          AMP PEAK 20(11Q13.3) MUTATED
  ASIAN                                               29
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               59
                           clus
vv                          AMP PEAK 20(11Q13.3) WILD-TYPE
  ASIAN                                                 12
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V10, binary
                                cls
clus                              0  1
  AMP PEAK 20(11Q13.3) MUTATED    0 50
  AMP PEAK 20(11Q13.3) WILD-TYPE  3 31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(11Q13.3) MUTATED      0   50
  AMP PEAK 20(11Q13.3) WILD-TYPE    3   31
                        clus
vv                       AMP PEAK 20(11Q13.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           50
                        clus
vv                       AMP PEAK 20(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                             31
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(12P12.1) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 21(12P12.1) MUTATED   42 31
  AMP PEAK 21(12P12.1) WILD-TYPE 58 40
  AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE 
                            73                             98 
  AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE 
                            31                             40 
$`AMP PEAK 21(12P12.1) MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3QL 
        7.63         5.92        16.24         4.21        32.45        20.09 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5S3 
        2.63        20.12        18.64         3.88         0.53        23.41 
TCGA-IG-A97H TCGA-JY-A93D TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OI 
       14.50        31.56         0.30         4.31        24.00        19.99 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88S 
       47.93        18.35         3.32         4.90        29.00         6.94 
TCGA-L5-A88Y TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NQ TCGA-L5-A8NT 
        0.36         2.66        16.47        13.22        21.37        27.12 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O 
       46.09        10.36         5.92        10.45        12.66        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A3 
        0.10        13.15         0.10        13.25        12.59        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.59         0.10        15.52        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-R6-A6DN 
       25.25        10.52        12.00        13.18         0.13         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8WG 
        7.59         5.06        29.59         6.35        53.95        12.69 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       20.02        20.38        19.96         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
       28.11        18.18        10.16         3.42         2.10         2.66 
TCGA-ZR-A9CJ 
       19.73 

$`AMP PEAK 21(12P12.1) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        31.27        14.30        58.55        13.94         8.94 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QT 
        7.69         6.21        33.27         0.85        20.78         9.30 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03         0.79        12.82         9.96        14.86         4.67 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
       12.16       122.10        44.75        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E 
       41.52        42.77        25.41        21.70        23.18        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         8.94         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
        4.70        32.61        21.01         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
       58.59         7.13         7.43         8.71         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH 
        7.40         3.95         3.02        55.50        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
       13.48        13.55         7.76         5.49         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49N TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y 
       83.24        52.57        12.43        15.35         0.10        12.46 
TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A7HX TCGA-LN-A7HY 
       12.49        22.39        11.54        12.33        12.23        12.03 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y2 
       33.11         5.16         7.82        14.70         7.04         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC 
       15.78         2.89         1.45         7.00         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ 
        4.80        15.35         9.27         4.44        18.81        22.82 
TCGA-VR-A8ER TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       12.43        30.71        42.87        46.19        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I 
        9.17        15.91 

  AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE 
                           0.1                            0.1 
  AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE 
                         53.95                         122.10 
  AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE 
                        12.660                         12.445 
[1] "0.1 - 54.0 (12.7)"  "0.1 - 122.1 (12.4)"
[1] "hr=" "1.4"
D21V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 21(12P12.1) MUTATED         0        1        3        1        21
  AMP PEAK 21(12P12.1) WILD-TYPE       8        4        4        0        18
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 21(12P12.1) MUTATED           8        10          5          4
  AMP PEAK 21(12P12.1) WILD-TYPE        21        15          7          6
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 21(12P12.1) MUTATED            6        3         3
  AMP PEAK 21(12P12.1) WILD-TYPE          1        2         1
D21V3, multiclass
            clus
vv           AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE
  STAGE I                               0                              8
  STAGE IA                              1                              4
  STAGE IB                              3                              4
  STAGE II                              1                              0
  STAGE IIA                            21                             18
  STAGE IIB                             8                             21
  STAGE III                            10                             15
  STAGE IIIA                            5                              7
  STAGE IIIB                            4                              6
  STAGE IIIC                            6                              1
  STAGE IV                              3                              2
  STAGE IVA                             3                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 21(12P12.1) MUTATED       7 17 43  0
  AMP PEAK 21(12P12.1) WILD-TYPE    24 19 42  5
D21V4, multiclass
       clus
vv      AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE
  T0+T1                            7                             24
  T2                              17                             19
  T3                              43                             42
  T4                               0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 21(12P12.1) MUTATED   31 25  4  6
  AMP PEAK 21(12P12.1) WILD-TYPE 40 39  8  2
D21V5, multiclass
    clus
vv   AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE
  N0                           31                             40
  N1                           25                             39
  N2                            4                              8
  N3                            6                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                                cls
clus                              0  1
  AMP PEAK 21(12P12.1) MUTATED   49  6
  AMP PEAK 21(12P12.1) WILD-TYPE 77  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(12P12.1) MUTATED     49    6
  AMP PEAK 21(12P12.1) WILD-TYPE   77    3
   clus
vv  AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE
  0                           49                             77
  1                            6                              3
[1] 2 2
[1] FALSE
D21V7, binary
                                cls
clus                              0  1
  AMP PEAK 21(12P12.1) MUTATED    3 71
  AMP PEAK 21(12P12.1) WILD-TYPE 21 78
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(12P12.1) MUTATED      3   71
  AMP PEAK 21(12P12.1) WILD-TYPE   21   78
        clus
vv       AMP PEAK 21(12P12.1) MUTATED AMP PEAK 21(12P12.1) WILD-TYPE
  FEMALE                            3                             21
  MALE                             71                             78
[1] 2 2
[1] FALSE
D21V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(12P12.1) MUTATED      25                         0    43
  AMP PEAK 21(12P12.1) WILD-TYPE    16                         2    68
D21V9, multiclass
                           clus
vv                          AMP PEAK 21(12P12.1) MUTATED
  ASIAN                                               25
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               43
                           clus
vv                          AMP PEAK 21(12P12.1) WILD-TYPE
  ASIAN                                                 16
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V10, binary
                                cls
clus                              0  1
  AMP PEAK 21(12P12.1) MUTATED    1 43
  AMP PEAK 21(12P12.1) WILD-TYPE  2 38
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(12P12.1) MUTATED      1   43
  AMP PEAK 21(12P12.1) WILD-TYPE    2   38
                        clus
vv                       AMP PEAK 21(12P12.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           43
                        clus
vv                       AMP PEAK 21(12P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             38
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(12Q15) MUTATION ANALYSIS
D22V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 22(12Q15) MUTATED   25 23
  AMP PEAK 22(12Q15) WILD-TYPE 75 48
  AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE 
                          48                          123 
  AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE 
                          23                           48 
$`AMP PEAK 22(12Q15) MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A50L TCGA-IG-A8O2 TCGA-L5-A43J 
        7.63        16.24        32.45         0.53         4.67         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OT 
        8.94        24.00        21.01        47.93         3.32         4.90 
TCGA-L5-A88S TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NN 
        6.94        55.50         2.66        13.48        13.22         5.49 
TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49V 
       27.12        52.57        46.09        10.36        10.45         0.10 
TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       13.25        12.59        12.59         0.10        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A9FO TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-R6-A6XQ 
       12.33         4.47         0.13         7.59        29.59         6.35 
TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EX 
       12.69        20.38         3.42        19.96         1.55        28.11 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       18.18        42.87        11.24        10.16         2.10        19.73 

$`AMP PEAK 22(12Q15) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94         4.21         7.69         6.21        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
       14.86        14.50        12.16       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       68.02         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
       30.25         0.30         3.68         4.70        32.61        19.99 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU 
       18.35         7.17         1.38         3.16        58.59        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
        7.13         7.43         8.71         2.60        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ 
        7.40         3.95         3.02        35.97        12.92        16.47 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.55         7.76        21.37         8.71        13.41        83.24 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
        5.92        12.66        12.43        13.41         0.10        13.15 
TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 
       15.35         0.10        12.46        12.49        12.76        22.39 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       13.22        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        13.18        33.11         5.16         7.82         8.02 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        5.06        14.70         7.04        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        2.89         1.45         7.00        20.02         5.29         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         9.27         4.44        18.81        22.82        12.43 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D 
       18.31         8.12        30.71        46.19        15.06         9.17 
TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-AAPN 
       15.91         3.42         2.66 

  AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE 
                         0.1                          0.1 
  AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE 
                        55.5                        122.1 
  AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE 
                      11.935                       12.760 
[1] "0.1 - 55.5 (11.9)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "1.4"
D22V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 22(12Q15) MUTATED         1        1        3        1         9
  AMP PEAK 22(12Q15) WILD-TYPE       7        4        4        0        30
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 22(12Q15) MUTATED           4         7          3          3
  AMP PEAK 22(12Q15) WILD-TYPE        25        18          9          7
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 22(12Q15) MUTATED            4        3         3
  AMP PEAK 22(12Q15) WILD-TYPE          3        2         1
D22V3, multiclass
            clus
vv           AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE
  STAGE I                             1                            7
  STAGE IA                            1                            4
  STAGE IB                            3                            4
  STAGE II                            1                            0
  STAGE IIA                           9                           30
  STAGE IIB                           4                           25
  STAGE III                           7                           18
  STAGE IIIA                          3                            9
  STAGE IIIB                          3                            7
  STAGE IIIC                          4                            3
  STAGE IV                            3                            2
  STAGE IVA                           3                            1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3 T4
  AMP PEAK 22(12Q15) MUTATED       5 10 29  0
  AMP PEAK 22(12Q15) WILD-TYPE    26 26 56  5
D22V4, multiclass
       clus
vv      AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE
  T0+T1                          5                           26
  T2                            10                           26
  T3                            29                           56
  T4                             0                            5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2 N3
  AMP PEAK 22(12Q15) MUTATED   17 18  4  5
  AMP PEAK 22(12Q15) WILD-TYPE 54 46  8  3
D22V5, multiclass
    clus
vv   AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE
  N0                         17                           54
  N1                         18                           46
  N2                          4                            8
  N3                          5                            3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                              cls
clus                            0  1
  AMP PEAK 22(12Q15) MUTATED   29  6
  AMP PEAK 22(12Q15) WILD-TYPE 97  3
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(12Q15) MUTATED     29    6
  AMP PEAK 22(12Q15) WILD-TYPE   97    3
   clus
vv  AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE
  0                         29                           97
  1                          6                            3
[1] 2 2
[1] FALSE
D22V7, binary
                              cls
clus                             0   1
  AMP PEAK 22(12Q15) MUTATED     5  44
  AMP PEAK 22(12Q15) WILD-TYPE  19 105
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(12Q15) MUTATED      5   44
  AMP PEAK 22(12Q15) WILD-TYPE   19  105
        clus
vv       AMP PEAK 22(12Q15) MUTATED AMP PEAK 22(12Q15) WILD-TYPE
  FEMALE                          5                           19
  MALE                           44                          105
[1] 2 2
[1] FALSE
D22V8, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(12Q15) MUTATED      14                         1    29
  AMP PEAK 22(12Q15) WILD-TYPE    27                         1    82
D22V9, multiclass
                           clus
vv                          AMP PEAK 22(12Q15) MUTATED
  ASIAN                                             14
  BLACK OR AFRICAN AMERICAN                          1
  WHITE                                             29
                           clus
vv                          AMP PEAK 22(12Q15) WILD-TYPE
  ASIAN                                               27
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V10, binary
                              cls
clus                            0  1
  AMP PEAK 22(12Q15) MUTATED    1 22
  AMP PEAK 22(12Q15) WILD-TYPE  2 59
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(12Q15) MUTATED      1   22
  AMP PEAK 22(12Q15) WILD-TYPE    2   59
                        clus
vv                       AMP PEAK 22(12Q15) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         22
                        clus
vv                       AMP PEAK 22(12Q15) WILD-TYPE
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           59
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 23(13Q22.1) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 23(13Q22.1) MUTATED   38 24
  AMP PEAK 23(13Q22.1) WILD-TYPE 62 47
  AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE 
                            62                            109 
  AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE 
                            24                             47 
$`AMP PEAK 23(13Q22.1) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IC-A6RE 
       31.27        14.30         5.92        13.94         4.21         7.69 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FH 
        0.53         0.79        14.50       122.10         3.68        42.77 
TCGA-JY-A93C TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OG 
       23.18        31.56         3.16        30.25         8.94         4.70 
TCGA-L5-A4OI TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88S 
       19.99         7.17         1.38        58.59         7.13         6.94 
TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NK 
        0.36         3.02        55.50         2.66        12.92        13.55 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49R 
        8.71        13.41        27.12        46.09        10.45         0.10 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4MQ 
       15.35         0.10        12.59        12.59         0.10        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 
       25.25        12.00        12.23         7.82         8.02        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WG 
        7.04        29.59        53.95         9.30        15.78        12.69 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EZ TCGA-VR-AA4D 
       20.02         5.29         3.42         9.27        18.18        46.19 
TCGA-X8-AAAR TCGA-ZR-A9CJ 
       10.16        19.73 

$`AMP PEAK 23(13Q22.1) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR 
       25.78        58.55         7.63         8.94        16.24        32.45 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        6.21        33.27        20.09         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 
       20.12        18.64         3.88         9.30        17.03        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA 
       12.82         9.96        14.86         4.67        12.16        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93E 
       60.39        68.02        41.52        25.41        21.70        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF 
       24.03         6.28         0.30         4.31        24.00         3.68 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR 
       32.61        21.01        47.93        18.35         3.32         3.16 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        4.90        29.00         7.43         8.71         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL 
        7.40         3.95        35.97        13.48        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A6VZ 
        7.76         5.49        21.37        83.24        52.57        10.36 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49W 
        5.92        12.66        12.43        13.41        13.15        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A8 
        0.10        12.46        12.49        12.76        22.39        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HY 
       11.54        13.22         4.47        12.33        10.52        12.03 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DQ TCGA-R6-A6KZ 
       13.18         0.13        33.11         5.16         7.59         5.06 
TCGA-R6-A6XQ TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RE 
        6.35         2.89         1.45         7.00        20.38         4.80 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         4.44        18.81        19.96        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 
        1.55        18.31         8.12        28.11        30.71        42.87 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE 
       15.06        11.24         9.17        15.91         3.42         2.10 
TCGA-Z6-AAPN 
        2.66 

  AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE 
                           0.1                            0.1 
  AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE 
                        122.10                          83.24 
  AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE 
                         12.28                          12.76 
[1] "0.1 - 122.1 (12.3)" "0.1 - 83.2 (12.8)" 
[1] "hr=" "1.1"
D23V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 23(13Q22.1) MUTATED         4        1        4        1         9
  AMP PEAK 23(13Q22.1) WILD-TYPE       4        4        3        0        30
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 23(13Q22.1) MUTATED           9         8          3          2
  AMP PEAK 23(13Q22.1) WILD-TYPE        20        17          9          8
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 23(13Q22.1) MUTATED            4        1         2
  AMP PEAK 23(13Q22.1) WILD-TYPE          3        4         2
D23V3, multiclass
            clus
vv           AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              1                              4
  STAGE IB                              4                              3
  STAGE II                              1                              0
  STAGE IIA                             9                             30
  STAGE IIB                             9                             20
  STAGE III                             8                             17
  STAGE IIIA                            3                              9
  STAGE IIIB                            2                              8
  STAGE IIIC                            4                              3
  STAGE IV                              1                              4
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 23(13Q22.1) MUTATED      14 12 26  0
  AMP PEAK 23(13Q22.1) WILD-TYPE    17 24 59  5
D23V4, multiclass
       clus
vv      AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE
  T0+T1                           14                             17
  T2                              12                             24
  T3                              26                             59
  T4                               0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 23(13Q22.1) MUTATED   21 22  4  4
  AMP PEAK 23(13Q22.1) WILD-TYPE 50 42  8  4
D23V5, multiclass
    clus
vv   AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE
  N0                           21                             50
  N1                           22                             42
  N2                            4                              8
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                                cls
clus                              0  1
  AMP PEAK 23(13Q22.1) MUTATED   39  3
  AMP PEAK 23(13Q22.1) WILD-TYPE 87  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(13Q22.1) MUTATED     39    3
  AMP PEAK 23(13Q22.1) WILD-TYPE   87    6
   clus
vv  AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE
  0                           39                             87
  1                            3                              6
[1] 2 2
[1] FALSE
D23V7, binary
                                cls
clus                              0  1
  AMP PEAK 23(13Q22.1) MUTATED    8 54
  AMP PEAK 23(13Q22.1) WILD-TYPE 16 95
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(13Q22.1) MUTATED      8   54
  AMP PEAK 23(13Q22.1) WILD-TYPE   16   95
        clus
vv       AMP PEAK 23(13Q22.1) MUTATED AMP PEAK 23(13Q22.1) WILD-TYPE
  FEMALE                            8                             16
  MALE                             54                             95
[1] 2 2
[1] FALSE
D23V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(13Q22.1) MUTATED      14                         1    38
  AMP PEAK 23(13Q22.1) WILD-TYPE    27                         1    73
D23V9, multiclass
                           clus
vv                          AMP PEAK 23(13Q22.1) MUTATED
  ASIAN                                               14
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               38
                           clus
vv                          AMP PEAK 23(13Q22.1) WILD-TYPE
  ASIAN                                                 27
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V10, binary
                                cls
clus                              0  1
  AMP PEAK 23(13Q22.1) MUTATED    3 27
  AMP PEAK 23(13Q22.1) WILD-TYPE  0 54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(13Q22.1) MUTATED      3   27
  AMP PEAK 23(13Q22.1) WILD-TYPE    0   54
                        clus
vv                       AMP PEAK 23(13Q22.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           27
                        clus
vv                       AMP PEAK 23(13Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  0
  NOT HISPANIC OR LATINO                             54
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 24(14Q21.1) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 24(14Q21.1) MUTATED   30 24
  AMP PEAK 24(14Q21.1) WILD-TYPE 70 47
  AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE 
                            54                            117 
  AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE 
                            24                             47 
$`AMP PEAK 24(14Q21.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4P3 
       25.78         5.92        32.45         0.85        20.78        18.64 
TCGA-IG-A50L TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FH TCGA-JY-A93C 
        0.53         9.96         4.67        12.16        42.77        23.18 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OR TCGA-L5-A4OX TCGA-L5-A8NG 
        3.16        30.25         4.31         3.16         7.43        35.97 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O 
        5.49        21.37        13.41         5.92        10.45        13.41 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A5 
       13.15        15.35         0.10        12.59        12.59        22.39 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       11.54        13.22        12.33        12.23        12.03        13.18 
TCGA-LN-A9FO TCGA-R6-A6DN TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-S8-A6BV TCGA-S8-A6BW 
        0.13         8.02        29.59        53.95        20.02        20.38 
TCGA-V5-AASX TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA4D 
        4.44        12.43         8.12        28.11        18.18        46.19 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       11.24         9.17        15.91         3.42         2.10        19.73 

$`AMP PEAK 24(14Q21.1) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21         7.69         6.21        33.27        20.09 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 
        2.63        20.12         3.88         9.30        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA 
       23.41        12.82        14.86        14.50       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 
       60.39        68.02         3.68        41.52        25.41        21.70 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43M 
       31.56        25.22        24.03         6.28         0.30         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
       24.00         3.68         4.70        32.61        19.99        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       47.93        18.35         3.32         7.17         1.38        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
        4.90        29.00         7.13         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       25.12         0.36         7.40         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        7.76         8.71        27.12        83.24        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49X 
       10.36        12.66        12.43         0.10        13.25         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ 
       12.46        12.49        12.76         0.10        15.52        12.33 
TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-M9-A5M8 TCGA-Q9-A6FU 
        4.47        25.25        10.52        12.00        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ 
        7.82         7.59         5.06        14.70         7.04         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         1.45        12.69         7.00 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO 
        5.29         3.42         4.80        15.35         9.27        18.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8Q7 
       19.96        22.82         1.55        18.31        30.71        42.87 
TCGA-VR-AA4G TCGA-X8-AAAR TCGA-Z6-AAPN 
       15.06        10.16         2.66 

  AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE 
                           0.1                            0.1 
  AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE 
                         53.95                         122.10 
  AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE 
                         12.51                          12.66 
[1] "0.1 - 54.0 (12.5)"  "0.1 - 122.1 (12.7)"
[1] "hr=" "1.3"
D24V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 24(14Q21.1) MUTATED         1        1        2        0        16
  AMP PEAK 24(14Q21.1) WILD-TYPE       7        4        5        1        23
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 24(14Q21.1) MUTATED           9         8          5          3
  AMP PEAK 24(14Q21.1) WILD-TYPE        20        17          7          7
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 24(14Q21.1) MUTATED            3        1         1
  AMP PEAK 24(14Q21.1) WILD-TYPE          4        4         3
D24V3, multiclass
            clus
vv           AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE
  STAGE I                               1                              7
  STAGE IA                              1                              4
  STAGE IB                              2                              5
  STAGE II                              0                              1
  STAGE IIA                            16                             23
  STAGE IIB                             9                             20
  STAGE III                             8                             17
  STAGE IIIA                            5                              7
  STAGE IIIB                            3                              7
  STAGE IIIC                            3                              4
  STAGE IV                              1                              4
  STAGE IVA                             1                              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 24(14Q21.1) MUTATED       4 16 26  4
  AMP PEAK 24(14Q21.1) WILD-TYPE    27 20 59  1
D24V4, multiclass
       clus
vv      AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE
  T0+T1                            4                             27
  T2                              16                             20
  T3                              26                             59
  T4                               4                              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                             N0 N1 N2 N3
  AMP PEAK 24(14Q21.1) MUTATED   25 18  3  4
  AMP PEAK 24(14Q21.1) WILD-TYPE 46 46  9  4
D24V5, multiclass
    clus
vv   AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE
  N0                           25                             46
  N1                           18                             46
  N2                            3                              9
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                                cls
clus                              0  1
  AMP PEAK 24(14Q21.1) MUTATED   43  2
  AMP PEAK 24(14Q21.1) WILD-TYPE 83  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(14Q21.1) MUTATED     43    2
  AMP PEAK 24(14Q21.1) WILD-TYPE   83    7
   clus
vv  AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE
  0                           43                             83
  1                            2                              7
[1] 2 2
[1] FALSE
D24V7, binary
                                cls
clus                              0  1
  AMP PEAK 24(14Q21.1) MUTATED    1 54
  AMP PEAK 24(14Q21.1) WILD-TYPE 23 95
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(14Q21.1) MUTATED      1   54
  AMP PEAK 24(14Q21.1) WILD-TYPE   23   95
        clus
vv       AMP PEAK 24(14Q21.1) MUTATED AMP PEAK 24(14Q21.1) WILD-TYPE
  FEMALE                            1                             23
  MALE                             54                             95
[1] 2 2
[1] FALSE
D24V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(14Q21.1) MUTATED      21                         0    28
  AMP PEAK 24(14Q21.1) WILD-TYPE    20                         2    83
D24V9, multiclass
                           clus
vv                          AMP PEAK 24(14Q21.1) MUTATED
  ASIAN                                               21
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               28
                           clus
vv                          AMP PEAK 24(14Q21.1) WILD-TYPE
  ASIAN                                                 20
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V10, binary
                                cls
clus                              0  1
  AMP PEAK 24(14Q21.1) MUTATED    0 33
  AMP PEAK 24(14Q21.1) WILD-TYPE  3 48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(14Q21.1) MUTATED      0   33
  AMP PEAK 24(14Q21.1) WILD-TYPE    3   48
                        clus
vv                       AMP PEAK 24(14Q21.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           33
                        clus
vv                       AMP PEAK 24(14Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                             48
[1] 2 2
[1] FALSE

Clustering(25) Variable = AMP PEAK 25(15Q26.1) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 25(15Q26.1) MUTATED   29 25
  AMP PEAK 25(15Q26.1) WILD-TYPE 71 46
  AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE 
                            54                            117 
  AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE 
                            25                             46 
$`AMP PEAK 25(15Q26.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IG-A50L 
       25.78        58.55         7.63         8.94        32.45         0.53 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A43M 
      122.10        60.39         3.68        42.77         3.16         8.94 
TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       47.93         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 
       29.00         7.13         6.94         2.60         0.36         3.95 
TCGA-L5-A8NE TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NW TCGA-L7-A6VZ 
       55.50        16.47        21.37        13.41        46.09        10.36 
TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A7HV TCGA-LN-A7HW 
       10.45         0.10        22.39        13.22        10.52        12.00 
TCGA-LN-A7HX TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       12.23        33.11         7.82         7.59        14.70         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-S8-A6BW TCGA-VR-A8EP 
        6.35        53.95         9.30        15.78        20.38        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-AA7B TCGA-VR-AA7D TCGA-ZR-A9CJ 
       22.82         1.55        18.31        11.24         9.17        19.73 

$`AMP PEAK 25(15Q26.1) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       31.27        14.30         5.92        13.94        16.24         4.21 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        7.69         6.21        33.27        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
        2.63        20.12        18.64         3.88         9.30        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A938 
       14.50        12.16        44.75        68.02        41.52        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
       30.25         0.30         4.31        24.00         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OX 
       32.61        19.99        21.01        18.35         3.32         7.43 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG 
        8.71        25.12         7.40         3.02         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        13.55        13.22         7.76         5.49 
TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49M 
        8.71        27.12        83.24        52.57         5.92        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.43        13.41        13.15        15.35         0.10        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 
        0.10        15.52        11.54        12.33         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-R6-A6DN 
       25.25        12.03        13.18         0.13         5.16         8.02 
TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        5.06        29.59         2.89         1.45        12.69         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.02         5.29         3.42         4.80        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
        4.44        18.81        12.43         8.12        28.11        30.71 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7I TCGA-X8-AAAR 
       18.18        42.87        46.19        15.06        15.91        10.16 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
        3.42         2.10         2.66 

  AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE 
                           0.1                            0.1 
  AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE 
                        122.10                          83.24 
  AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE 
                         11.62                          12.66 
[1] "0.1 - 122.1 (11.6)" "0.1 - 83.2 (12.7)" 
[1] "hr=" "1.1"
D25V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 25(15Q26.1) MUTATED         3        3        3        0        11
  AMP PEAK 25(15Q26.1) WILD-TYPE       5        2        4        1        28
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 25(15Q26.1) MUTATED           5         8          2          2
  AMP PEAK 25(15Q26.1) WILD-TYPE        24        17         10          8
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 25(15Q26.1) MUTATED            3        3         1
  AMP PEAK 25(15Q26.1) WILD-TYPE          4        2         3
D25V3, multiclass
            clus
vv           AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE
  STAGE I                               3                              5
  STAGE IA                              3                              2
  STAGE IB                              3                              4
  STAGE II                              0                              1
  STAGE IIA                            11                             28
  STAGE IIB                             5                             24
  STAGE III                             8                             17
  STAGE IIIA                            2                             10
  STAGE IIIB                            2                              8
  STAGE IIIC                            3                              4
  STAGE IV                              3                              2
  STAGE IVA                             1                              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 25(15Q26.1) MUTATED       8 15 24  0
  AMP PEAK 25(15Q26.1) WILD-TYPE    23 21 61  5
D25V4, multiclass
       clus
vv      AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE
  T0+T1                            8                             23
  T2                              15                             21
  T3                              24                             61
  T4                               0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 25(15Q26.1) MUTATED   21 18  4  4
  AMP PEAK 25(15Q26.1) WILD-TYPE 50 46  8  4
D25V5, multiclass
    clus
vv   AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE
  N0                           21                             50
  N1                           18                             46
  N2                            4                              8
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
                                cls
clus                              0  1
  AMP PEAK 25(15Q26.1) MUTATED   32  4
  AMP PEAK 25(15Q26.1) WILD-TYPE 94  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(15Q26.1) MUTATED     32    4
  AMP PEAK 25(15Q26.1) WILD-TYPE   94    5
   clus
vv  AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE
  0                           32                             94
  1                            4                              5
[1] 2 2
[1] FALSE
D25V7, binary
                                cls
clus                               0   1
  AMP PEAK 25(15Q26.1) MUTATED     7  47
  AMP PEAK 25(15Q26.1) WILD-TYPE  17 102
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(15Q26.1) MUTATED      7   47
  AMP PEAK 25(15Q26.1) WILD-TYPE   17  102
        clus
vv       AMP PEAK 25(15Q26.1) MUTATED AMP PEAK 25(15Q26.1) WILD-TYPE
  FEMALE                            7                             17
  MALE                             47                            102
[1] 2 2
[1] FALSE
D25V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(15Q26.1) MUTATED       8                         0    37
  AMP PEAK 25(15Q26.1) WILD-TYPE    33                         2    74
D25V9, multiclass
                           clus
vv                          AMP PEAK 25(15Q26.1) MUTATED
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               37
                           clus
vv                          AMP PEAK 25(15Q26.1) WILD-TYPE
  ASIAN                                                 33
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V10, binary
                                cls
clus                              0  1
  AMP PEAK 25(15Q26.1) MUTATED    1 18
  AMP PEAK 25(15Q26.1) WILD-TYPE  2 63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(15Q26.1) MUTATED      1   18
  AMP PEAK 25(15Q26.1) WILD-TYPE    2   63
                        clus
vv                       AMP PEAK 25(15Q26.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           18
                        clus
vv                       AMP PEAK 25(15Q26.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             63
[1] 2 2
[1] FALSE

Clustering(26) Variable = AMP PEAK 26(17Q12) MUTATION ANALYSIS
D26V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 26(17Q12) MUTATED   42 29
  AMP PEAK 26(17Q12) WILD-TYPE 58 42
  AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE 
                          71                          100 
  AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE 
                          29                           42 
$`AMP PEAK 26(17Q12) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IC-A6RE 
       25.78        14.30        58.55        13.94         8.94         7.69 
TCGA-IG-A3QL TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-JY-A6FB TCGA-JY-A938 
       20.09         0.53        17.03        12.82        60.39        25.41 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OE 
       23.18        31.56        25.22        30.25         0.30        24.00 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
       18.35         3.32         1.38        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        7.13         2.60         7.40        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NT TCGA-LN-A49L 
       16.47        13.22         5.49         8.71        27.12        10.45 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.10        13.15        15.35         0.10        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.59        15.52        13.18        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W5 
        7.59         5.06         7.04        29.59        53.95        15.78 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        1.45        12.69        20.38         3.42         4.80        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX 
        9.27         4.44        12.43         1.55        18.31        28.11 
TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JE 
       46.19        11.24        15.91        10.16         2.10 

$`AMP PEAK 26(17Q12) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
       31.27         7.63         5.92        16.24         4.21        32.45 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
        6.21        33.27         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS 
       18.64         3.88         9.30         0.79        23.41         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93F 
       68.02         3.68        41.52        42.77        21.70        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG 
        6.28         3.16         4.31         8.94         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR 
       32.61        19.99        21.01        47.93         7.17         3.16 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A891 
        7.43         6.94         8.71        25.12         0.36         3.95 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ 
        3.02        55.50         2.66        13.55         7.76        21.37 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
       13.41        83.24        52.57        46.09        10.36         5.92 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       12.66        12.43        13.41        13.25         0.10        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        22.39         0.10        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-R6-A6L4 TCGA-R6-A6XQ TCGA-R6-A6Y2 
       12.03         0.13         5.16        14.70         6.35         9.30 
TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-VR-A8EO TCGA-VR-A8EP 
        2.89         7.00        20.02         5.29        18.81        19.96 
TCGA-VR-A8EQ TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G 
       22.82         8.12        30.71        18.18        42.87        15.06 
TCGA-VR-AA7D TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        9.17         3.42         2.66        19.73 

  AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE 
                         0.1                          0.1 
  AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE 
                       60.39                       122.10 
  AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE 
                       12.92                        12.28 
[1] "0.1 - 60.4 (12.9)"  "0.1 - 122.1 (12.3)"
[1] "hr=" "1"  
D26V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 26(17Q12) MUTATED         3        0        3        0        11
  AMP PEAK 26(17Q12) WILD-TYPE       5        5        4        1        28
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 26(17Q12) MUTATED          10        16          4          4
  AMP PEAK 26(17Q12) WILD-TYPE        19         9          8          6
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 26(17Q12) MUTATED            2        4         2
  AMP PEAK 26(17Q12) WILD-TYPE          5        1         2
D26V3, multiclass
            clus
vv           AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE
  STAGE I                             3                            5
  STAGE IA                            0                            5
  STAGE IB                            3                            4
  STAGE II                            0                            1
  STAGE IIA                          11                           28
  STAGE IIB                          10                           19
  STAGE III                          16                            9
  STAGE IIIA                          4                            8
  STAGE IIIB                          4                            6
  STAGE IIIC                          2                            5
  STAGE IV                            4                            1
  STAGE IVA                           2                            2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3 T4
  AMP PEAK 26(17Q12) MUTATED      14  9 35  2
  AMP PEAK 26(17Q12) WILD-TYPE    17 27 50  3
D26V4, multiclass
       clus
vv      AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE
  T0+T1                         14                           17
  T2                             9                           27
  T3                            35                           50
  T4                             2                            3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2 N3
  AMP PEAK 26(17Q12) MUTATED   21 31  5  3
  AMP PEAK 26(17Q12) WILD-TYPE 50 33  7  5
D26V5, multiclass
    clus
vv   AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE
  N0                         21                           50
  N1                         31                           33
  N2                          5                            7
  N3                          3                            5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                              cls
clus                            0  1
  AMP PEAK 26(17Q12) MUTATED   47  6
  AMP PEAK 26(17Q12) WILD-TYPE 79  3
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(17Q12) MUTATED     47    6
  AMP PEAK 26(17Q12) WILD-TYPE   79    3
   clus
vv  AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE
  0                         47                           79
  1                          6                            3
[1] 2 2
[1] FALSE
D26V7, binary
                              cls
clus                            0  1
  AMP PEAK 26(17Q12) MUTATED    6 65
  AMP PEAK 26(17Q12) WILD-TYPE 18 84
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(17Q12) MUTATED      6   65
  AMP PEAK 26(17Q12) WILD-TYPE   18   84
        clus
vv       AMP PEAK 26(17Q12) MUTATED AMP PEAK 26(17Q12) WILD-TYPE
  FEMALE                          6                           18
  MALE                           65                           84
[1] 2 2
[1] FALSE
D26V8, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 26(17Q12) MUTATED      13                         2    46
  AMP PEAK 26(17Q12) WILD-TYPE    28                         0    65
D26V9, multiclass
                           clus
vv                          AMP PEAK 26(17Q12) MUTATED
  ASIAN                                             13
  BLACK OR AFRICAN AMERICAN                          2
  WHITE                                             46
                           clus
vv                          AMP PEAK 26(17Q12) WILD-TYPE
  ASIAN                                               28
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V10, binary
                              cls
clus                            0  1
  AMP PEAK 26(17Q12) MUTATED    1 32
  AMP PEAK 26(17Q12) WILD-TYPE  2 49
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(17Q12) MUTATED      1   32
  AMP PEAK 26(17Q12) WILD-TYPE    2   49
                        clus
vv                       AMP PEAK 26(17Q12) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         32
                        clus
vv                       AMP PEAK 26(17Q12) WILD-TYPE
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           49
[1] 2 2
[1] FALSE

Clustering(27) Variable = AMP PEAK 27(18P11.32) MUTATION ANALYSIS
D27V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 27(18P11.32) MUTATED   37 25
  AMP PEAK 27(18P11.32) WILD-TYPE 63 46
  AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE 
                             62                             109 
  AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE 
                             25                              46 
$`AMP PEAK 27(18P11.32) MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A50L 
        7.63        13.94        16.24         4.21        32.45         0.53 
TCGA-IG-A625 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE 
       12.82        14.50        12.16        44.75        60.39         3.68 
TCGA-JY-A938 TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OM TCGA-L5-A4OO 
       25.41         3.16         4.31         8.94        47.93         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Y 
        1.38         3.16         4.90         7.13         2.60         0.36 
TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ 
        2.66        13.48        16.47        13.22         5.49        21.37 
TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U 
       27.12        46.09        10.36        13.41        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10        13.25         0.10        12.46        12.76        12.59 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HY TCGA-LN-A7HZ 
       12.33        13.22         4.47        25.25        12.03        13.18 
TCGA-R6-A6KZ TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE 
        5.06        53.95        12.69        20.38         3.42         4.80 
TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7D TCGA-Z6-A8JD 
       28.11        18.18        42.87        11.24         9.17         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN 
        2.10         2.66 

$`AMP PEAK 27(18P11.32) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        31.27        14.30        58.55         5.92         8.94 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        7.69         6.21        33.27        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
        2.63        20.12        18.64         3.88         9.30        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 
        0.79        23.41         9.96        14.86         4.67       122.10 
TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       68.02        41.52        42.77        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OE 
       25.22        24.03         6.28        30.25         0.30        24.00 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON 
        3.68         4.70        32.61        19.99        21.01        18.35 
TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        7.17        58.59        29.00         7.43         6.94         8.71 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NG 
       25.12         7.40         3.95         3.02        55.50        35.97 
TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       12.92        13.55         7.76         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R 
       52.57         5.92        10.45        12.66        12.43         0.10 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.59        12.49        22.39         0.10        15.52        11.54 
TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A9FO TCGA-M9-A5M8 
       12.33        10.52        12.00        12.23         0.13        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
        5.16         7.82         8.02         7.59        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
       29.59         6.35         9.30        15.78         2.89         1.45 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        7.00        20.02         5.29        15.35         9.27         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       18.81        19.96        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7I TCGA-X8-AAAR 
        8.12        30.71        46.19        15.06        15.91        10.16 
TCGA-ZR-A9CJ 
       19.73 

  AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE 
                            0.1                             0.1 
  AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE 
                          60.39                          122.10 
  AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE 
                         12.395                          12.660 
[1] "0.1 - 60.4 (12.4)"  "0.1 - 122.1 (12.7)"
[1] "hr=" "1.2"
D27V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 27(18P11.32) MUTATED         1        2        3        0        15
  AMP PEAK 27(18P11.32) WILD-TYPE       7        3        4        1        24
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 27(18P11.32) MUTATED           8        13          4          1
  AMP PEAK 27(18P11.32) WILD-TYPE        21        12          8          9
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 27(18P11.32) MUTATED            4        3         3
  AMP PEAK 27(18P11.32) WILD-TYPE          3        2         1
D27V3, multiclass
            clus
vv           AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE
  STAGE I                                1                               7
  STAGE IA                               2                               3
  STAGE IB                               3                               4
  STAGE II                               0                               1
  STAGE IIA                             15                              24
  STAGE IIB                              8                              21
  STAGE III                             13                              12
  STAGE IIIA                             4                               8
  STAGE IIIB                             1                               9
  STAGE IIIC                             4                               3
  STAGE IV                               3                               2
  STAGE IVA                              3                               1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3 T4
  AMP PEAK 27(18P11.32) MUTATED       8 11 40  0
  AMP PEAK 27(18P11.32) WILD-TYPE    23 25 45  5
D27V4, multiclass
       clus
vv      AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE
  T0+T1                             8                              23
  T2                               11                              25
  T3                               40                              45
  T4                                0                               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  AMP PEAK 27(18P11.32) MUTATED   25 25  3  5
  AMP PEAK 27(18P11.32) WILD-TYPE 46 39  9  3
D27V5, multiclass
    clus
vv   AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE
  N0                            25                              46
  N1                            25                              39
  N2                             3                               9
  N3                             5                               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                                 cls
clus                               0  1
  AMP PEAK 27(18P11.32) MUTATED   44  6
  AMP PEAK 27(18P11.32) WILD-TYPE 82  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(18P11.32) MUTATED     44    6
  AMP PEAK 27(18P11.32) WILD-TYPE   82    3
   clus
vv  AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE
  0                            44                              82
  1                             6                               3
[1] 2 2
[1] FALSE
D27V7, binary
                                 cls
clus                               0  1
  AMP PEAK 27(18P11.32) MUTATED    4 60
  AMP PEAK 27(18P11.32) WILD-TYPE 20 89
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(18P11.32) MUTATED      4   60
  AMP PEAK 27(18P11.32) WILD-TYPE   20   89
        clus
vv       AMP PEAK 27(18P11.32) MUTATED AMP PEAK 27(18P11.32) WILD-TYPE
  FEMALE                             4                              20
  MALE                              60                              89
[1] 2 2
[1] FALSE
D27V8, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 27(18P11.32) MUTATED      21                         1    33
  AMP PEAK 27(18P11.32) WILD-TYPE    20                         1    78
D27V9, multiclass
                           clus
vv                          AMP PEAK 27(18P11.32) MUTATED
  ASIAN                                                21
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                33
                           clus
vv                          AMP PEAK 27(18P11.32) WILD-TYPE
  ASIAN                                                  20
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                  78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V10, binary
                                 cls
clus                               0  1
  AMP PEAK 27(18P11.32) MUTATED    1 29
  AMP PEAK 27(18P11.32) WILD-TYPE  2 52
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(18P11.32) MUTATED      1   29
  AMP PEAK 27(18P11.32) WILD-TYPE    2   52
                        clus
vv                       AMP PEAK 27(18P11.32) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            29
                        clus
vv                       AMP PEAK 27(18P11.32) WILD-TYPE
  HISPANIC OR LATINO                                   2
  NOT HISPANIC OR LATINO                              52
[1] 2 2
[1] FALSE

Clustering(28) Variable = AMP PEAK 28(18Q11.2) MUTATION ANALYSIS
D28V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 28(18Q11.2) MUTATED   33 22
  AMP PEAK 28(18Q11.2) WILD-TYPE 67 49
  AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE 
                            55                            116 
  AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE 
                            22                             49 
$`AMP PEAK 28(18Q11.2) MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A50L 
       58.55         7.63        13.94         4.21        33.27         0.53 
TCGA-IG-A625 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M 
       12.82        60.39        42.77         3.16        30.25         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OW 
       24.00         4.70        18.35         3.32         3.16         7.13 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI 
        2.60         0.36         3.02        55.50         2.66        13.48 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
       13.22         5.49        13.41        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 
       46.09        10.36         5.92         0.10        12.76        12.59 
TCGA-LN-A4MQ TCGA-LN-A5U7 TCGA-LN-A7HZ TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.33        25.25        13.18         7.82         7.59         5.06 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RE 
       29.59        53.95        15.78        12.69        20.38         4.80 
TCGA-VR-A8EQ TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7I TCGA-Z6-A8JE 
       22.82        18.18        42.87        11.24        15.91         2.10 
TCGA-Z6-AAPN 
        2.66 

$`AMP PEAK 28(18Q11.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27        14.30         5.92         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69         6.21        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
        2.63        20.12        18.64         3.88         9.30        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        23.41         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       25.41        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI 
        6.28         0.30         4.31         3.68        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       21.01        47.93         7.17         1.38        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z 
       29.00         7.43         6.94         8.71        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM 
        3.95        35.97        12.92        16.47        13.55         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       21.37         8.71        10.45        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y 
        0.10        13.15        15.35         0.10        13.25        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.59        12.49        22.39         0.10        15.52        11.54 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       13.22         4.47        12.33        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6L4 
       12.03         0.13        33.11         5.16         8.02        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
        7.04         6.35         9.30         2.89         1.45         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
       20.02         5.29         3.42        15.35         9.27         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       18.81        19.96        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR 
       28.11        30.71        46.19        15.06         9.17        10.16 
TCGA-Z6-A8JD TCGA-ZR-A9CJ 
        3.42        19.73 

  AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE 
                           0.1                            0.1 
  AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE 
                         83.24                         122.10 
  AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE 
                        12.760                         12.445 
[1] "0.1 - 83.2 (12.8)"  "0.1 - 122.1 (12.4)"
[1] "hr=" "1.3"
D28V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 28(18Q11.2) MUTATED         5        1        3        0         8
  AMP PEAK 28(18Q11.2) WILD-TYPE       3        4        4        1        31
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 28(18Q11.2) MUTATED           8        11          3          3
  AMP PEAK 28(18Q11.2) WILD-TYPE        21        14          9          7
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 28(18Q11.2) MUTATED            3        1         2
  AMP PEAK 28(18Q11.2) WILD-TYPE          4        4         2
D28V3, multiclass
            clus
vv           AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE
  STAGE I                               5                              3
  STAGE IA                              1                              4
  STAGE IB                              3                              4
  STAGE II                              0                              1
  STAGE IIA                             8                             31
  STAGE IIB                             8                             21
  STAGE III                            11                             14
  STAGE IIIA                            3                              9
  STAGE IIIB                            3                              7
  STAGE IIIC                            3                              4
  STAGE IV                              1                              4
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 28(18Q11.2) MUTATED      11  9 29  1
  AMP PEAK 28(18Q11.2) WILD-TYPE    20 27 56  4
D28V4, multiclass
       clus
vv      AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE
  T0+T1                           11                             20
  T2                               9                             27
  T3                              29                             56
  T4                               1                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 28(18Q11.2) MUTATED   21 21  4  4
  AMP PEAK 28(18Q11.2) WILD-TYPE 50 43  8  4
D28V5, multiclass
    clus
vv   AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE
  N0                           21                             50
  N1                           21                             43
  N2                            4                              8
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                                cls
clus                              0  1
  AMP PEAK 28(18Q11.2) MUTATED   39  3
  AMP PEAK 28(18Q11.2) WILD-TYPE 87  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(18Q11.2) MUTATED     39    3
  AMP PEAK 28(18Q11.2) WILD-TYPE   87    6
   clus
vv  AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE
  0                           39                             87
  1                            3                              6
[1] 2 2
[1] FALSE
D28V7, binary
                                cls
clus                               0   1
  AMP PEAK 28(18Q11.2) MUTATED     7  49
  AMP PEAK 28(18Q11.2) WILD-TYPE  17 100
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(18Q11.2) MUTATED      7   49
  AMP PEAK 28(18Q11.2) WILD-TYPE   17  100
        clus
vv       AMP PEAK 28(18Q11.2) MUTATED AMP PEAK 28(18Q11.2) WILD-TYPE
  FEMALE                            7                             17
  MALE                             49                            100
[1] 2 2
[1] FALSE
D28V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 28(18Q11.2) MUTATED      10                         0    40
  AMP PEAK 28(18Q11.2) WILD-TYPE    31                         2    71
D28V9, multiclass
                           clus
vv                          AMP PEAK 28(18Q11.2) MUTATED
  ASIAN                                               10
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               40
                           clus
vv                          AMP PEAK 28(18Q11.2) WILD-TYPE
  ASIAN                                                 31
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V10, binary
                                cls
clus                              0  1
  AMP PEAK 28(18Q11.2) MUTATED    1 22
  AMP PEAK 28(18Q11.2) WILD-TYPE  2 59
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(18Q11.2) MUTATED      1   22
  AMP PEAK 28(18Q11.2) WILD-TYPE    2   59
                        clus
vv                       AMP PEAK 28(18Q11.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           22
                        clus
vv                       AMP PEAK 28(18Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             59
[1] 2 2
[1] FALSE

Clustering(29) Variable = AMP PEAK 29(19P13.2) MUTATION ANALYSIS
D29V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 29(19P13.2) MUTATED   22  8
  AMP PEAK 29(19P13.2) WILD-TYPE 78 63
  AMP PEAK 29(19P13.2) MUTATED AMP PEAK 29(19P13.2) WILD-TYPE 
                            30                            141 
  AMP PEAK 29(19P13.2) MUTATED AMP PEAK 29(19P13.2) WILD-TYPE 
                             8                             63 
$`AMP PEAK 29(19P13.2) MUTATED`
TCGA-2H-A9GH TCGA-IG-A3QL TCGA-IG-A3YC TCGA-IG-A51D TCGA-L5-A43C TCGA-L5-A43J 
       31.27        20.09        20.12        17.03         3.16         4.31 
TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NF 
        3.16        29.00         2.60         0.36         3.95         2.66 
TCGA-L5-A8NK TCGA-L5-A8NT TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49V TCGA-LN-A4A1 
       13.55        27.12         5.92        13.41         0.10        12.59 
TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-R6-A8W8 TCGA-S8-A6BW 
       12.76         0.10        25.25        12.00         2.89        20.38 
TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EX TCGA-VR-AA7I TCGA-X8-AAAR 
       15.35         9.27        18.81        28.11        15.91        10.16 

$`AMP PEAK 29(19P13.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
        8.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS 
       33.27         0.85        20.78         2.63        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30         0.53         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       60.39        68.02         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
       30.25         0.30         8.94        24.00         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       32.61        19.99        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
        7.17         1.38        58.59         4.90         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE 
        6.94         8.71        25.12         7.40         3.02        55.50 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
       35.97        12.92        13.48        16.47        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R 
       46.09        10.36        10.45        12.66        12.43         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
       13.15        15.35        13.25         0.10        12.46        12.49 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        22.39        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
        4.47        12.33        10.52        12.23        12.03        13.18 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.13        33.11         5.16         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        14.70         7.04        29.59         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
        9.30        15.78         1.45        12.69         7.00        20.02 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ 
        5.29         3.42         4.80         4.44        19.96        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43         1.55        18.31         8.12        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-Z6-A8JD 
       42.87        46.19        15.06        11.24         9.17         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.10         2.66        19.73 

  AMP PEAK 29(19P13.2) MUTATED AMP PEAK 29(19P13.2) WILD-TYPE 
                           0.1                            0.1 
  AMP PEAK 29(19P13.2) MUTATED AMP PEAK 29(19P13.2) WILD-TYPE 
                         31.27                         122.10 
  AMP PEAK 29(19P13.2) MUTATED AMP PEAK 29(19P13.2) WILD-TYPE 
                        12.675                         12.490 
[1] "0.1 - 31.3 (12.7)"  "0.1 - 122.1 (12.5)"
[1] "hr=" "1.2"
D29V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 29(19P13.2) MUTATED         0        1        1        1         8
  AMP PEAK 29(19P13.2) WILD-TYPE       8        4        6        0        31
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 29(19P13.2) MUTATED           6         3          1          1
  AMP PEAK 29(19P13.2) WILD-TYPE        23        22         11          9
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 29(19P13.2) MUTATED            0        0         2
  AMP PEAK 29(19P13.2) WILD-TYPE          7        5         2
D29V3, multiclass
            clus
vv           AMP PEAK 29(19P13.2) MUTATED AMP PEAK 29(19P13.2) WILD-TYPE
  STAGE I                               0                              8
  STAGE IA                              1                              4
  STAGE IB                              1                              6
  STAGE II                              1                              0
  STAGE IIA                             8                             31
  STAGE IIB                             6                             23
  STAGE III                             3                             22
  STAGE IIIA                            1                             11
  STAGE IIIB                            1                              9
  STAGE IIIC                            0                              7
  STAGE IV                              0                              5
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 29(19P13.2) MUTATED       7  4 15  1
  AMP PEAK 29(19P13.2) WILD-TYPE    24 32 70  4
D29V4, multiclass
       clus
vv      AMP PEAK 29(19P13.2) MUTATED AMP PEAK 29(19P13.2) WILD-TYPE
  T0+T1                            7                             24
  T2                               4                             32
  T3                              15                             70
  T4                               1                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 29(19P13.2) MUTATED   19  8  0  0
  AMP PEAK 29(19P13.2) WILD-TYPE 52 56 12  8
D29V5, multiclass
    clus
vv   AMP PEAK 29(19P13.2) MUTATED AMP PEAK 29(19P13.2) WILD-TYPE
  N0                           19                             52
  N1                            8                             56
  N2                            0                             12
  N3                            0                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                                cls
clus                               0   1
  AMP PEAK 29(19P13.2) MUTATED    18   2
  AMP PEAK 29(19P13.2) WILD-TYPE 108   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(19P13.2) MUTATED     18    2
  AMP PEAK 29(19P13.2) WILD-TYPE  108    7
   clus
vv  AMP PEAK 29(19P13.2) MUTATED AMP PEAK 29(19P13.2) WILD-TYPE
  0                           18                            108
  1                            2                              7
[1] 2 2
[1] FALSE
D29V7, binary
                                cls
clus                               0   1
  AMP PEAK 29(19P13.2) MUTATED     1  29
  AMP PEAK 29(19P13.2) WILD-TYPE  23 120
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(19P13.2) MUTATED      1   29
  AMP PEAK 29(19P13.2) WILD-TYPE   23  120
        clus
vv       AMP PEAK 29(19P13.2) MUTATED AMP PEAK 29(19P13.2) WILD-TYPE
  FEMALE                            1                             23
  MALE                             29                            120
[1] 2 2
[1] FALSE
D29V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 29(19P13.2) MUTATED       8                         1    19
  AMP PEAK 29(19P13.2) WILD-TYPE    33                         1    92
D29V9, multiclass
                           clus
vv                          AMP PEAK 29(19P13.2) MUTATED
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               19
                           clus
vv                          AMP PEAK 29(19P13.2) WILD-TYPE
  ASIAN                                                 33
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V10, binary
                                cls
clus                              0  1
  AMP PEAK 29(19P13.2) MUTATED    0 16
  AMP PEAK 29(19P13.2) WILD-TYPE  3 65
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(19P13.2) MUTATED      0   16
  AMP PEAK 29(19P13.2) WILD-TYPE    3   65
                        clus
vv                       AMP PEAK 29(19P13.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           16
                        clus
vv                       AMP PEAK 29(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                             65
[1] 2 2
[1] FALSE

Clustering(30) Variable = AMP PEAK 30(19Q12) MUTATION ANALYSIS
D30V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 30(19Q12) MUTATED   30 19
  AMP PEAK 30(19Q12) WILD-TYPE 70 52
  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE 
                          49                          122 
  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE 
                          19                           52 
$`AMP PEAK 30(19Q12) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-IC-A6RE TCGA-IG-A3QL 
       31.27        58.55         7.63         8.94         7.69        20.09 
TCGA-IG-A4QS TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A4OE 
        3.88        23.41        14.50        42.77         3.16        24.00 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
        3.68        32.61        18.35         3.32         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NK TCGA-L5-A8NN 
       58.59         3.95        55.50        35.97        13.55         5.49 
TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
        8.71        27.12        52.57        46.09        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49U TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A7HW TCGA-LN-A9FO 
       10.45        15.35        12.59        22.39        12.00         0.13 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8WG 
        5.06        14.70        29.59        53.95        15.78        12.69 
TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-X8-AAAR 
       20.38        15.35        28.11        42.87        15.91        10.16 
TCGA-Z6-A8JE 
        2.10 

$`AMP PEAK 30(19Q12) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        14.30         5.92        13.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       32.45         6.21        33.27         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         9.30         0.53        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
       12.82         9.96        14.86         4.67        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 
       44.75        60.39        68.02         3.68        41.52        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI 
       30.25         0.30         4.31         8.94         4.70        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
       21.01        47.93         7.17         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
        7.43         6.94         8.71         2.60        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        7.40         3.02         2.66        12.92        13.48        16.47 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49M 
       13.22         7.76        21.37        13.41        83.24        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W 
       12.43        13.41         0.10        13.15         0.10        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 
        0.10        12.46        12.59        12.49        12.76         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 
       25.25        10.52        12.23        12.03        13.18        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ 
        5.16         7.82         8.02         7.59         7.04         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        9.30         2.89         1.45         7.00        20.02         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        3.42         4.80         9.27         4.44        18.81        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
       22.82        12.43         1.55        18.31         8.12        30.71 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-Z6-A8JD 
       18.18        46.19        15.06        11.24         9.17         3.42 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE 
                        0.13                         0.10 
  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE 
                       58.59                       122.10 
  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE 
                       14.70                        12.38 
[1] "0.1 - 58.6 (14.7)"  "0.1 - 122.1 (12.4)"
[1] "hr=" "1.5"
D30V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 30(19Q12) MUTATED         2        1        2        0        10
  AMP PEAK 30(19Q12) WILD-TYPE       6        4        5        1        29
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 30(19Q12) MUTATED          12         7          3          2
  AMP PEAK 30(19Q12) WILD-TYPE        17        18          9          8
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 30(19Q12) MUTATED            2        0         2
  AMP PEAK 30(19Q12) WILD-TYPE          5        5         2
D30V3, multiclass
            clus
vv           AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE
  STAGE I                             2                            6
  STAGE IA                            1                            4
  STAGE IB                            2                            5
  STAGE II                            0                            1
  STAGE IIA                          10                           29
  STAGE IIB                          12                           17
  STAGE III                           7                           18
  STAGE IIIA                          3                            9
  STAGE IIIB                          2                            8
  STAGE IIIC                          2                            5
  STAGE IV                            0                            5
  STAGE IVA                           2                            2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3 T4
  AMP PEAK 30(19Q12) MUTATED       9 11 24  1
  AMP PEAK 30(19Q12) WILD-TYPE    22 25 61  4
D30V4, multiclass
       clus
vv      AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE
  T0+T1                          9                           22
  T2                            11                           25
  T3                            24                           61
  T4                             1                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2 N3
  AMP PEAK 30(19Q12) MUTATED   18 21  3  2
  AMP PEAK 30(19Q12) WILD-TYPE 53 43  9  6
D30V5, multiclass
    clus
vv   AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE
  N0                         18                           53
  N1                         21                           43
  N2                          3                            9
  N3                          2                            6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                              cls
clus                            0  1
  AMP PEAK 30(19Q12) MUTATED   34  2
  AMP PEAK 30(19Q12) WILD-TYPE 92  7
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 30(19Q12) MUTATED     34    2
  AMP PEAK 30(19Q12) WILD-TYPE   92    7
   clus
vv  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE
  0                         34                           92
  1                          2                            7
[1] 2 2
[1] FALSE
D30V7, binary
                              cls
clus                             0   1
  AMP PEAK 30(19Q12) MUTATED     4  47
  AMP PEAK 30(19Q12) WILD-TYPE  20 102
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 30(19Q12) MUTATED      4   47
  AMP PEAK 30(19Q12) WILD-TYPE   20  102
        clus
vv       AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE
  FEMALE                          4                           20
  MALE                           47                          102
[1] 2 2
[1] FALSE
D30V8, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 30(19Q12) MUTATED      10                         1    34
  AMP PEAK 30(19Q12) WILD-TYPE    31                         1    77
D30V9, multiclass
                           clus
vv                          AMP PEAK 30(19Q12) MUTATED
  ASIAN                                             10
  BLACK OR AFRICAN AMERICAN                          1
  WHITE                                             34
                           clus
vv                          AMP PEAK 30(19Q12) WILD-TYPE
  ASIAN                                               31
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V10, binary
                              cls
clus                            0  1
  AMP PEAK 30(19Q12) MUTATED    1 24
  AMP PEAK 30(19Q12) WILD-TYPE  2 57
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 30(19Q12) MUTATED      1   24
  AMP PEAK 30(19Q12) WILD-TYPE    2   57
                        clus
vv                       AMP PEAK 30(19Q12) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         24
                        clus
vv                       AMP PEAK 30(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           57
[1] 2 2
[1] FALSE

Clustering(31) Variable = AMP PEAK 31(XQ28) MUTATION ANALYSIS
D31V1, survival
                             sevent
clus2                          0  1
  AMP PEAK 31(XQ28) MUTATED   34 28
  AMP PEAK 31(XQ28) WILD-TYPE 66 43
  AMP PEAK 31(XQ28) MUTATED AMP PEAK 31(XQ28) WILD-TYPE 
                         62                         109 
  AMP PEAK 31(XQ28) MUTATED AMP PEAK 31(XQ28) WILD-TYPE 
                         28                          43 
$`AMP PEAK 31(XQ28) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GO TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4QS 
       14.30         5.92        16.24        20.09        20.78         3.88 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 
        0.53        17.03        23.41        12.82         9.96         4.67 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A938 TCGA-JY-A93C TCGA-L5-A43E TCGA-L5-A43J 
      122.10        44.75        25.41        23.18        30.25         4.31 
TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A8NK 
       24.00        19.99        47.93        18.35         1.38        13.55 
TCGA-L5-A8NQ TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       21.37        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 
        0.10         0.10         0.10        12.59        12.49        12.59 
TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A9FO 
       22.39        13.22        25.25        12.00        13.18         0.13 
TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-S8-A6BV 
        8.02        14.70        15.78         2.89        12.69        20.02 
TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
        5.29        15.35         4.44        18.31         8.12        30.71 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7I TCGA-Z6-A8JD 
       18.18        42.87        46.19        11.24        15.91         3.42 
TCGA-Z6-A8JE TCGA-ZR-A9CJ 
        2.10        19.73 

$`AMP PEAK 31(XQ28) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        31.27        58.55         7.63        13.94         8.94 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 
        4.21        32.45         7.69         6.21        33.27         0.85 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A7DP 
        2.63        20.12        18.64         9.30         0.79        14.86 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       14.50        12.16        60.39        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       42.77        21.70        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        3.16         0.30         8.94         3.68         4.70        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       21.01         3.32         7.17         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
       29.00         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       25.12         0.36         7.40         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL 
        2.66        35.97        12.92        13.48        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
        7.76         5.49         8.71        13.41        27.12        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
       52.57        46.09        13.41        13.15        15.35        13.25 
TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.46        12.76         0.10        15.52        11.54        12.33 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-M9-A5M8 
        4.47        12.33        10.52        12.23        12.03        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG 
        5.16         7.82         7.59         5.06         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW 
        6.35        53.95         9.30         1.45         7.00        20.38 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
        3.42         4.80         9.27        18.81        19.96        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR 
       12.43         1.55        28.11        15.06         9.17        10.16 
TCGA-Z6-AAPN 
        2.66 

  AMP PEAK 31(XQ28) MUTATED AMP PEAK 31(XQ28) WILD-TYPE 
                        0.1                         0.1 
  AMP PEAK 31(XQ28) MUTATED AMP PEAK 31(XQ28) WILD-TYPE 
                     122.10                       83.24 
  AMP PEAK 31(XQ28) MUTATED AMP PEAK 31(XQ28) WILD-TYPE 
                      13.20                       12.16 
[1] "0.1 - 122.1 (13.2)" "0.1 - 83.2 (12.2)" 
[1] "hr=" "1.2"
D31V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 31(XQ28) MUTATED         2        1        1        0        17
  AMP PEAK 31(XQ28) WILD-TYPE       6        4        6        1        22
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 31(XQ28) MUTATED          12         5          6          6
  AMP PEAK 31(XQ28) WILD-TYPE        17        20          6          4
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 31(XQ28) MUTATED            4        2         2
  AMP PEAK 31(XQ28) WILD-TYPE          3        3         2
D31V3, multiclass
            clus
vv           AMP PEAK 31(XQ28) MUTATED AMP PEAK 31(XQ28) WILD-TYPE
  STAGE I                            2                           6
  STAGE IA                           1                           4
  STAGE IB                           1                           6
  STAGE II                           0                           1
  STAGE IIA                         17                          22
  STAGE IIB                         12                          17
  STAGE III                          5                          20
  STAGE IIIA                         6                           6
  STAGE IIIB                         6                           4
  STAGE IIIC                         4                           3
  STAGE IV                           2                           3
  STAGE IVA                          2                           2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  AMP PEAK 31(XQ28) MUTATED       8 14 35  2
  AMP PEAK 31(XQ28) WILD-TYPE    23 22 50  3
D31V4, multiclass
       clus
vv      AMP PEAK 31(XQ28) MUTATED AMP PEAK 31(XQ28) WILD-TYPE
  T0+T1                         8                          23
  T2                           14                          22
  T3                           35                          50
  T4                            2                           3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2 N3
  AMP PEAK 31(XQ28) MUTATED   28 19  7  5
  AMP PEAK 31(XQ28) WILD-TYPE 43 45  5  3
D31V5, multiclass
    clus
vv   AMP PEAK 31(XQ28) MUTATED AMP PEAK 31(XQ28) WILD-TYPE
  N0                        28                          43
  N1                        19                          45
  N2                         7                           5
  N3                         5                           3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                             cls
clus                           0  1
  AMP PEAK 31(XQ28) MUTATED   44  4
  AMP PEAK 31(XQ28) WILD-TYPE 82  5
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 31(XQ28) MUTATED     44    4
  AMP PEAK 31(XQ28) WILD-TYPE   82    5
   clus
vv  AMP PEAK 31(XQ28) MUTATED AMP PEAK 31(XQ28) WILD-TYPE
  0                        44                          82
  1                         4                           5
[1] 2 2
[1] FALSE
D31V7, binary
                             cls
clus                           0  1
  AMP PEAK 31(XQ28) MUTATED    5 59
  AMP PEAK 31(XQ28) WILD-TYPE 19 90
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 31(XQ28) MUTATED      5   59
  AMP PEAK 31(XQ28) WILD-TYPE   19   90
        clus
vv       AMP PEAK 31(XQ28) MUTATED AMP PEAK 31(XQ28) WILD-TYPE
  FEMALE                         5                          19
  MALE                          59                          90
[1] 2 2
[1] FALSE
D31V8, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 31(XQ28) MUTATED      24                         1    35
  AMP PEAK 31(XQ28) WILD-TYPE    17                         1    76
D31V9, multiclass
                           clus
vv                          AMP PEAK 31(XQ28) MUTATED
  ASIAN                                            24
  BLACK OR AFRICAN AMERICAN                         1
  WHITE                                            35
                           clus
vv                          AMP PEAK 31(XQ28) WILD-TYPE
  ASIAN                                              17
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V10, binary
                             cls
clus                           0  1
  AMP PEAK 31(XQ28) MUTATED    2 38
  AMP PEAK 31(XQ28) WILD-TYPE  1 43
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 31(XQ28) MUTATED      2   38
  AMP PEAK 31(XQ28) WILD-TYPE    1   43
                        clus
vv                       AMP PEAK 31(XQ28) MUTATED AMP PEAK 31(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             2                           1
  NOT HISPANIC OR LATINO                        38                          43
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK  1(1P36.11) MUTATION ANALYSIS
D32V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  1(1P36.11) MUTATED   39 31
  DEL PEAK  1(1P36.11) WILD-TYPE 61 40
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            70                            101 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            31                             40 
$`DEL PEAK  1(1P36.11) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A4P3 
       16.24        32.45         7.69        33.27        20.09        18.64 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A625 TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH 
        3.88         0.53        12.82       122.10        60.39        42.77 
TCGA-JY-A93C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
       23.18         0.30         4.31         8.94        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        4.70         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE 
        7.43         2.60         0.36         7.40         3.02        55.50 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NS 
       35.97        12.92        16.47        13.22         5.49        13.41 
TCGA-LN-A49K TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW 
        5.92         0.10        13.25        12.33        25.25        12.00 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A8W8 
       12.03        13.18         8.02         7.59         5.06         2.89 
TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
        1.45        20.38         3.42         4.80         9.27         4.44 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX 
       19.96        22.82        12.43         1.55         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       30.71        42.87         2.66        19.73 

$`DEL PEAK  1(1P36.11) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-IC-A6RF TCGA-IG-A3Y9 TCGA-IG-A3YA 
       25.78         5.92         4.21         6.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        2.63        20.12         9.30        17.03         0.79        23.41 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
        9.96        14.86         4.67        14.50        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D 
       68.02         3.68        41.52        25.41        21.70        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OH 
       25.22        24.03         6.28         3.16        30.25        32.61 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       19.99        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A8NF 
        1.38         6.94         8.71        25.12         3.95         2.66 
TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT 
       13.48        13.55         7.76        21.37         8.71        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       83.24        52.57        46.09        10.36        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
       12.43        13.41        13.15        15.35         0.10         0.10 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
        0.10        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       10.52        12.23         0.13        33.11         5.16         7.82 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       14.70         7.04        29.59         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASV 
       15.78        12.69         7.00        20.02         5.29        15.35 
TCGA-VR-A8EO TCGA-VR-A8EU TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       18.81        18.31        18.18        46.19        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE 
        9.17        15.91        10.16         3.42         2.10 

  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           0.1                            0.1 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                        122.10                          83.24 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                         12.18                          12.66 
[1] "0.1 - 122.1 (12.2)" "0.1 - 83.2 (12.7)" 
[1] "hr=" "1.1"
D32V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  1(1P36.11) MUTATED         5        1        2        0        11
  DEL PEAK  1(1P36.11) WILD-TYPE       3        4        5        1        28
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  1(1P36.11) MUTATED          14        14          2          6
  DEL PEAK  1(1P36.11) WILD-TYPE        15        11         10          4
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  1(1P36.11) MUTATED            1        2         2
  DEL PEAK  1(1P36.11) WILD-TYPE          6        3         2
D32V3, multiclass
            clus
vv           DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  STAGE I                               5                              3
  STAGE IA                              1                              4
  STAGE IB                              2                              5
  STAGE II                              0                              1
  STAGE IIA                            11                             28
  STAGE IIB                            14                             15
  STAGE III                            14                             11
  STAGE IIIA                            2                             10
  STAGE IIIB                            6                              4
  STAGE IIIC                            1                              6
  STAGE IV                              2                              3
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK  1(1P36.11) MUTATED      15 12 34  1
  DEL PEAK  1(1P36.11) WILD-TYPE    16 24 51  4
D32V4, multiclass
       clus
vv      DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  T0+T1                           15                             16
  T2                              12                             24
  T3                              34                             51
  T4                               1                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK  1(1P36.11) MUTATED   23 31  7  1
  DEL PEAK  1(1P36.11) WILD-TYPE 48 33  5  7
D32V5, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                           23                             48
  N1                           31                             33
  N2                            7                              5
  N3                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.11) MUTATED   49  4
  DEL PEAK  1(1P36.11) WILD-TYPE 77  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     49    4
  DEL PEAK  1(1P36.11) WILD-TYPE   77    5
   clus
vv  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  0                           49                             77
  1                            4                              5
[1] 2 2
[1] FALSE
D32V7, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.11) MUTATED    9 61
  DEL PEAK  1(1P36.11) WILD-TYPE 15 88
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      9   61
  DEL PEAK  1(1P36.11) WILD-TYPE   15   88
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  FEMALE                            9                             15
  MALE                             61                             88
[1] 2 2
[1] FALSE
D32V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.11) MUTATED      12                         1    45
  DEL PEAK  1(1P36.11) WILD-TYPE    29                         1    66
D32V9, multiclass
                           clus
vv                          DEL PEAK  1(1P36.11) MUTATED
  ASIAN                                               12
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               45
                           clus
vv                          DEL PEAK  1(1P36.11) WILD-TYPE
  ASIAN                                                 29
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V10, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.11) MUTATED    0 26
  DEL PEAK  1(1P36.11) WILD-TYPE  3 55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      0   26
  DEL PEAK  1(1P36.11) WILD-TYPE    3   55
                        clus
vv                       DEL PEAK  1(1P36.11) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           26
                        clus
vv                       DEL PEAK  1(1P36.11) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                             55
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK  2(1P13.2) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  2(1P13.2) MUTATED   31 26
  DEL PEAK  2(1P13.2) WILD-TYPE 69 45
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           57                           114 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           26                            45 
$`DEL PEAK  2(1P13.2) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       14.30         7.63        13.94         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
       33.27        20.09         2.63        18.64         3.88         0.53 
TCGA-IG-A5B8 TCGA-IG-A8O2 TCGA-JY-A6FE TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE 
        0.79         4.67         3.68         0.30         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        4.70        32.61         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NF 
        6.94         2.60         0.36         7.40        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NS TCGA-LN-A49K 
       35.97        12.92        13.48        16.47        13.41         5.92 
TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A5U7 
       13.25        12.59        12.59        11.54        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6Y0 
       10.52        12.00        13.18        33.11         7.59        53.95 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASW TCGA-V5-AASX 
        2.89         1.45        20.38         3.42         9.27         4.44 
TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-AA4D 
       12.43         8.12        46.19 

$`DEL PEAK  2(1P13.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27        58.55         5.92         8.94        16.24 
TCGA-IC-A6RF TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A51D 
        6.21         0.85        20.78        20.12         9.30        17.03 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I 
       23.41        12.82         9.96        14.86        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        60.39        68.02        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       25.41        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OI 
        6.28         3.16        30.25         4.31         3.68        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 
        3.16        58.59         8.71        25.12         3.95         3.02 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L 
       27.12        83.24        52.57        46.09        10.36        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.66        12.43        13.41         0.10        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 
        0.10         0.10        12.46        12.49        12.76        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HX 
        0.10        15.52        12.33        13.22         4.47        12.23 
TCGA-LN-A7HY TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ 
       12.03         0.13         5.16         7.82         8.02         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 
       14.70         7.04        29.59         6.35         9.30        15.78 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
       12.69         7.00        20.02         5.29         4.80        15.35 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX 
       18.81        19.96        22.82         1.55        18.31        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       30.71        18.18        42.87        15.06        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       15.91        10.16         3.42         2.10         2.66        19.73 

  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                          0.3                           0.1 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                         55.5                         122.1 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                       10.520                        13.185 
[1] "0.3 - 55.5 (10.5)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.5"
D33V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  2(1P13.2) MUTATED         2        0        4        0        12
  DEL PEAK  2(1P13.2) WILD-TYPE       6        5        3        1        27
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  2(1P13.2) MUTATED          10        12          2          4
  DEL PEAK  2(1P13.2) WILD-TYPE        19        13         10          6
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  2(1P13.2) MUTATED            0        2         1
  DEL PEAK  2(1P13.2) WILD-TYPE          7        3         3
D33V3, multiclass
            clus
vv           DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  STAGE I                              2                             6
  STAGE IA                             0                             5
  STAGE IB                             4                             3
  STAGE II                             0                             1
  STAGE IIA                           12                            27
  STAGE IIB                           10                            19
  STAGE III                           12                            13
  STAGE IIIA                           2                            10
  STAGE IIIB                           4                             6
  STAGE IIIC                           0                             7
  STAGE IV                             2                             3
  STAGE IVA                            1                             3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  2(1P13.2) MUTATED       9 12 29  1
  DEL PEAK  2(1P13.2) WILD-TYPE    22 24 56  4
D33V4, multiclass
       clus
vv      DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  T0+T1                           9                            22
  T2                             12                            24
  T3                             29                            56
  T4                              1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK  2(1P13.2) MUTATED   21 25  5  0
  DEL PEAK  2(1P13.2) WILD-TYPE 50 39  7  8
D33V5, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  N0                          21                            50
  N1                          25                            39
  N2                           5                             7
  N3                           0                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED   42  3
  DEL PEAK  2(1P13.2) WILD-TYPE 84  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     42    3
  DEL PEAK  2(1P13.2) WILD-TYPE   84    6
   clus
vv  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  0                          42                            84
  1                           3                             6
[1] 2 2
[1] FALSE
D33V7, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED    6 52
  DEL PEAK  2(1P13.2) WILD-TYPE 18 97
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      6   52
  DEL PEAK  2(1P13.2) WILD-TYPE   18   97
        clus
vv       DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  FEMALE                           6                            18
  MALE                            52                            97
[1] 2 2
[1] FALSE
D33V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P13.2) MUTATED      14                         1    34
  DEL PEAK  2(1P13.2) WILD-TYPE    27                         1    77
D33V9, multiclass
                           clus
vv                          DEL PEAK  2(1P13.2) MUTATED
  ASIAN                                              14
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              34
                           clus
vv                          DEL PEAK  2(1P13.2) WILD-TYPE
  ASIAN                                                27
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V10, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED    0 27
  DEL PEAK  2(1P13.2) WILD-TYPE  3 54
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      0   27
  DEL PEAK  2(1P13.2) WILD-TYPE    3   54
                        clus
vv                       DEL PEAK  2(1P13.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          27
                        clus
vv                       DEL PEAK  2(1P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            54
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK  3(1Q44) MUTATION ANALYSIS
D34V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  3(1Q44) MUTATED    8  9
  DEL PEAK  3(1Q44) WILD-TYPE 92 62
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         17                         154 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                          9                          62 
$`DEL PEAK  3(1Q44) MUTATED`
TCGA-IG-A4QS TCGA-IG-A6QS TCGA-L5-A4OE TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A8NG 
        3.88         9.96        24.00        21.01         3.32        35.97 
TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49Y TCGA-LN-A4A5 
       83.24        10.36         5.92        13.41        12.46        22.39 
TCGA-LN-A7HW TCGA-R6-A6DQ TCGA-R6-A6Y0 TCGA-VR-A8ER TCGA-VR-AA7D 
       12.00         7.59        53.95        12.43         9.17 

$`DEL PEAK  3(1Q44) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        6.21        33.27        20.09         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       23.41        12.82        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
      122.10        44.75        60.39        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       42.77        25.41        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       24.03         6.28         3.16        30.25         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OM 
        8.94         3.68         4.70        32.61        19.99        47.93 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
       29.00         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       25.12         0.36         7.40         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
        7.76         5.49        21.37         8.71        13.41        27.12 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R 
       52.57        46.09        10.45        12.66        12.43         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 
       13.15        15.35         0.10        13.25         0.10        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.76        12.59         0.10        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU 
       12.23        12.03        13.18         0.13        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.82         8.02         5.06        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35         9.30        15.78         2.89         1.45        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        7.00        20.02        20.38         5.29         3.42         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         4.44        18.81        19.96        22.82 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR 
       42.87        46.19        15.06        11.24        15.91        10.16 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        3.42         2.10         2.66        19.73 

  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                       3.32                        0.10 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                      83.24                      122.10 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                     12.430                      12.625 
[1] "3.3 - 83.2 (12.4)"  "0.1 - 122.1 (12.6)"
[1] "hr=" "1.1"
D34V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  3(1Q44) MUTATED         1        0        0        0         6
  DEL PEAK  3(1Q44) WILD-TYPE       7        5        7        1        33
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  3(1Q44) MUTATED           1         2          0          2
  DEL PEAK  3(1Q44) WILD-TYPE        28        23         12          8
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  3(1Q44) MUTATED            3        0         0
  DEL PEAK  3(1Q44) WILD-TYPE          4        5         4
D34V3, multiclass
            clus
vv           DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  STAGE I                            1                           7
  STAGE IA                           0                           5
  STAGE IB                           0                           7
  STAGE II                           0                           1
  STAGE IIA                          6                          33
  STAGE IIB                          1                          28
  STAGE III                          2                          23
  STAGE IIIA                         0                          12
  STAGE IIIB                         2                           8
  STAGE IIIC                         3                           4
  STAGE IV                           0                           5
  STAGE IVA                          0                           4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  DEL PEAK  3(1Q44) MUTATED       1  4  9  1
  DEL PEAK  3(1Q44) WILD-TYPE    30 32 76  4
D34V4, multiclass
       clus
vv      DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  T0+T1                         1                          30
  T2                            4                          32
  T3                            9                          76
  T4                            1                           4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2 N3
  DEL PEAK  3(1Q44) MUTATED    7  3  2  3
  DEL PEAK  3(1Q44) WILD-TYPE 64 61 10  5
D34V5, multiclass
    clus
vv   DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  N0                         7                          64
  N1                         3                          61
  N2                         2                          10
  N3                         3                           5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED    13   0
  DEL PEAK  3(1Q44) WILD-TYPE 113   9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED     13    0
  DEL PEAK  3(1Q44) WILD-TYPE  113    9
   clus
vv  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  0                        13                         113
  1                         0                           9
[1] 2 2
[1] FALSE
D34V7, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED     2  15
  DEL PEAK  3(1Q44) WILD-TYPE  22 134
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED      2   15
  DEL PEAK  3(1Q44) WILD-TYPE   22  134
        clus
vv       DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  FEMALE                         2                          22
  MALE                          15                         134
[1] 2 2
[1] FALSE
D34V8, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(1Q44) MUTATED       5                         0    10
  DEL PEAK  3(1Q44) WILD-TYPE    36                         2   101
D34V9, multiclass
                           clus
vv                          DEL PEAK  3(1Q44) MUTATED
  ASIAN                                             5
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                            10
                           clus
vv                          DEL PEAK  3(1Q44) WILD-TYPE
  ASIAN                                              36
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                             101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V10, binary
                             cls
clus                           0  1
  DEL PEAK  3(1Q44) MUTATED    0 10
  DEL PEAK  3(1Q44) WILD-TYPE  3 71
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED      0   10
  DEL PEAK  3(1Q44) WILD-TYPE    3   71
                        clus
vv                       DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  HISPANIC OR LATINO                             0                           3
  NOT HISPANIC OR LATINO                        10                          71
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK  4(2Q22.1) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  4(2Q22.1) MUTATED   29 23
  DEL PEAK  4(2Q22.1) WILD-TYPE 71 48
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           52                           119 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           23                            48 
$`DEL PEAK  4(2Q22.1) MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC 
       58.55         4.21        33.27         0.85         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A8O2 
       18.64         0.53        17.03         0.79         9.96         4.67 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-L5-A43C TCGA-L5-A43H 
       12.16        44.75        68.02        41.52         3.16         0.30 
TCGA-L5-A4OE TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NK 
       24.00        58.59         7.43         7.40         3.02        13.55 
TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49Y TCGA-LN-A4MQ TCGA-LN-A5U5 
       52.57        10.36        10.45        12.46        12.33         4.47 
TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A9FO 
       12.33        10.52        12.00        12.23        13.18         0.13 
TCGA-Q9-A6FU TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-S8-A6BW TCGA-V5-A7RB 
        5.16        29.59        53.95         2.89        20.38         5.29 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       12.43        18.31         8.12        30.71        18.18        42.87 
TCGA-VR-AA7B TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-AAPN 
       11.24        15.91         3.42         2.66 

$`DEL PEAK  4(2Q22.1) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL 
        8.94        16.24        32.45         7.69         6.21        20.09 
TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP 
       20.78         3.88         9.30        23.41        12.82        14.86 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A938 
       14.50       122.10        60.39         3.68        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
       30.25         4.31         8.94         3.68         4.70        32.61 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       19.99        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S 
        1.38         3.16         4.90        29.00         7.13         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NE 
        8.71         2.60        25.12         0.36         3.95        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL 
        2.66        35.97        12.92        13.48        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
        7.76         5.49        21.37         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       83.24        46.09         5.92        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
        0.10        13.15        15.35         0.10        13.25         0.10 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HY TCGA-M9-A5M8 
       15.52        11.54        13.22        25.25        12.03        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        14.70         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        6.35         9.30        15.78         1.45        12.69         7.00 
TCGA-S8-A6BV TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
       20.02         3.42         4.80        15.35         9.27         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-AA4D 
       18.81        19.96        22.82         1.55        28.11        46.19 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       15.06         9.17        10.16         2.10        19.73 

  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                         0.13                          0.10 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                        68.02                        122.10 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                       12.195                        12.820 
[1] "0.1 - 68.0 (12.2)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "1"  
D35V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  4(2Q22.1) MUTATED         2        0        2        0        15
  DEL PEAK  4(2Q22.1) WILD-TYPE       6        5        5        1        24
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  4(2Q22.1) MUTATED           8         6          5          4
  DEL PEAK  4(2Q22.1) WILD-TYPE        21        19          7          6
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  4(2Q22.1) MUTATED            2        3         0
  DEL PEAK  4(2Q22.1) WILD-TYPE          5        2         4
D35V3, multiclass
            clus
vv           DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  STAGE I                              2                             6
  STAGE IA                             0                             5
  STAGE IB                             2                             5
  STAGE II                             0                             1
  STAGE IIA                           15                            24
  STAGE IIB                            8                            21
  STAGE III                            6                            19
  STAGE IIIA                           5                             7
  STAGE IIIB                           4                             6
  STAGE IIIC                           2                             5
  STAGE IV                             3                             2
  STAGE IVA                            0                             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  4(2Q22.1) MUTATED       6 14 25  3
  DEL PEAK  4(2Q22.1) WILD-TYPE    25 22 60  2
D35V4, multiclass
       clus
vv      DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  T0+T1                           6                            25
  T2                             14                            22
  T3                             25                            60
  T4                              3                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK  4(2Q22.1) MUTATED   21 20  4  3
  DEL PEAK  4(2Q22.1) WILD-TYPE 50 44  8  5
D35V5, multiclass
    clus
vv   DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  N0                          21                            50
  N1                          20                            44
  N2                           4                             8
  N3                           3                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q22.1) MUTATED   41  3
  DEL PEAK  4(2Q22.1) WILD-TYPE 85  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED     41    3
  DEL PEAK  4(2Q22.1) WILD-TYPE   85    6
   clus
vv  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  0                          41                            85
  1                           3                             6
[1] 2 2
[1] FALSE
D35V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED     9  43
  DEL PEAK  4(2Q22.1) WILD-TYPE  15 106
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      9   43
  DEL PEAK  4(2Q22.1) WILD-TYPE   15  106
        clus
vv       DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  FEMALE                           9                            15
  MALE                            43                           106
[1] 2 2
[1] FALSE
D35V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q22.1) MUTATED      15                         0    33
  DEL PEAK  4(2Q22.1) WILD-TYPE    26                         2    78
D35V9, multiclass
                           clus
vv                          DEL PEAK  4(2Q22.1) MUTATED
  ASIAN                                              15
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              33
                           clus
vv                          DEL PEAK  4(2Q22.1) WILD-TYPE
  ASIAN                                                26
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V10, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q22.1) MUTATED    1 29
  DEL PEAK  4(2Q22.1) WILD-TYPE  2 52
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      1   29
  DEL PEAK  4(2Q22.1) WILD-TYPE    2   52
                        clus
vv                       DEL PEAK  4(2Q22.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          29
                        clus
vv                       DEL PEAK  4(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            52
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK  5(2Q33.3) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  5(2Q33.3) MUTATED   22  9
  DEL PEAK  5(2Q33.3) WILD-TYPE 78 62
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                           31                           140 
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                            9                            62 
$`DEL PEAK  5(2Q33.3) MUTATED`
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A5B8 
       20.09         0.85         2.63        20.12        18.64         0.79 
TCGA-JY-A6FD TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4OS TCGA-L5-A88S TCGA-L5-A893 
       68.02        25.22         0.30        58.59         6.94         3.02 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NN TCGA-LN-A49K TCGA-LN-A49V TCGA-LN-A4MQ 
       16.47        13.55         5.49         5.92         0.10        12.33 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-R6-A6DN TCGA-R6-A8W8 TCGA-R6-A8WC 
       10.52        12.23        13.18         8.02         2.89         1.45 
TCGA-S8-A6BV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8Q7 TCGA-Z6-AAPN 
       20.02        18.81        19.96        12.43        42.87         2.66 
TCGA-ZR-A9CJ 
       19.73 

$`DEL PEAK  5(2Q33.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        6.21        33.27        20.78         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE 
       14.50        12.16       122.10        44.75        60.39         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       41.52        42.77        25.41        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M 
       24.03         6.28         3.16        30.25         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
       24.00         3.68         4.70        32.61        19.99        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V 
        4.90        29.00         7.13         7.43         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         0.36         7.40         3.95        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ 
       35.97        12.92        13.48        13.22         7.76        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        8.71        13.41        27.12        83.24        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       10.36        10.45        12.66        12.43        13.41         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        15.35        13.25         0.10        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39         0.10        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW 
       11.54        13.22         4.47        12.33        25.25        12.00 
TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ 
       12.03         0.13        33.11         5.16         7.82         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        14.70         7.04        29.59         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        9.30        15.78        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ 
        3.42         4.80        15.35         9.27         4.44        22.82 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        30.71        18.18 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        15.06        11.24         9.17        15.91        10.16 
TCGA-Z6-A8JD TCGA-Z6-A8JE 
        3.42         2.10 

  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                          0.1                           0.1 
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                        68.02                        122.10 
  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE 
                       12.330                        12.625 
[1] "0.1 - 68.0 (12.3)"  "0.1 - 122.1 (12.6)"
[1] "hr=" "1.3"
D36V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  5(2Q33.3) MUTATED         1        0        2        0         8
  DEL PEAK  5(2Q33.3) WILD-TYPE       7        5        5        1        31
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  5(2Q33.3) MUTATED           4         5          6          2
  DEL PEAK  5(2Q33.3) WILD-TYPE        25        20          6          8
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  5(2Q33.3) MUTATED            1        0         0
  DEL PEAK  5(2Q33.3) WILD-TYPE          6        5         4
D36V3, multiclass
            clus
vv           DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  STAGE I                              1                             7
  STAGE IA                             0                             5
  STAGE IB                             2                             5
  STAGE II                             0                             1
  STAGE IIA                            8                            31
  STAGE IIB                            4                            25
  STAGE III                            5                            20
  STAGE IIIA                           6                             6
  STAGE IIIB                           2                             8
  STAGE IIIC                           1                             6
  STAGE IV                             0                             5
  STAGE IVA                            0                             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  5(2Q33.3) MUTATED       1  6 20  2
  DEL PEAK  5(2Q33.3) WILD-TYPE    30 30 65  3
D36V4, multiclass
       clus
vv      DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  T0+T1                           1                            30
  T2                              6                            30
  T3                             20                            65
  T4                              2                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK  5(2Q33.3) MUTATED   14 13  1  1
  DEL PEAK  5(2Q33.3) WILD-TYPE 57 51 11  7
D36V5, multiclass
    clus
vv   DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  N0                          14                            57
  N1                          13                            51
  N2                           1                            11
  N3                           1                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q33.3) MUTATED    26   0
  DEL PEAK  5(2Q33.3) WILD-TYPE 100   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q33.3) MUTATED     26    0
  DEL PEAK  5(2Q33.3) WILD-TYPE  100    9
   clus
vv  DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  0                          26                           100
  1                           0                             9
[1] 2 2
[1] FALSE
D36V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q33.3) MUTATED     4  28
  DEL PEAK  5(2Q33.3) WILD-TYPE  20 121
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q33.3) MUTATED      4   28
  DEL PEAK  5(2Q33.3) WILD-TYPE   20  121
        clus
vv       DEL PEAK  5(2Q33.3) MUTATED DEL PEAK  5(2Q33.3) WILD-TYPE
  FEMALE                           4                            20
  MALE                            28                           121
[1] 2 2
[1] FALSE
D36V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(2Q33.3) MUTATED       8                         0    23
  DEL PEAK  5(2Q33.3) WILD-TYPE    33                         2    88
D36V9, multiclass
                           clus
vv                          DEL PEAK  5(2Q33.3) MUTATED
  ASIAN                                               8
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              23
                           clus
vv                          DEL PEAK  5(2Q33.3) WILD-TYPE
  ASIAN                                                33
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V10, binary
                               cls
clus                             0  1
  DEL PEAK  5(2Q33.3) MUTATED    0 19
  DEL PEAK  5(2Q33.3) WILD-TYPE  3 62
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q33.3) MUTATED      0   19
  DEL PEAK  5(2Q33.3) WILD-TYPE    3   62
                        clus
vv                       DEL PEAK  5(2Q33.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          19
                        clus
vv                       DEL PEAK  5(2Q33.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            62
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK  6(3P26.2) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  6(3P26.2) MUTATED   64 35
  DEL PEAK  6(3P26.2) WILD-TYPE 36 36
  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                           99                            72 
  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                           35                            36 
$`DEL PEAK  6(3P26.2) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       14.30         5.92        13.94         8.94        16.24         4.21 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69        33.27        20.09         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       20.12         3.88         0.53        17.03         0.79        23.41 
TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FB TCGA-JY-A6FD TCGA-L5-A43E 
        9.96        14.50        12.16        60.39        68.02        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OM 
        0.30         4.31         8.94         4.70        32.61        47.93 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW 
        3.32         7.17         3.16        58.59         4.90         7.13 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        6.94         2.60         7.40        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NV TCGA-LN-A49K 
       12.92        16.47        13.55         5.49        52.57         5.92 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X 
       12.43        13.41         0.10        13.15        15.35         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.46        12.49        12.76        12.59        22.39         0.10 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       15.52        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 
       10.52        12.00        12.23        13.18         0.13        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A8W8 TCGA-R6-A8WG 
        7.82         7.59         7.04        29.59         2.89        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EO 
        7.00        20.02        20.38         3.42         9.27        18.81 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ 
       19.96        12.43        18.31         8.12        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       42.87        46.19        15.06        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE 
       10.16         3.42         2.10 

$`DEL PEAK  6(3P26.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GR TCGA-IC-A6RF 
       25.78        31.27        58.55         7.63        32.45         6.21 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 
       18.64         9.30        12.82        14.86         4.67       122.10 
TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       44.75         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OQ 
       24.00         3.68        19.99        21.01        18.35         1.38 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A891 
       29.00         7.43         8.71        25.12         0.36         3.95 
TCGA-L5-A893 TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR 
        3.02        13.48        13.22         7.76        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L 
       13.41        27.12        83.24        46.09        10.36        10.45 
TCGA-LN-A49M TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A9 TCGA-LN-A7HY 
       12.66         0.10        13.25        12.59        11.54        12.03 
TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.16         8.02         5.06        14.70         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
        9.30        15.78         1.45         5.29         4.80        15.35 
TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EX TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        4.44        22.82         1.55        28.11         2.66        19.73 

  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                          0.1                           0.1 
  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                        68.02                        122.10 
  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                       12.430                        13.235 
[1] "0.1 - 68.0 (12.4)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.2"
D37V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  6(3P26.2) MUTATED         4        3        4        1        26
  DEL PEAK  6(3P26.2) WILD-TYPE       4        2        3        0        13
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  6(3P26.2) MUTATED          15        15          9          5
  DEL PEAK  6(3P26.2) WILD-TYPE        14        10          3          5
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  6(3P26.2) MUTATED            3        5         2
  DEL PEAK  6(3P26.2) WILD-TYPE          4        0         2
D37V3, multiclass
            clus
vv           DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE
  STAGE I                              4                             4
  STAGE IA                             3                             2
  STAGE IB                             4                             3
  STAGE II                             1                             0
  STAGE IIA                           26                            13
  STAGE IIB                           15                            14
  STAGE III                           15                            10
  STAGE IIIA                           9                             3
  STAGE IIIB                           5                             5
  STAGE IIIC                           3                             4
  STAGE IV                             5                             0
  STAGE IVA                            2                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  6(3P26.2) MUTATED      17 20 53  4
  DEL PEAK  6(3P26.2) WILD-TYPE    14 16 32  1
D37V4, multiclass
       clus
vv      DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE
  T0+T1                          17                            14
  T2                             20                            16
  T3                             53                            32
  T4                              4                             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                            N0 N1 N2 N3
  DEL PEAK  6(3P26.2) MUTATED   45 38  6  4
  DEL PEAK  6(3P26.2) WILD-TYPE 26 26  6  4
D37V5, multiclass
    clus
vv   DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE
  N0                          45                            26
  N1                          38                            26
  N2                           6                             6
  N3                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                               cls
clus                             0  1
  DEL PEAK  6(3P26.2) MUTATED   77  7
  DEL PEAK  6(3P26.2) WILD-TYPE 49  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.2) MUTATED     77    7
  DEL PEAK  6(3P26.2) WILD-TYPE   49    2
   clus
vv  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE
  0                          77                            49
  1                           7                             2
[1] 2 2
[1] FALSE
D37V7, binary
                               cls
clus                             0  1
  DEL PEAK  6(3P26.2) MUTATED   16 85
  DEL PEAK  6(3P26.2) WILD-TYPE  8 64
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.2) MUTATED     16   85
  DEL PEAK  6(3P26.2) WILD-TYPE    8   64
        clus
vv       DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE
  FEMALE                          16                             8
  MALE                            85                            64
[1] 2 2
[1] FALSE
D37V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(3P26.2) MUTATED      30                         1    59
  DEL PEAK  6(3P26.2) WILD-TYPE    11                         1    52
D37V9, multiclass
                           clus
vv                          DEL PEAK  6(3P26.2) MUTATED
  ASIAN                                              30
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              59
                           clus
vv                          DEL PEAK  6(3P26.2) WILD-TYPE
  ASIAN                                                11
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V10, binary
                               cls
clus                             0  1
  DEL PEAK  6(3P26.2) MUTATED    1 54
  DEL PEAK  6(3P26.2) WILD-TYPE  2 27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.2) MUTATED      1   54
  DEL PEAK  6(3P26.2) WILD-TYPE    2   27
                        clus
vv                       DEL PEAK  6(3P26.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          54
                        clus
vv                       DEL PEAK  6(3P26.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            27
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK  7(3P14.3) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  7(3P14.3) MUTATED   71 43
  DEL PEAK  7(3P14.3) WILD-TYPE 29 28
  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                          114                            57 
  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                           43                            28 
$`DEL PEAK  7(3P14.3) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       14.30         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12        18.64         3.88         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
        0.79        23.41         9.96        14.50        12.16        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
       60.39        68.02        30.25         0.30         4.31         8.94 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO 
        3.68         4.70        32.61        21.01        47.93         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        7.17         1.38         7.13         7.43         6.94         2.60 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ 
        0.36         7.40         2.66        35.97        12.92        16.47 
TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
       13.55         5.49         8.71        13.41        83.24        52.57 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
        5.92        10.45        12.66        12.43        13.41         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        15.35        13.25         0.10        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39         0.10        15.52 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 
       12.00        12.23        12.03        13.18         0.13        33.11 
TCGA-Q9-A6FU TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A8W8 TCGA-R6-A8WG 
        5.16         7.59         7.04        29.59         2.89        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EO 
        7.00        20.02        20.38         3.42         9.27        18.81 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       19.96        12.43        18.31         8.12        28.11        30.71 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        42.87        46.19        15.06        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       15.91        10.16         3.42         2.10         2.66        19.73 

$`DEL PEAK  7(3P14.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-IC-A6RF TCGA-IG-A4QT 
       25.78        31.27        58.55         7.63         6.21         9.30 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG 
       12.82        14.86         4.67       122.10         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       42.77        25.41        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A4ON 
       24.03         6.28         3.16        24.00        19.99        18.35 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88W 
        3.16        58.59         4.90        29.00         8.71        25.12 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM 
        3.95         3.02        55.50        13.48        13.22         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49V TCGA-LN-A4A9 
       21.37        27.12        46.09        10.36         0.10        11.54 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.82         8.02         5.06        14.70         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
        9.30        15.78         1.45         5.29         4.80        15.35 
TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ET 
        4.44        22.82         1.55 

  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                          0.1                           0.1 
  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                        83.24                        122.10 
  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE 
                       12.445                        13.480 
[1] "0.1 - 83.2 (12.4)"  "0.1 - 122.1 (13.5)"
[1] "hr=" "1"  
D38V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  7(3P14.3) MUTATED         5        2        4        1        32
  DEL PEAK  7(3P14.3) WILD-TYPE       3        3        3        0         7
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  7(3P14.3) MUTATED          18        18         10          5
  DEL PEAK  7(3P14.3) WILD-TYPE        11         7          2          5
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  7(3P14.3) MUTATED            4        4         3
  DEL PEAK  7(3P14.3) WILD-TYPE          3        1         1
D38V3, multiclass
            clus
vv           DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE
  STAGE I                              5                             3
  STAGE IA                             2                             3
  STAGE IB                             4                             3
  STAGE II                             1                             0
  STAGE IIA                           32                             7
  STAGE IIB                           18                            11
  STAGE III                           18                             7
  STAGE IIIA                          10                             2
  STAGE IIIB                           5                             5
  STAGE IIIC                           4                             3
  STAGE IV                             4                             1
  STAGE IVA                            3                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  7(3P14.3) MUTATED      20 25 60  4
  DEL PEAK  7(3P14.3) WILD-TYPE    11 11 25  1
D38V4, multiclass
       clus
vv      DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE
  T0+T1                          20                            11
  T2                             25                            11
  T3                             60                            25
  T4                              4                             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                            N0 N1 N2 N3
  DEL PEAK  7(3P14.3) MUTATED   53 43  7  5
  DEL PEAK  7(3P14.3) WILD-TYPE 18 21  5  3
D38V5, multiclass
    clus
vv   DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE
  N0                          53                            18
  N1                          43                            21
  N2                           7                             5
  N3                           5                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                               cls
clus                             0  1
  DEL PEAK  7(3P14.3) MUTATED   89  7
  DEL PEAK  7(3P14.3) WILD-TYPE 37  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.3) MUTATED     89    7
  DEL PEAK  7(3P14.3) WILD-TYPE   37    2
   clus
vv  DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE
  0                          89                            37
  1                           7                             2
[1] 2 2
[1] FALSE
D38V7, binary
                               cls
clus                             0  1
  DEL PEAK  7(3P14.3) MUTATED   18 98
  DEL PEAK  7(3P14.3) WILD-TYPE  6 51
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.3) MUTATED     18   98
  DEL PEAK  7(3P14.3) WILD-TYPE    6   51
        clus
vv       DEL PEAK  7(3P14.3) MUTATED DEL PEAK  7(3P14.3) WILD-TYPE
  FEMALE                          18                             6
  MALE                            98                            51
[1] 2 2
[1] FALSE
D38V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(3P14.3) MUTATED      36                         1    65
  DEL PEAK  7(3P14.3) WILD-TYPE     5                         1    46
D38V9, multiclass
                           clus
vv                          DEL PEAK  7(3P14.3) MUTATED
  ASIAN                                              36
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              65
                           clus
vv                          DEL PEAK  7(3P14.3) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V10, binary
                               cls
clus                             0  1
  DEL PEAK  7(3P14.3) MUTATED    1 61
  DEL PEAK  7(3P14.3) WILD-TYPE  2 20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.3) MUTATED      1   61
  DEL PEAK  7(3P14.3) WILD-TYPE    2   20
                        clus
vv                       DEL PEAK  7(3P14.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          61
                        clus
vv                       DEL PEAK  7(3P14.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            20
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK  8(3P14.2) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  8(3P14.2) MUTATED   69 43
  DEL PEAK  8(3P14.2) WILD-TYPE 31 28
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                          112                            59 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                           43                            28 
$`DEL PEAK  8(3P14.2) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       14.30         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12        18.64         3.88         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
        0.79        23.41         9.96        14.50        12.16        44.75 
TCGA-JY-A6FD TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       68.02        30.25         0.30         4.31         8.94        24.00 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO 
        3.68         4.70        32.61        21.01        47.93         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        7.17         1.38         7.13         7.43         6.94         2.60 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ 
        0.36         7.40         2.66        35.97        12.92        16.47 
TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-LN-A49K 
       13.55         5.49         8.71        13.41        52.57         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U 
       10.45        12.66        12.43        13.41        13.15        15.35 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25         0.10        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        22.39         0.10        15.52        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN 
       12.03        13.18         0.13        33.11         5.16         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
        7.59         7.04         2.89        12.69         7.00        20.02 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP 
       20.38         3.42         4.80         9.27        18.81        19.96 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43        18.31         8.12        28.11        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       42.87        46.19        15.06        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
       10.16         3.42         2.10         2.66 

$`DEL PEAK  8(3P14.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-IC-A6RF TCGA-IG-A4QT 
       25.78        31.27        58.55         7.63         6.21         9.30 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE 
       12.82        14.86         4.67       122.10        60.39         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       41.52        42.77        25.41        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A4OI TCGA-L5-A4ON 
       25.22        24.03         6.28         3.16        19.99        18.35 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88W 
        3.16        58.59         4.90        29.00         8.71        25.12 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM 
        3.95         3.02        55.50        13.48        13.22         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49R 
       21.37        27.12        83.24        46.09        10.36         0.10 
TCGA-LN-A49V TCGA-LN-A4A9 TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG 
        0.10        11.54         7.82         5.06        14.70        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-V5-A7RB 
        6.35        53.95         9.30        15.78         1.45         5.29 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-ZR-A9CJ 
       15.35         4.44        22.82         1.55        19.73 

  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                          0.1                           0.1 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                        68.02                        122.10 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                        12.38                         14.86 
[1] "0.1 - 68.0 (12.4)"  "0.1 - 122.1 (14.9)"
[1] "hr=" "1.2"
D39V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  8(3P14.2) MUTATED         4        2        5        1        31
  DEL PEAK  8(3P14.2) WILD-TYPE       4        3        2        0         8
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  8(3P14.2) MUTATED          18        17         10          6
  DEL PEAK  8(3P14.2) WILD-TYPE        11         8          2          4
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  8(3P14.2) MUTATED            3        4         3
  DEL PEAK  8(3P14.2) WILD-TYPE          4        1         1
D39V3, multiclass
            clus
vv           DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  STAGE I                              4                             4
  STAGE IA                             2                             3
  STAGE IB                             5                             2
  STAGE II                             1                             0
  STAGE IIA                           31                             8
  STAGE IIB                           18                            11
  STAGE III                           17                             8
  STAGE IIIA                          10                             2
  STAGE IIIB                           6                             4
  STAGE IIIC                           3                             4
  STAGE IV                             4                             1
  STAGE IVA                            3                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  8(3P14.2) MUTATED      20 24 59  4
  DEL PEAK  8(3P14.2) WILD-TYPE    11 12 26  1
D39V4, multiclass
       clus
vv      DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  T0+T1                          20                            11
  T2                             24                            12
  T3                             59                            26
  T4                              4                             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                            N0 N1 N2 N3
  DEL PEAK  8(3P14.2) MUTATED   52 42  8  4
  DEL PEAK  8(3P14.2) WILD-TYPE 19 22  4  4
D39V5, multiclass
    clus
vv   DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  N0                          52                            19
  N1                          42                            22
  N2                           8                             4
  N3                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                               cls
clus                             0  1
  DEL PEAK  8(3P14.2) MUTATED   87  7
  DEL PEAK  8(3P14.2) WILD-TYPE 39  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.2) MUTATED     87    7
  DEL PEAK  8(3P14.2) WILD-TYPE   39    2
   clus
vv  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  0                          87                            39
  1                           7                             2
[1] 2 2
[1] FALSE
D39V7, binary
                               cls
clus                             0  1
  DEL PEAK  8(3P14.2) MUTATED   18 96
  DEL PEAK  8(3P14.2) WILD-TYPE  6 53
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.2) MUTATED     18   96
  DEL PEAK  8(3P14.2) WILD-TYPE    6   53
        clus
vv       DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  FEMALE                          18                             6
  MALE                            96                            53
[1] 2 2
[1] FALSE
D39V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(3P14.2) MUTATED      35                         1    64
  DEL PEAK  8(3P14.2) WILD-TYPE     6                         1    47
D39V9, multiclass
                           clus
vv                          DEL PEAK  8(3P14.2) MUTATED
  ASIAN                                              35
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              64
                           clus
vv                          DEL PEAK  8(3P14.2) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V10, binary
                               cls
clus                             0  1
  DEL PEAK  8(3P14.2) MUTATED    1 60
  DEL PEAK  8(3P14.2) WILD-TYPE  2 21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.2) MUTATED      1   60
  DEL PEAK  8(3P14.2) WILD-TYPE    2   21
                        clus
vv                       DEL PEAK  8(3P14.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          60
                        clus
vv                       DEL PEAK  8(3P14.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            21
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK  9(3Q11.1) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  9(3Q11.1) MUTATED   19 13
  DEL PEAK  9(3Q11.1) WILD-TYPE 81 58
  DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE 
                           32                           139 
  DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE 
                           13                            58 
$`DEL PEAK  9(3Q11.1) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3YB 
       14.30        13.94         4.21        32.45         7.69         2.63 
TCGA-IG-A3YC TCGA-IG-A5S3 TCGA-JY-A6FD TCGA-JY-A938 TCGA-L5-A43E TCGA-L5-A43H 
       20.12        23.41        68.02        25.41        30.25         0.30 
TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OX TCGA-L5-A88Y TCGA-L5-A8NH TCGA-LN-A49L 
       32.61         3.32         7.43         0.36        12.92        10.45 
TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A6 TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HX 
        0.10        12.46         0.10         4.47        12.33        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-AASW 
       12.03        13.18         2.89        12.69         7.00         9.27 
TCGA-VR-AA4D TCGA-X8-AAAR 
       46.19        10.16 

$`DEL PEAK  9(3Q11.1) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        31.27        58.55         7.63         5.92         8.94 
TCGA-2H-A9GO TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       16.24         6.21        33.27        20.09         0.85        20.78 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        60.39         3.68        41.52        42.77 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        3.16         4.31         8.94        24.00         3.68         4.70 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
       19.99        21.01        47.93        18.35         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S 
        3.16        58.59         4.90        29.00         7.13         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        8.71         2.60        25.12         7.40         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        35.97        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
       27.12        83.24        52.57        46.09        10.36         5.92 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.66        12.43        13.41        13.15        15.35         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25         0.10        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U7 
       22.39        15.52        11.54        12.33        13.22        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       10.52        12.00         0.13        33.11         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-S8-A6BV 
        6.35        53.95         9.30        15.78         1.45        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX 
       20.38         5.29         3.42         4.80        15.35         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       18.81        19.96        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G 
        8.12        28.11        30.71        18.18        42.87        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
       11.24         9.17        15.91         3.42         2.10         2.66 
TCGA-ZR-A9CJ 
       19.73 

  DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE 
                          0.1                           0.1 
  DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE 
                        68.02                        122.10 
  DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE 
                        12.13                         12.76 
[1] "0.1 - 68.0 (12.1)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "1.1"
D40V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  9(3Q11.1) MUTATED         2        0        1        1         6
  DEL PEAK  9(3Q11.1) WILD-TYPE       6        5        6        0        33
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  9(3Q11.1) MUTATED           7         5          2          0
  DEL PEAK  9(3Q11.1) WILD-TYPE        22        20         10         10
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  9(3Q11.1) MUTATED            1        2         0
  DEL PEAK  9(3Q11.1) WILD-TYPE          6        3         4
D40V3, multiclass
            clus
vv           DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE
  STAGE I                              2                             6
  STAGE IA                             0                             5
  STAGE IB                             1                             6
  STAGE II                             1                             0
  STAGE IIA                            6                            33
  STAGE IIB                            7                            22
  STAGE III                            5                            20
  STAGE IIIA                           2                            10
  STAGE IIIB                           0                            10
  STAGE IIIC                           1                             6
  STAGE IV                             2                             3
  STAGE IVA                            0                             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK  9(3Q11.1) MUTATED       9  6 14  0
  DEL PEAK  9(3Q11.1) WILD-TYPE    22 30 71  5
D40V4, multiclass
       clus
vv      DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE
  T0+T1                           9                            22
  T2                              6                            30
  T3                             14                            71
  T4                              0                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK  9(3Q11.1) MUTATED   13 15  0  1
  DEL PEAK  9(3Q11.1) WILD-TYPE 58 49 12  7
D40V5, multiclass
    clus
vv   DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE
  N0                          13                            58
  N1                          15                            49
  N2                           0                            12
  N3                           1                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                               cls
clus                              0   1
  DEL PEAK  9(3Q11.1) MUTATED    25   2
  DEL PEAK  9(3Q11.1) WILD-TYPE 101   7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3Q11.1) MUTATED     25    2
  DEL PEAK  9(3Q11.1) WILD-TYPE  101    7
   clus
vv  DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE
  0                          25                           101
  1                           2                             7
[1] 2 2
[1] FALSE
D40V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(3Q11.1) MUTATED     3  29
  DEL PEAK  9(3Q11.1) WILD-TYPE  21 120
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3Q11.1) MUTATED      3   29
  DEL PEAK  9(3Q11.1) WILD-TYPE   21  120
        clus
vv       DEL PEAK  9(3Q11.1) MUTATED DEL PEAK  9(3Q11.1) WILD-TYPE
  FEMALE                           3                            21
  MALE                            29                           120
[1] 2 2
[1] FALSE
D40V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(3Q11.1) MUTATED      10                         0    18
  DEL PEAK  9(3Q11.1) WILD-TYPE    31                         2    93
D40V9, multiclass
                           clus
vv                          DEL PEAK  9(3Q11.1) MUTATED
  ASIAN                                              10
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              18
                           clus
vv                          DEL PEAK  9(3Q11.1) WILD-TYPE
  ASIAN                                                31
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V10, binary
                               cls
clus                             0  1
  DEL PEAK  9(3Q11.1) MUTATED    1 17
  DEL PEAK  9(3Q11.1) WILD-TYPE  2 64
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3Q11.1) MUTATED      1   17
  DEL PEAK  9(3Q11.1) WILD-TYPE    2   64
                        clus
vv                       DEL PEAK  9(3Q11.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          17
                        clus
vv                       DEL PEAK  9(3Q11.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            64
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 10(3Q26.31) MUTATION ANALYSIS
D41V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 10(3Q26.31) MUTATED    5 10
  DEL PEAK 10(3Q26.31) WILD-TYPE 95 61
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                            15                            156 
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                            10                             61 
$`DEL PEAK 10(3Q26.31) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GM TCGA-IC-A6RE TCGA-JY-A938 TCGA-JY-A93D 
       25.78        14.30        13.94         7.69        25.41        31.56 
TCGA-L5-A4OH TCGA-L5-A4OX TCGA-L5-A891 TCGA-L5-A8NH TCGA-L5-A8NW TCGA-R6-A6DN 
       32.61         7.43         3.95        12.92        46.09         8.02 
TCGA-RE-A7BO TCGA-VR-A8EU TCGA-X8-AAAR 
        7.00        18.31        10.16 

$`DEL PEAK 10(3Q26.31) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        58.55         7.63         5.92         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         6.21        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       60.39        68.02         3.68        41.52        42.77        21.70 
TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       23.18        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        0.30         4.31         8.94        24.00         3.68         4.70 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       19.99        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
        6.94         8.71         2.60        25.12         0.36         7.40 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        35.97        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K 
       13.41        27.12        83.24        52.57        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.45        12.66        12.43        13.41         0.10        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35         0.10        13.25         0.10        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39         0.10        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO 
       10.52        12.00        12.23        12.03        13.18         0.13 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         5.16         7.82         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        29.59         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         1.45        12.69        20.02        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42         4.80        15.35         9.27         4.44        18.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX 
       19.96        22.82        12.43         1.55         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       30.71        18.18        42.87        46.19        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        9.17        15.91         3.42         2.10         2.66        19.73 

  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                          3.95                           0.10 
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                         46.09                         122.10 
  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE 
                        13.940                         12.475 
[1] "4.0 - 46.1 (13.9)"  "0.1 - 122.1 (12.5)"
[1] "hr=" "1.5"
D41V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 10(3Q26.31) MUTATED         1        0        1        0         0
  DEL PEAK 10(3Q26.31) WILD-TYPE       7        5        6        1        39
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 10(3Q26.31) MUTATED           5         2          0          0
  DEL PEAK 10(3Q26.31) WILD-TYPE        24        23         12         10
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 10(3Q26.31) MUTATED            1        2         0
  DEL PEAK 10(3Q26.31) WILD-TYPE          6        3         4
D41V3, multiclass
            clus
vv           DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  STAGE I                               1                              7
  STAGE IA                              0                              5
  STAGE IB                              1                              6
  STAGE II                              0                              1
  STAGE IIA                             0                             39
  STAGE IIB                             5                             24
  STAGE III                             2                             23
  STAGE IIIA                            0                             12
  STAGE IIIB                            0                             10
  STAGE IIIC                            1                              6
  STAGE IV                              2                              3
  STAGE IVA                             0                              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 10(3Q26.31) MUTATED       7  3  4  0
  DEL PEAK 10(3Q26.31) WILD-TYPE    24 33 81  5
D41V4, multiclass
       clus
vv      DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  T0+T1                            7                             24
  T2                               3                             33
  T3                               4                             81
  T4                               0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 10(3Q26.31) MUTATED    3 10  0  1
  DEL PEAK 10(3Q26.31) WILD-TYPE 68 54 12  7
D41V5, multiclass
    clus
vv   DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  N0                            3                             68
  N1                           10                             54
  N2                            0                             12
  N3                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                                cls
clus                               0   1
  DEL PEAK 10(3Q26.31) MUTATED    11   2
  DEL PEAK 10(3Q26.31) WILD-TYPE 115   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q26.31) MUTATED     11    2
  DEL PEAK 10(3Q26.31) WILD-TYPE  115    7
   clus
vv  DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  0                           11                            115
  1                            2                              7
[1] 2 2
[1] FALSE
D41V7, binary
                                cls
clus                               0   1
  DEL PEAK 10(3Q26.31) MUTATED     1  14
  DEL PEAK 10(3Q26.31) WILD-TYPE  23 135
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q26.31) MUTATED      1   14
  DEL PEAK 10(3Q26.31) WILD-TYPE   23  135
        clus
vv       DEL PEAK 10(3Q26.31) MUTATED DEL PEAK 10(3Q26.31) WILD-TYPE
  FEMALE                            1                             23
  MALE                             14                            135
[1] 2 2
[1] FALSE
D41V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(3Q26.31) MUTATED       0                         0    12
  DEL PEAK 10(3Q26.31) WILD-TYPE    41                         2    99
D41V9, multiclass
                           clus
vv                          DEL PEAK 10(3Q26.31) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               12
                           clus
vv                          DEL PEAK 10(3Q26.31) WILD-TYPE
  ASIAN                                                 41
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V10, binary
                                cls
clus                              0  1
  DEL PEAK 10(3Q26.31) MUTATED    0  4
  DEL PEAK 10(3Q26.31) WILD-TYPE  3 77
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(3Q26.31) MUTATED      0    4
  DEL PEAK 10(3Q26.31) WILD-TYPE    3   77
                        clus
vv                       DEL PEAK 10(3Q26.31) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            4
                        clus
vv                       DEL PEAK 10(3Q26.31) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                             77
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 11(4P15.2) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 11(4P15.2) MUTATED   53 46
  DEL PEAK 11(4P15.2) WILD-TYPE 47 25
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                           99                            72 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                           46                            25 
$`DEL PEAK 11(4P15.2) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        14.30        58.55         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 
       20.78        20.12        18.64         3.88         0.53         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB 
       12.82         9.96         4.67        12.16        44.75        60.39 
TCGA-JY-A6FH TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       42.77        25.22         3.16         8.94        24.00         4.70 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW 
       21.01        47.93         3.32         3.16         4.90         7.13 
TCGA-L5-A4OX TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ 
        7.43         7.40         3.95        35.97        12.92        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
       13.55        13.22         5.49         8.71        13.41        27.12 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       12.43         0.10        15.35         0.10        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U6 
       12.49        12.76         0.10        15.52        13.22        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-R6-A6DN 
       25.25        12.00        12.23        13.18         0.13         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 
        7.59         5.06         7.04         6.35         9.30         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE 
        1.45        12.69         7.00        20.38         3.42         4.80 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         4.44        19.96        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       18.31         8.12        18.18        42.87        46.19        15.06 
TCGA-VR-AA7B TCGA-VR-AA7I TCGA-Z6-A8JD 
       11.24        15.91         3.42 

$`DEL PEAK 11(4P15.2) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GK TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3YB TCGA-IG-A4QT 
       31.27         7.63         7.69         6.21         2.63         9.30 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A7DP TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FD 
       17.03        23.41        14.86        14.50       122.10        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        25.41        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OF 
       24.03         6.28        30.25         0.30         4.31         3.68 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       32.61        19.99        18.35         7.17         1.38        58.59 
TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
       29.00         6.94         8.71         2.60        25.12         0.36 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NQ 
        3.02        55.50         2.66        13.48         7.76        21.37 
TCGA-L5-A8NU TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A4 
       83.24        13.41        13.15         0.10        13.25        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HY 
       22.39        11.54        12.33         4.47        10.52        12.03 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 
       33.11         5.16         7.82        14.70        29.59        53.95 
TCGA-R6-A8W5 TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EX 
       15.78        20.02         5.29        15.35        18.81        28.11 
TCGA-VR-A8EY TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       30.71         9.17        10.16         2.10         2.66        19.73 

  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                          0.1                           0.1 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                        60.39                        122.10 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                       12.430                        13.445 
[1] "0.1 - 60.4 (12.4)"  "0.1 - 122.1 (13.4)"
[1] "hr=" "1.7"
D42V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 11(4P15.2) MUTATED         4        2        5        1        22
  DEL PEAK 11(4P15.2) WILD-TYPE       4        3        2        0        17
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 11(4P15.2) MUTATED          15        15          7          6
  DEL PEAK 11(4P15.2) WILD-TYPE        14        10          5          4
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 11(4P15.2) MUTATED            3        4         1
  DEL PEAK 11(4P15.2) WILD-TYPE          4        1         3
D42V3, multiclass
            clus
vv           DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  STAGE I                              4                             4
  STAGE IA                             2                             3
  STAGE IB                             5                             2
  STAGE II                             1                             0
  STAGE IIA                           22                            17
  STAGE IIB                           15                            14
  STAGE III                           15                            10
  STAGE IIIA                           7                             5
  STAGE IIIB                           6                             4
  STAGE IIIC                           3                             4
  STAGE IV                             4                             1
  STAGE IVA                            1                             3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 11(4P15.2) MUTATED      13 24 46  4
  DEL PEAK 11(4P15.2) WILD-TYPE    18 12 39  1
D42V4, multiclass
       clus
vv      DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  T0+T1                          13                            18
  T2                             24                            12
  T3                             46                            39
  T4                              4                             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                            N0 N1 N2 N3
  DEL PEAK 11(4P15.2) MUTATED   39 36  8  4
  DEL PEAK 11(4P15.2) WILD-TYPE 32 28  4  4
D42V5, multiclass
    clus
vv   DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  N0                          39                            32
  N1                          36                            28
  N2                           8                             4
  N3                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V6, binary
                               cls
clus                             0  1
  DEL PEAK 11(4P15.2) MUTATED   76  5
  DEL PEAK 11(4P15.2) WILD-TYPE 50  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED     76    5
  DEL PEAK 11(4P15.2) WILD-TYPE   50    4
   clus
vv  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  0                          76                            50
  1                           5                             4
[1] 2 2
[1] FALSE
D42V7, binary
                               cls
clus                             0  1
  DEL PEAK 11(4P15.2) MUTATED   13 87
  DEL PEAK 11(4P15.2) WILD-TYPE 11 62
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED     13   87
  DEL PEAK 11(4P15.2) WILD-TYPE   11   62
        clus
vv       DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  FEMALE                          13                            11
  MALE                            87                            62
[1] 2 2
[1] FALSE
D42V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(4P15.2) MUTATED      26                         1    60
  DEL PEAK 11(4P15.2) WILD-TYPE    15                         1    51
D42V9, multiclass
                           clus
vv                          DEL PEAK 11(4P15.2) MUTATED
  ASIAN                                              26
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              60
                           clus
vv                          DEL PEAK 11(4P15.2) WILD-TYPE
  ASIAN                                                15
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V10, binary
                               cls
clus                             0  1
  DEL PEAK 11(4P15.2) MUTATED    2 49
  DEL PEAK 11(4P15.2) WILD-TYPE  1 32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED      2   49
  DEL PEAK 11(4P15.2) WILD-TYPE    1   32
                        clus
vv                       DEL PEAK 11(4P15.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          49
                        clus
vv                       DEL PEAK 11(4P15.2) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            32
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 12(4Q22.1) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 12(4Q22.1) MUTATED   54 45
  DEL PEAK 12(4Q22.1) WILD-TYPE 46 26
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                           99                            72 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                           45                            26 
$`DEL PEAK 12(4Q22.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A8O2 
        0.85         3.88         0.53         0.79        12.82         4.67 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93E 
       12.16        44.75        60.39        42.77        23.18        25.22 
TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OO 
        3.16         4.31         8.94        24.00         4.70         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38         3.16        58.59         4.90         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF 
        6.94         2.60         7.40         3.95        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NR 
       35.97        12.92        13.48        16.47        13.22         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
       13.41        27.12        83.24        52.57        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U 
        5.92        10.45        12.66        13.41         0.10        15.35 
TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ 
       13.25        12.46        12.59        12.76         0.10        12.33 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HZ 
        4.47        12.33        25.25        10.52        12.00        13.18 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         7.59         5.06         7.04        29.59         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
        9.30        15.78         1.45        12.69         7.00        20.02 
TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       20.38         4.80         9.27         4.44        18.81        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B 
       22.82         1.55        28.11        42.87        15.06        11.24 
TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-AAPN 
       15.91         3.42         2.66 

$`DEL PEAK 12(4Q22.1) WILD-TYPE`
TCGA-2H-A9GJ TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       58.55         7.69         6.21        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP 
       18.64         9.30        17.03        23.41         9.96        14.86 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 
       14.50       122.10        68.02         3.68        41.52        25.41 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
       21.70        31.56        24.03         6.28        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        3.68        32.61        19.99        21.01        47.93        18.35 
TCGA-L5-A4OP TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A893 
        7.17        29.00         8.71        25.12         0.36         3.02 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-LN-A49N TCGA-LN-A49S 
       13.55         7.76         5.49        21.37        12.43        13.15 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
        0.10         0.10        12.49        12.59        22.39        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 
       11.54        13.22        12.23        12.03         0.13        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-V5-A7RB 
        5.16         7.82        14.70        53.95         2.89         5.29 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
        3.42        15.35        12.43        18.31         8.12        30.71 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       18.18        46.19         9.17        10.16         2.10        19.73 

  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                          0.1                           0.1 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                        83.24                        122.10 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                       12.330                        13.385 
[1] "0.1 - 83.2 (12.3)"  "0.1 - 122.1 (13.4)"
[1] "hr=" "1.5"
D43V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 12(4Q22.1) MUTATED         2        1        5        1        19
  DEL PEAK 12(4Q22.1) WILD-TYPE       6        4        2        0        20
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 12(4Q22.1) MUTATED          16        18          7          7
  DEL PEAK 12(4Q22.1) WILD-TYPE        13         7          5          3
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 12(4Q22.1) MUTATED            2        4         4
  DEL PEAK 12(4Q22.1) WILD-TYPE          5        1         0
D43V3, multiclass
            clus
vv           DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  STAGE I                              2                             6
  STAGE IA                             1                             4
  STAGE IB                             5                             2
  STAGE II                             1                             0
  STAGE IIA                           19                            20
  STAGE IIB                           16                            13
  STAGE III                           18                             7
  STAGE IIIA                           7                             5
  STAGE IIIB                           7                             3
  STAGE IIIC                           2                             5
  STAGE IV                             4                             1
  STAGE IVA                            4                             0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 12(4Q22.1) MUTATED      11 22 53  2
  DEL PEAK 12(4Q22.1) WILD-TYPE    20 14 32  3
D43V4, multiclass
       clus
vv      DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  T0+T1                          11                            20
  T2                             22                            14
  T3                             53                            32
  T4                              2                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 12(4Q22.1) MUTATED   36 40  9  3
  DEL PEAK 12(4Q22.1) WILD-TYPE 35 24  3  5
D43V5, multiclass
    clus
vv   DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  N0                          36                            35
  N1                          40                            24
  N2                           9                             3
  N3                           3                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                               cls
clus                             0  1
  DEL PEAK 12(4Q22.1) MUTATED   70  8
  DEL PEAK 12(4Q22.1) WILD-TYPE 56  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED     70    8
  DEL PEAK 12(4Q22.1) WILD-TYPE   56    1
   clus
vv  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  0                          70                            56
  1                           8                             1
[1] 2 2
[1] FALSE
D43V7, binary
                               cls
clus                             0  1
  DEL PEAK 12(4Q22.1) MUTATED   11 89
  DEL PEAK 12(4Q22.1) WILD-TYPE 13 60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED     11   89
  DEL PEAK 12(4Q22.1) WILD-TYPE   13   60
        clus
vv       DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  FEMALE                          11                            13
  MALE                            89                            60
[1] 2 2
[1] FALSE
D43V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(4Q22.1) MUTATED      24                         0    62
  DEL PEAK 12(4Q22.1) WILD-TYPE    17                         2    49
D43V9, multiclass
                           clus
vv                          DEL PEAK 12(4Q22.1) MUTATED
  ASIAN                                              24
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              62
                           clus
vv                          DEL PEAK 12(4Q22.1) WILD-TYPE
  ASIAN                                                17
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V10, binary
                               cls
clus                             0  1
  DEL PEAK 12(4Q22.1) MUTATED    2 44
  DEL PEAK 12(4Q22.1) WILD-TYPE  1 37
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED      2   44
  DEL PEAK 12(4Q22.1) WILD-TYPE    1   37
                        clus
vv                       DEL PEAK 12(4Q22.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          44
                        clus
vv                       DEL PEAK 12(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            37
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 13(4Q34.3) MUTATION ANALYSIS
D44V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 13(4Q34.3) MUTATED   49 44
  DEL PEAK 13(4Q34.3) WILD-TYPE 51 27
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                           93                            78 
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                           44                            27 
$`DEL PEAK 13(4Q34.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        14.30         5.92         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 
       32.45        33.27         0.85         3.88         0.53         0.79 
TCGA-IG-A625 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FG TCGA-JY-A6FH 
       12.82       122.10        44.75        60.39        41.52        42.77 
TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       23.18        25.22         3.16         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS 
        4.70        18.35         3.32         7.17         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88Y TCGA-L5-A88Z 
        4.90         7.13         7.43         6.94         0.36         7.40 
TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ 
        3.95        55.50         2.66        35.97        12.92        16.47 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
       13.22         5.49         8.71        13.41        27.12        83.24 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O 
       46.09        10.36         5.92        10.45        12.66        13.41 
TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ 
        0.10        13.25        12.59        12.76         0.10        12.33 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ 
        4.47        12.33        10.52        12.00        12.23        13.18 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 
        5.16         7.82         8.02         7.59         5.06         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       29.59         6.35         9.30         2.89         1.45        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP 
        7.00        20.38         4.80         9.27         4.44        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 
       22.82         1.55         8.12        28.11        18.18        42.87 
TCGA-VR-AA4G TCGA-VR-AA7I TCGA-ZR-A9CJ 
       15.06        15.91        19.73 

$`DEL PEAK 13(4Q34.3) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-IC-A6RE TCGA-IC-A6RF 
       31.27        58.55         7.63        13.94         7.69         6.21 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
       20.09        20.78         2.63        20.12        18.64         9.30 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       17.03        23.41         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D 
       12.16        68.02         3.68        25.41        21.70        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
       24.03         6.28        30.25         0.30         3.68        32.61 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A88T 
       19.99        21.01        47.93         1.38        29.00         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A893 TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM 
        2.60        25.12         3.02        13.48        13.55         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       21.37        52.57        12.43        13.15        15.35         0.10 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
        0.10        12.46        12.49        12.59        22.39        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 
       11.54        13.22        25.25        12.03         0.13        33.11 
TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC 
       14.70        53.95        15.78        20.02         5.29         3.42 
TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-AA4D 
       15.35        18.81        12.43        18.31        30.71        46.19 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
       11.24         9.17        10.16         3.42         2.10         2.66 

  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                          0.1                           0.1 
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                       122.10                         68.02 
  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE 
                       10.520                        13.745 
[1] "0.1 - 122.1 (10.5)" "0.1 - 68.0 (13.7)" 
[1] "hr=" "1.5"
D44V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 13(4Q34.3) MUTATED         3        2        5        1        14
  DEL PEAK 13(4Q34.3) WILD-TYPE       5        3        2        0        25
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 13(4Q34.3) MUTATED          13        17          5          8
  DEL PEAK 13(4Q34.3) WILD-TYPE        16         8          7          2
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 13(4Q34.3) MUTATED            4        3         3
  DEL PEAK 13(4Q34.3) WILD-TYPE          3        2         1
D44V3, multiclass
            clus
vv           DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  STAGE I                              3                             5
  STAGE IA                             2                             3
  STAGE IB                             5                             2
  STAGE II                             1                             0
  STAGE IIA                           14                            25
  STAGE IIB                           13                            16
  STAGE III                           17                             8
  STAGE IIIA                           5                             7
  STAGE IIIB                           8                             2
  STAGE IIIC                           4                             3
  STAGE IV                             3                             2
  STAGE IVA                            3                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 13(4Q34.3) MUTATED      13 20 46  2
  DEL PEAK 13(4Q34.3) WILD-TYPE    18 16 39  3
D44V4, multiclass
       clus
vv      DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  T0+T1                          13                            18
  T2                             20                            16
  T3                             46                            39
  T4                              2                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 13(4Q34.3) MUTATED   31 36 10  4
  DEL PEAK 13(4Q34.3) WILD-TYPE 40 28  2  4
D44V5, multiclass
    clus
vv   DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  N0                          31                            40
  N1                          36                            28
  N2                          10                             2
  N3                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                               cls
clus                             0  1
  DEL PEAK 13(4Q34.3) MUTATED   64  6
  DEL PEAK 13(4Q34.3) WILD-TYPE 62  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q34.3) MUTATED     64    6
  DEL PEAK 13(4Q34.3) WILD-TYPE   62    3
   clus
vv  DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  0                          64                            62
  1                           6                             3
[1] 2 2
[1] FALSE
D44V7, binary
                               cls
clus                             0  1
  DEL PEAK 13(4Q34.3) MUTATED   12 82
  DEL PEAK 13(4Q34.3) WILD-TYPE 12 67
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q34.3) MUTATED     12   82
  DEL PEAK 13(4Q34.3) WILD-TYPE   12   67
        clus
vv       DEL PEAK 13(4Q34.3) MUTATED DEL PEAK 13(4Q34.3) WILD-TYPE
  FEMALE                          12                            12
  MALE                            82                            67
[1] 2 2
[1] FALSE
D44V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(4Q34.3) MUTATED      22                         0    61
  DEL PEAK 13(4Q34.3) WILD-TYPE    19                         2    50
D44V9, multiclass
                           clus
vv                          DEL PEAK 13(4Q34.3) MUTATED
  ASIAN                                              22
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              61
                           clus
vv                          DEL PEAK 13(4Q34.3) WILD-TYPE
  ASIAN                                                19
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V10, binary
                               cls
clus                             0  1
  DEL PEAK 13(4Q34.3) MUTATED    2 39
  DEL PEAK 13(4Q34.3) WILD-TYPE  1 42
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q34.3) MUTATED      2   39
  DEL PEAK 13(4Q34.3) WILD-TYPE    1   42
                        clus
vv                       DEL PEAK 13(4Q34.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          39
                        clus
vv                       DEL PEAK 13(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            42
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 14(5Q12.1) MUTATION ANALYSIS
D45V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 14(5Q12.1) MUTATED   59 45
  DEL PEAK 14(5Q12.1) WILD-TYPE 41 26
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                          104                            67 
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                           45                            26 
$`DEL PEAK 14(5Q12.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A8O2 
        0.85         2.63         3.88         0.53        17.03         4.67 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A93D TCGA-JY-A93E 
      122.10        44.75        60.39        42.77        31.56        25.22 
TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
       30.25         4.31        24.00         3.68         4.70        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS 
       21.01        47.93         3.32         7.17         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 
        4.90         7.13         2.60         0.36         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK 
       55.50         2.66        35.97        12.92        13.48        13.55 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        27.12        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49R 
       46.09        10.36         5.92        10.45        12.43         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 
       13.15        15.35         0.10        13.25        12.46        12.49 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       22.39        15.52        12.33         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 
       10.52        12.00        12.23        12.03        13.18        33.11 
TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        5.16         5.06        29.59         6.35        53.95         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-A7RC TCGA-V5-AASW 
        2.89         1.45        12.69        20.02         3.42         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU 
        4.44        18.81        19.96        22.82        12.43        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7I TCGA-Z6-A8JE 
        8.12        28.11        42.87        11.24        15.91         2.10 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

$`DEL PEAK 14(5Q12.1) WILD-TYPE`
TCGA-2H-A9GH TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 
       31.27         7.69         6.21        20.78        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        9.30         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 
       14.50        12.16        68.02         3.68        41.52        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       21.70        23.18        24.03         6.28         3.16         0.30 
TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OX 
        8.94        19.99        18.35         1.38        29.00         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NJ TCGA-L5-A8NL 
        6.94         8.71        25.12         7.40        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49X TCGA-LN-A4A1 
        7.76        83.24        12.66        13.41         0.10        12.59 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A9FO 
       12.76        12.59         0.10        11.54        13.22         0.13 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A8W5 
        7.82         8.02         7.59        14.70         7.04        15.78 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8ET 
        7.00        20.38         5.29         4.80        15.35         1.55 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR 
       30.71        18.18        46.19        15.06         9.17        10.16 
TCGA-Z6-A8JD 
        3.42 

  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                          0.1                           0.1 
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                       122.10                         83.24 
  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE 
                       12.475                        12.590 
[1] "0.1 - 122.1 (12.5)" "0.1 - 83.2 (12.6)" 
[1] "hr=" "1"  
D45V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 14(5Q12.1) MUTATED         8        3        1        0        21
  DEL PEAK 14(5Q12.1) WILD-TYPE       0        2        6        1        18
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 14(5Q12.1) MUTATED          15        18          7          7
  DEL PEAK 14(5Q12.1) WILD-TYPE        14         7          5          3
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 14(5Q12.1) MUTATED            4        5         3
  DEL PEAK 14(5Q12.1) WILD-TYPE          3        0         1
D45V3, multiclass
            clus
vv           DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  STAGE I                              8                             0
  STAGE IA                             3                             2
  STAGE IB                             1                             6
  STAGE II                             0                             1
  STAGE IIA                           21                            18
  STAGE IIB                           15                            14
  STAGE III                           18                             7
  STAGE IIIA                           7                             5
  STAGE IIIB                           7                             3
  STAGE IIIC                           4                             3
  STAGE IV                             5                             0
  STAGE IVA                            3                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 14(5Q12.1) MUTATED      19 19 53  3
  DEL PEAK 14(5Q12.1) WILD-TYPE    12 17 32  2
D45V4, multiclass
       clus
vv      DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  T0+T1                          19                            12
  T2                             19                            17
  T3                             53                            32
  T4                              3                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 14(5Q12.1) MUTATED   42 41  6  5
  DEL PEAK 14(5Q12.1) WILD-TYPE 29 23  6  3
D45V5, multiclass
    clus
vv   DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  N0                          42                            29
  N1                          41                            23
  N2                           6                             6
  N3                           5                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                               cls
clus                             0  1
  DEL PEAK 14(5Q12.1) MUTATED   75  8
  DEL PEAK 14(5Q12.1) WILD-TYPE 51  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q12.1) MUTATED     75    8
  DEL PEAK 14(5Q12.1) WILD-TYPE   51    1
   clus
vv  DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  0                          75                            51
  1                           8                             1
[1] 2 2
[1] FALSE
D45V7, binary
                               cls
clus                             0  1
  DEL PEAK 14(5Q12.1) MUTATED   12 93
  DEL PEAK 14(5Q12.1) WILD-TYPE 12 56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q12.1) MUTATED     12   93
  DEL PEAK 14(5Q12.1) WILD-TYPE   12   56
        clus
vv       DEL PEAK 14(5Q12.1) MUTATED DEL PEAK 14(5Q12.1) WILD-TYPE
  FEMALE                          12                            12
  MALE                            93                            56
[1] 2 2
[1] FALSE
D45V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(5Q12.1) MUTATED      26                         1    63
  DEL PEAK 14(5Q12.1) WILD-TYPE    15                         1    48
D45V9, multiclass
                           clus
vv                          DEL PEAK 14(5Q12.1) MUTATED
  ASIAN                                              26
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              63
                           clus
vv                          DEL PEAK 14(5Q12.1) WILD-TYPE
  ASIAN                                                15
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V10, binary
                               cls
clus                             0  1
  DEL PEAK 14(5Q12.1) MUTATED    2 44
  DEL PEAK 14(5Q12.1) WILD-TYPE  1 37
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q12.1) MUTATED      2   44
  DEL PEAK 14(5Q12.1) WILD-TYPE    1   37
                        clus
vv                       DEL PEAK 14(5Q12.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          44
                        clus
vv                       DEL PEAK 14(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            37
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 15(6P25.3) MUTATION ANALYSIS
D46V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 15(6P25.3) MUTATED   36 32
  DEL PEAK 15(6P25.3) WILD-TYPE 64 39
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           68                           103 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           32                            39 
$`DEL PEAK 15(6P25.3) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ 
       14.30        58.55         7.63        13.94         8.94         4.21 
TCGA-IG-A3I8 TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5S3 TCGA-IG-A97I 
       33.27        18.64         3.88         0.53        23.41        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A93C TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A43E 
      122.10        60.39        23.18        31.56         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
        0.30         4.31         4.70        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A88Y TCGA-L5-A8NF TCGA-L5-A8NG 
        1.38         3.16         7.13         0.36         2.66        35.97 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L5-A8NT 
       13.48        16.47        13.55        13.22        13.41        27.12 
TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49V TCGA-LN-A49W 
       52.57        10.36         5.92        12.43         0.10        13.25 
TCGA-LN-A4A2 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU 
       12.49        12.33        25.25        13.18        33.11         5.16 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG 
        7.59        14.70         9.30        15.78         2.89        12.69 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW 
       20.02        20.38         5.29         3.42        15.35         9.27 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B 
       12.43        18.31         8.12        18.18        15.06        11.24 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

$`DEL PEAK 15(6P25.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE 
       25.78        31.27         5.92        16.24        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
        6.21        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        9.30        17.03         0.79        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        4.67        14.50        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       42.77        25.41        21.70        25.22        24.03         6.28 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        8.94        24.00         3.68        32.61        19.99        21.01 
TCGA-L5-A4OM TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S 
       47.93        58.59         4.90        29.00         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        8.71         2.60        25.12         7.40         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       55.50        12.92         7.76         5.49        21.37         8.71 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R 
       83.24        46.09        10.45        12.66        13.41         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 
       13.15        15.35         0.10        12.46        12.59        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39         0.10        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       13.22         4.47        10.52        12.00        12.23        12.03 
TCGA-LN-A9FO TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG 
        0.13         7.82         8.02         5.06         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RE TCGA-V5-AASX 
        6.35        53.95         1.45         7.00         4.80         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EY 
       18.81        19.96        22.82         1.55        28.11        30.71 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD 
       42.87        46.19         9.17        15.91        10.16         3.42 
TCGA-Z6-A8JE 
        2.10 

  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                          0.1                           0.1 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                       122.10                         83.24 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                        12.59                         12.59 
[1] "0.1 - 122.1 (12.6)" "0.1 - 83.2 (12.6)" 
[1] "hr=" "1.3"
D46V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 15(6P25.3) MUTATED         5        2        1        0        12
  DEL PEAK 15(6P25.3) WILD-TYPE       3        3        6        1        27
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 15(6P25.3) MUTATED          12        11          4          4
  DEL PEAK 15(6P25.3) WILD-TYPE        17        14          8          6
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 15(6P25.3) MUTATED            5        2         2
  DEL PEAK 15(6P25.3) WILD-TYPE          2        3         2
D46V3, multiclass
            clus
vv           DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  STAGE I                              5                             3
  STAGE IA                             2                             3
  STAGE IB                             1                             6
  STAGE II                             0                             1
  STAGE IIA                           12                            27
  STAGE IIB                           12                            17
  STAGE III                           11                            14
  STAGE IIIA                           4                             8
  STAGE IIIB                           4                             6
  STAGE IIIC                           5                             2
  STAGE IV                             2                             3
  STAGE IVA                            2                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 15(6P25.3) MUTATED      13 12 36  1
  DEL PEAK 15(6P25.3) WILD-TYPE    18 24 49  4
D46V4, multiclass
       clus
vv      DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  T0+T1                          13                            18
  T2                             12                            24
  T3                             36                            49
  T4                              1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 15(6P25.3) MUTATED   27 23  6  6
  DEL PEAK 15(6P25.3) WILD-TYPE 44 41  6  2
D46V5, multiclass
    clus
vv   DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  N0                          27                            44
  N1                          23                            41
  N2                           6                             6
  N3                           6                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                               cls
clus                             0  1
  DEL PEAK 15(6P25.3) MUTATED   46  4
  DEL PEAK 15(6P25.3) WILD-TYPE 80  5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED     46    4
  DEL PEAK 15(6P25.3) WILD-TYPE   80    5
   clus
vv  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  0                          46                            80
  1                           4                             5
[1] 2 2
[1] FALSE
D46V7, binary
                               cls
clus                             0  1
  DEL PEAK 15(6P25.3) MUTATED   10 60
  DEL PEAK 15(6P25.3) WILD-TYPE 14 89
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED     10   60
  DEL PEAK 15(6P25.3) WILD-TYPE   14   89
        clus
vv       DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  FEMALE                          10                            14
  MALE                            60                            89
[1] 2 2
[1] FALSE
D46V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(6P25.3) MUTATED      13                         2    45
  DEL PEAK 15(6P25.3) WILD-TYPE    28                         0    66
D46V9, multiclass
                           clus
vv                          DEL PEAK 15(6P25.3) MUTATED
  ASIAN                                              13
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              45
                           clus
vv                          DEL PEAK 15(6P25.3) WILD-TYPE
  ASIAN                                                28
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V10, binary
                               cls
clus                             0  1
  DEL PEAK 15(6P25.3) MUTATED    3 28
  DEL PEAK 15(6P25.3) WILD-TYPE  0 53
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED      3   28
  DEL PEAK 15(6P25.3) WILD-TYPE    0   53
                        clus
vv                       DEL PEAK 15(6P25.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          28
                        clus
vv                       DEL PEAK 15(6P25.3) WILD-TYPE
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            53
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 16(6Q16.3) MUTATION ANALYSIS
D47V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 16(6Q16.3) MUTATED   30 20
  DEL PEAK 16(6Q16.3) WILD-TYPE 70 51
  DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE 
                           50                           121 
  DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE 
                           20                            51 
$`DEL PEAK 16(6Q16.3) MUTATED`
TCGA-2H-A9GF TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A50L TCGA-IG-A8O2 
       25.78         7.69        33.27        20.09         0.53         4.67 
TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A93E TCGA-L5-A43C 
       14.50        44.75        60.39        42.77        25.22         3.16 
TCGA-L5-A43M TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A88Y TCGA-L5-A8NJ TCGA-L5-A8NK 
        8.94        18.35         3.16         0.36        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49R 
       13.22        13.41        83.24        52.57         5.92         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A4MR 
       13.25         0.10        12.59        22.39        12.33        13.22 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A9FO TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6XG 
       12.33        25.25         0.13         8.02         5.06        29.59 
TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASW 
        2.89        12.69        20.02        20.38         3.42         9.27 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-Z6-A8JD 
       22.82        12.43        18.31         8.12        28.11         3.42 
TCGA-Z6-A8JE TCGA-ZR-A9CJ 
        2.10        19.73 

$`DEL PEAK 16(6Q16.3) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RF TCGA-IG-A3Y9 
        8.94        16.24         4.21        32.45         6.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 
       12.16       122.10        68.02         3.68        41.52        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E 
       21.70        23.18        31.56        24.03         6.28        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        0.30         4.31        24.00         3.68         4.70        32.61 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       19.99        21.01        47.93         3.32         7.17         1.38 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        8.71         2.60        25.12         7.40         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NM 
       55.50         2.66        35.97        12.92        13.48         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ 
        5.49        21.37         8.71        27.12        46.09        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U 
       10.45        12.66        12.43        13.41        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
        0.10        12.46        12.49        12.76        12.59         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       15.52        11.54         4.47        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ 
       12.03        13.18        33.11         5.16         7.82         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
       14.70         7.04         6.35        53.95         9.30        15.78 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX 
        1.45         7.00         5.29         4.80        15.35         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.81        19.96         1.55        30.71        18.18        42.87 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        15.06        11.24         9.17        15.91        10.16 
TCGA-Z6-AAPN 
        2.66 

  DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE 
                          0.1                           0.1 
  DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE 
                        83.24                        122.10 
  DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE 
                        13.22                         12.43 
[1] "0.1 - 83.2 (13.2)"  "0.1 - 122.1 (12.4)"
[1] "hr=" "1.1"
D47V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 16(6Q16.3) MUTATED         1        1        1        0        12
  DEL PEAK 16(6Q16.3) WILD-TYPE       7        4        6        1        27
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 16(6Q16.3) MUTATED           9         8          4          2
  DEL PEAK 16(6Q16.3) WILD-TYPE        20        17          8          8
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 16(6Q16.3) MUTATED            1        1         1
  DEL PEAK 16(6Q16.3) WILD-TYPE          6        4         3
D47V3, multiclass
            clus
vv           DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE
  STAGE I                              1                             7
  STAGE IA                             1                             4
  STAGE IB                             1                             6
  STAGE II                             0                             1
  STAGE IIA                           12                            27
  STAGE IIB                            9                            20
  STAGE III                            8                            17
  STAGE IIIA                           4                             8
  STAGE IIIB                           2                             8
  STAGE IIIC                           1                             6
  STAGE IV                             1                             4
  STAGE IVA                            1                             3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 16(6Q16.3) MUTATED       7 10 25  1
  DEL PEAK 16(6Q16.3) WILD-TYPE    24 26 60  4
D47V4, multiclass
       clus
vv      DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE
  T0+T1                           7                            24
  T2                             10                            26
  T3                             25                            60
  T4                              1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 16(6Q16.3) MUTATED   18 20  3  1
  DEL PEAK 16(6Q16.3) WILD-TYPE 53 44  9  7
D47V5, multiclass
    clus
vv   DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE
  N0                          18                            53
  N1                          20                            44
  N2                           3                             9
  N3                           1                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                               cls
clus                             0  1
  DEL PEAK 16(6Q16.3) MUTATED   34  2
  DEL PEAK 16(6Q16.3) WILD-TYPE 92  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6Q16.3) MUTATED     34    2
  DEL PEAK 16(6Q16.3) WILD-TYPE   92    7
   clus
vv  DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE
  0                          34                            92
  1                           2                             7
[1] 2 2
[1] FALSE
D47V7, binary
                               cls
clus                              0   1
  DEL PEAK 16(6Q16.3) MUTATED     3  48
  DEL PEAK 16(6Q16.3) WILD-TYPE  21 101
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6Q16.3) MUTATED      3   48
  DEL PEAK 16(6Q16.3) WILD-TYPE   21  101
        clus
vv       DEL PEAK 16(6Q16.3) MUTATED DEL PEAK 16(6Q16.3) WILD-TYPE
  FEMALE                           3                            21
  MALE                            48                           101
[1] 2 2
[1] FALSE
D47V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(6Q16.3) MUTATED      17                         1    29
  DEL PEAK 16(6Q16.3) WILD-TYPE    24                         1    82
D47V9, multiclass
                           clus
vv                          DEL PEAK 16(6Q16.3) MUTATED
  ASIAN                                              17
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              29
                           clus
vv                          DEL PEAK 16(6Q16.3) WILD-TYPE
  ASIAN                                                24
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V10, binary
                               cls
clus                             0  1
  DEL PEAK 16(6Q16.3) MUTATED    1 28
  DEL PEAK 16(6Q16.3) WILD-TYPE  2 53
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6Q16.3) MUTATED      1   28
  DEL PEAK 16(6Q16.3) WILD-TYPE    2   53
                        clus
vv                       DEL PEAK 16(6Q16.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          28
                        clus
vv                       DEL PEAK 16(6Q16.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            53
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 17(6Q26) MUTATION ANALYSIS
D48V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 17(6Q26) MUTATED   31 17
  DEL PEAK 17(6Q26) WILD-TYPE 69 54
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         48                         123 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         17                          54 
$`DEL PEAK 17(6Q26) MUTATED`
TCGA-2H-A9GF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FH 
       25.78        33.27        20.09         4.67        14.50        42.77 
TCGA-JY-A938 TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OR 
       25.41        25.22         3.16         4.31         8.94         3.16 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        0.36         7.40        13.48        16.47        13.55        13.22 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49R TCGA-LN-A49W 
       13.41        83.24        52.57         5.92         0.10        13.25 
TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4MQ 
        0.10        12.59        12.49        12.76        22.39        12.33 
TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-R6-A6DN TCGA-R6-A6XG 
       13.22        25.25        12.00        12.23         8.02        29.59 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW 
        1.45        12.69        20.38         3.42         4.80         9.27 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EX TCGA-Z6-A8JD TCGA-ZR-A9CJ 
       22.82        12.43         8.12        28.11         3.42        19.73 

$`DEL PEAK 17(6Q26) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
        8.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
        9.96        14.86        12.16       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       68.02         3.68        41.52        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OE TCGA-L5-A4OF 
       24.03         6.28        30.25         0.30        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        4.70        32.61        19.99        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         1.38        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        3.95         3.02        55.50         2.66        35.97        12.92 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NW 
        7.76         5.49        21.37         8.71        27.12        46.09 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S 
       10.36        10.45        12.66        12.43        13.41        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 
       15.35         0.10        12.46        12.59         0.10        15.52 
TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ 
       11.54         4.47        12.33        10.52        12.03        13.18 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.13        33.11         5.16         7.82         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
       14.70         7.04         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASX 
        2.89         7.00        20.02         5.29        15.35         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ 
       18.81        19.96         1.55        18.31        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       42.87        46.19        15.06        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-Z6-AAPN 
       10.16         2.10         2.66 

  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                        0.1                         0.1 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                      83.24                      122.10 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                     12.725                      12.430 
[1] "0.1 - 83.2 (12.7)"  "0.1 - 122.1 (12.4)"
[1] "hr=" "1.2"
D48V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 17(6Q26) MUTATED         0        1        2        0        15
  DEL PEAK 17(6Q26) WILD-TYPE       8        4        5        1        24
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 17(6Q26) MUTATED           6        10          1          2
  DEL PEAK 17(6Q26) WILD-TYPE        23        15         11          8
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 17(6Q26) MUTATED            1        0         1
  DEL PEAK 17(6Q26) WILD-TYPE          6        5         3
D48V3, multiclass
            clus
vv           DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  STAGE I                            0                           8
  STAGE IA                           1                           4
  STAGE IB                           2                           5
  STAGE II                           0                           1
  STAGE IIA                         15                          24
  STAGE IIB                          6                          23
  STAGE III                         10                          15
  STAGE IIIA                         1                          11
  STAGE IIIB                         2                           8
  STAGE IIIC                         1                           6
  STAGE IV                           0                           5
  STAGE IVA                          1                           3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  DEL PEAK 17(6Q26) MUTATED       5  8 27  1
  DEL PEAK 17(6Q26) WILD-TYPE    26 28 58  4
D48V4, multiclass
       clus
vv      DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  T0+T1                         5                          26
  T2                            8                          28
  T3                           27                          58
  T4                            1                           4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2 N3
  DEL PEAK 17(6Q26) MUTATED   22 14  3  1
  DEL PEAK 17(6Q26) WILD-TYPE 49 50  9  7
D48V5, multiclass
    clus
vv   DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  N0                        22                          49
  N1                        14                          50
  N2                         3                           9
  N3                         1                           7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                             cls
clus                           0  1
  DEL PEAK 17(6Q26) MUTATED   34  1
  DEL PEAK 17(6Q26) WILD-TYPE 92  8
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED     34    1
  DEL PEAK 17(6Q26) WILD-TYPE   92    8
   clus
vv  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  0                        34                          92
  1                         1                           8
[1] 2 2
[1] FALSE
D48V7, binary
                             cls
clus                            0   1
  DEL PEAK 17(6Q26) MUTATED     4  44
  DEL PEAK 17(6Q26) WILD-TYPE  20 105
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED      4   44
  DEL PEAK 17(6Q26) WILD-TYPE   20  105
        clus
vv       DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  FEMALE                         4                          20
  MALE                          44                         105
[1] 2 2
[1] FALSE
D48V8, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(6Q26) MUTATED      16                         1    27
  DEL PEAK 17(6Q26) WILD-TYPE    25                         1    84
D48V9, multiclass
                           clus
vv                          DEL PEAK 17(6Q26) MUTATED
  ASIAN                                            16
  BLACK OR AFRICAN AMERICAN                         1
  WHITE                                            27
                           clus
vv                          DEL PEAK 17(6Q26) WILD-TYPE
  ASIAN                                              25
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V10, binary
                             cls
clus                           0  1
  DEL PEAK 17(6Q26) MUTATED    1 25
  DEL PEAK 17(6Q26) WILD-TYPE  2 56
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED      1   25
  DEL PEAK 17(6Q26) WILD-TYPE    2   56
                        clus
vv                       DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             1                           2
  NOT HISPANIC OR LATINO                        25                          56
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 18(7Q31.1) MUTATION ANALYSIS
D49V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 18(7Q31.1) MUTATED   29 26
  DEL PEAK 18(7Q31.1) WILD-TYPE 71 45
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                           55                           116 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                           26                            45 
$`DEL PEAK 18(7Q31.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ 
       25.78        14.30         7.63         5.92         8.94         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS 
       32.45         7.69         0.85         2.63        20.12         3.88 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6FH TCGA-L5-A43C 
       17.03         0.79         9.96         4.67        42.77         3.16 
TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88V 
        3.68        47.93         3.16        29.00         6.94         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
       25.12         0.36        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NR TCGA-L7-A6VZ TCGA-LN-A49N TCGA-LN-A49R 
       16.47        13.55         8.71        10.36        12.43         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MR 
       13.25         0.10        12.46        12.76         0.10        13.22 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-R6-A6KZ TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-V5-A7RB 
        0.13        33.11         5.06        15.78         2.89         5.29 
TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
        4.44        22.82         1.55        15.06         9.17        15.91 
TCGA-Z6-AAPN 
        2.66 

$`DEL PEAK 18(7Q31.1) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GO TCGA-IC-A6RF TCGA-IG-A3I8 
       31.27        58.55        13.94        16.24         6.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5S3 
       20.09        20.78        18.64         9.30         0.53        23.41 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       12.82        14.86        14.50        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 
       60.39        68.02         3.68        41.52        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E 
       23.18        31.56        25.22        24.03         6.28        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH 
        0.30         4.31         8.94        24.00         4.70        32.61 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       19.99        21.01        18.35         3.32         7.17         1.38 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88Z 
       58.59         4.90         7.13         7.43         8.71         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NG TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
        3.95         3.02        35.97        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37        13.41        27.12        83.24        52.57        46.09 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U 
        5.92        10.45        12.66        13.41        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
        0.10        12.59        12.49        12.59        22.39        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       11.54        12.33         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.00        12.23        12.03        13.18         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         7.59        14.70         7.04        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
       53.95         9.30         1.45        12.69         7.00        20.02 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO 
       20.38         3.42         4.80        15.35         9.27        18.81 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       19.96        12.43        18.31         8.12        28.11        30.71 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-X8-AAAR TCGA-Z6-A8JD 
       18.18        42.87        46.19        11.24        10.16         3.42 
TCGA-Z6-A8JE TCGA-ZR-A9CJ 
        2.10        19.73 

  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                          0.1                           0.1 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                         55.5                         122.1 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                        8.940                        13.165 
[1] "0.1 - 55.5 (8.9)"   "0.1 - 122.1 (13.2)"
[1] "hr=" "1.9"
D49V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 18(7Q31.1) MUTATED         0        2        2        1        11
  DEL PEAK 18(7Q31.1) WILD-TYPE       8        3        5        0        28
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 18(7Q31.1) MUTATED           7        15          4          2
  DEL PEAK 18(7Q31.1) WILD-TYPE        22        10          8          8
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 18(7Q31.1) MUTATED            2        1         2
  DEL PEAK 18(7Q31.1) WILD-TYPE          5        4         2
D49V3, multiclass
            clus
vv           DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  STAGE I                              0                             8
  STAGE IA                             2                             3
  STAGE IB                             2                             5
  STAGE II                             1                             0
  STAGE IIA                           11                            28
  STAGE IIB                            7                            22
  STAGE III                           15                            10
  STAGE IIIA                           4                             8
  STAGE IIIB                           2                             8
  STAGE IIIC                           2                             5
  STAGE IV                             1                             4
  STAGE IVA                            2                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 18(7Q31.1) MUTATED       9  9 31  2
  DEL PEAK 18(7Q31.1) WILD-TYPE    22 27 54  3
D49V4, multiclass
       clus
vv      DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  T0+T1                           9                            22
  T2                              9                            27
  T3                             31                            54
  T4                              2                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 18(7Q31.1) MUTATED   21 25  3  2
  DEL PEAK 18(7Q31.1) WILD-TYPE 50 39  9  6
D49V5, multiclass
    clus
vv   DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  N0                          21                            50
  N1                          25                            39
  N2                           3                             9
  N3                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                               cls
clus                             0  1
  DEL PEAK 18(7Q31.1) MUTATED   39  3
  DEL PEAK 18(7Q31.1) WILD-TYPE 87  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(7Q31.1) MUTATED     39    3
  DEL PEAK 18(7Q31.1) WILD-TYPE   87    6
   clus
vv  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  0                          39                            87
  1                           3                             6
[1] 2 2
[1] FALSE
D49V7, binary
                               cls
clus                             0  1
  DEL PEAK 18(7Q31.1) MUTATED    4 51
  DEL PEAK 18(7Q31.1) WILD-TYPE 20 98
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(7Q31.1) MUTATED      4   51
  DEL PEAK 18(7Q31.1) WILD-TYPE   20   98
        clus
vv       DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  FEMALE                           4                            20
  MALE                            51                            98
[1] 2 2
[1] FALSE
D49V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(7Q31.1) MUTATED      10                         0    34
  DEL PEAK 18(7Q31.1) WILD-TYPE    31                         2    77
D49V9, multiclass
                           clus
vv                          DEL PEAK 18(7Q31.1) MUTATED
  ASIAN                                              10
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              34
                           clus
vv                          DEL PEAK 18(7Q31.1) WILD-TYPE
  ASIAN                                                31
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V10, binary
                               cls
clus                             0  1
  DEL PEAK 18(7Q31.1) MUTATED    1 23
  DEL PEAK 18(7Q31.1) WILD-TYPE  2 58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(7Q31.1) MUTATED      1   23
  DEL PEAK 18(7Q31.1) WILD-TYPE    2   58
                        clus
vv                       DEL PEAK 18(7Q31.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          23
                        clus
vv                       DEL PEAK 18(7Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            58
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 19(7Q36.3) MUTATION ANALYSIS
D50V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 19(7Q36.3) MUTATED   38 28
  DEL PEAK 19(7Q36.3) WILD-TYPE 62 43
  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE 
                           66                           105 
  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE 
                           28                            43 
$`DEL PEAK 19(7Q36.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        14.30         7.63         5.92         8.94        16.24 
TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A51D 
        4.21         7.69         0.85        20.12        18.64        17.03 
TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
        0.79         9.96        14.50        44.75        68.02         3.68 
TCGA-JY-A6FH TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON 
       42.77        25.22         3.16         3.68        47.93        18.35 
TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S 
        7.17         3.16        58.59        29.00         7.13         6.94 
TCGA-L5-A88Y TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK 
        0.36        55.50         2.66        12.92        13.48        13.55 
TCGA-L5-A8NR TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
        8.71        10.36        10.45        13.41         0.10        13.15 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ 
        0.10        12.46        12.59        12.76         0.10        12.33 
TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-R6-A6XG 
       13.22        25.25        33.11         7.82         5.06        29.59 
TCGA-R6-A8W5 TCGA-V5-A7RB TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET 
       15.78         5.29         4.44        18.81        12.43         1.55 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-AAPN 
       15.06        11.24         9.17        15.91         3.42         2.66 

$`DEL PEAK 19(7Q36.3) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IC-A6RF TCGA-IG-A3I8 
       31.27        58.55        13.94        32.45         6.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
       20.09        20.78         2.63         3.88         9.30         0.53 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
       23.41        12.82        14.86         4.67        12.16       122.10 
TCGA-JY-A6FB TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       60.39        41.52        25.41        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
       24.03         6.28        30.25         0.30         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO 
       24.00         4.70        32.61        19.99        21.01         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        1.38         4.90         7.43         8.71         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NG TCGA-L5-A8NJ TCGA-L5-A8NL 
        7.40         3.95         3.02        35.97        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
        7.76         5.49        21.37        13.41        27.12        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49U 
       52.57        46.09         5.92        12.66        12.43        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
        0.10        13.25        12.49        12.59        22.39        15.52 
TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       11.54         4.47        12.33        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.03        13.18         0.13         5.16         8.02         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 
       14.70         7.04         6.35        53.95         9.30         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC 
        1.45        12.69         7.00        20.02        20.38         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8EU 
        4.80        15.35         9.27        19.96        22.82        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        30.71        18.18        42.87        46.19 
TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       10.16         2.10        19.73 

  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE 
                          0.1                           0.1 
  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE 
                        68.02                        122.10 
  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE 
                        12.38                         12.69 
[1] "0.1 - 68.0 (12.4)"  "0.1 - 122.1 (12.7)"
[1] "hr=" "1.2"
D50V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 19(7Q36.3) MUTATED         0        3        2        1        15
  DEL PEAK 19(7Q36.3) WILD-TYPE       8        2        5        0        24
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 19(7Q36.3) MUTATED          12        14          4          2
  DEL PEAK 19(7Q36.3) WILD-TYPE        17        11          8          8
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 19(7Q36.3) MUTATED            2        2         3
  DEL PEAK 19(7Q36.3) WILD-TYPE          5        3         1
D50V3, multiclass
            clus
vv           DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE
  STAGE I                              0                             8
  STAGE IA                             3                             2
  STAGE IB                             2                             5
  STAGE II                             1                             0
  STAGE IIA                           15                            24
  STAGE IIB                           12                            17
  STAGE III                           14                            11
  STAGE IIIA                           4                             8
  STAGE IIIB                           2                             8
  STAGE IIIC                           2                             5
  STAGE IV                             2                             3
  STAGE IVA                            3                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 19(7Q36.3) MUTATED      11 13 35  3
  DEL PEAK 19(7Q36.3) WILD-TYPE    20 23 50  2
D50V4, multiclass
       clus
vv      DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE
  T0+T1                          11                            20
  T2                             13                            23
  T3                             35                            50
  T4                              3                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 19(7Q36.3) MUTATED   27 29  2  3
  DEL PEAK 19(7Q36.3) WILD-TYPE 44 35 10  5
D50V5, multiclass
    clus
vv   DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE
  N0                          27                            44
  N1                          29                            35
  N2                           2                            10
  N3                           3                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                               cls
clus                             0  1
  DEL PEAK 19(7Q36.3) MUTATED   48  5
  DEL PEAK 19(7Q36.3) WILD-TYPE 78  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(7Q36.3) MUTATED     48    5
  DEL PEAK 19(7Q36.3) WILD-TYPE   78    4
   clus
vv  DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE
  0                          48                            78
  1                           5                             4
[1] 2 2
[1] FALSE
D50V7, binary
                               cls
clus                             0  1
  DEL PEAK 19(7Q36.3) MUTATED    9 57
  DEL PEAK 19(7Q36.3) WILD-TYPE 15 92
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(7Q36.3) MUTATED      9   57
  DEL PEAK 19(7Q36.3) WILD-TYPE   15   92
        clus
vv       DEL PEAK 19(7Q36.3) MUTATED DEL PEAK 19(7Q36.3) WILD-TYPE
  FEMALE                           9                            15
  MALE                            57                            92
[1] 2 2
[1] FALSE
D50V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(7Q36.3) MUTATED      15                         0    38
  DEL PEAK 19(7Q36.3) WILD-TYPE    26                         2    73
D50V9, multiclass
                           clus
vv                          DEL PEAK 19(7Q36.3) MUTATED
  ASIAN                                              15
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              38
                           clus
vv                          DEL PEAK 19(7Q36.3) WILD-TYPE
  ASIAN                                                26
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V10, binary
                               cls
clus                             0  1
  DEL PEAK 19(7Q36.3) MUTATED    1 28
  DEL PEAK 19(7Q36.3) WILD-TYPE  2 53
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(7Q36.3) MUTATED      1   28
  DEL PEAK 19(7Q36.3) WILD-TYPE    2   53
                        clus
vv                       DEL PEAK 19(7Q36.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          28
                        clus
vv                       DEL PEAK 19(7Q36.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            53
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 20(8P23.2) MUTATION ANALYSIS
D51V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 20(8P23.2) MUTATED   50 30
  DEL PEAK 20(8P23.2) WILD-TYPE 50 41
  DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE 
                           80                            91 
  DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE 
                           30                            41 
$`DEL PEAK 20(8P23.2) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3Y9 
       25.78        31.27         5.92        13.94         4.21         0.85 
TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
        2.63        18.64         3.88         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE 
       23.41         9.96        14.50        44.75        60.39         3.68 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       42.77        25.41        23.18        31.56        25.22        24.03 
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OT 
        4.31        24.00         3.68        32.61         3.32         4.90 
TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NL 
        7.43         2.60         7.40         3.95         2.66        13.22 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L7-A6VZ TCGA-LN-A49L 
        5.49         8.71        13.41        27.12        10.36        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 
       12.66        12.43        13.15        13.25        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
       12.49        12.76        22.39        12.33        13.22        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
       25.25        12.00         0.13         5.16         7.82         8.02 
TCGA-R6-A6Y0 TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       53.95         1.45        20.38         5.29         3.42         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       15.35         9.27        12.43        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       30.71        42.87        15.06        11.24         9.17        15.91 
TCGA-Z6-A8JE TCGA-Z6-AAPN 
        2.10         2.66 

$`DEL PEAK 20(8P23.2) WILD-TYPE`
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR 
       14.30        58.55         7.63         8.94        16.24        32.45 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC 
        7.69         6.21        33.27        20.09        20.78        20.12 
TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
        9.30        12.82        14.86         4.67        12.16       122.10 
TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A939 TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       68.02        41.52        21.70         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
        0.30         8.94         4.70        19.99        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU 
       18.35         7.17         1.38         3.16        58.59        29.00 
TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A893 
        7.13         6.94         8.71        25.12         0.36         3.02 
TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50        35.97        12.92        13.48        16.47        13.55 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K 
        7.76        21.37        83.24        52.57        46.09         5.92 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A4 
       13.41         0.10        15.35         0.10         0.10        12.59 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX 
        0.10        15.52        11.54         4.47        10.52        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.03        13.18        33.11         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04        29.59         6.35         9.30        15.78         2.89 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       12.69         7.00        20.02         4.44        18.81        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-X8-AAAR TCGA-Z6-A8JD 
       22.82         1.55        18.18        46.19        10.16         3.42 
TCGA-ZR-A9CJ 
       19.73 

  DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE 
                         0.13                          0.10 
  DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE 
                        60.39                        122.10 
  DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE 
                        12.43                         12.92 
[1] "0.1 - 60.4 (12.4)"  "0.1 - 122.1 (12.9)"
[1] "hr=" "1"  
D51V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 20(8P23.2) MUTATED         2        0        4        0        15
  DEL PEAK 20(8P23.2) WILD-TYPE       6        5        3        1        24
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 20(8P23.2) MUTATED          18        13          7          6
  DEL PEAK 20(8P23.2) WILD-TYPE        11        12          5          4
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 20(8P23.2) MUTATED            4        3         2
  DEL PEAK 20(8P23.2) WILD-TYPE          3        2         2
D51V3, multiclass
            clus
vv           DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE
  STAGE I                              2                             6
  STAGE IA                             0                             5
  STAGE IB                             4                             3
  STAGE II                             0                             1
  STAGE IIA                           15                            24
  STAGE IIB                           18                            11
  STAGE III                           13                            12
  STAGE IIIA                           7                             5
  STAGE IIIB                           6                             4
  STAGE IIIC                           4                             3
  STAGE IV                             3                             2
  STAGE IVA                            2                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 20(8P23.2) MUTATED      12 19 42  3
  DEL PEAK 20(8P23.2) WILD-TYPE    19 17 43  2
D51V4, multiclass
       clus
vv      DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE
  T0+T1                          12                            19
  T2                             19                            17
  T3                             42                            43
  T4                              3                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 20(8P23.2) MUTATED   28 35  7  5
  DEL PEAK 20(8P23.2) WILD-TYPE 43 29  5  3
D51V5, multiclass
    clus
vv   DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE
  N0                          28                            43
  N1                          35                            29
  N2                           7                             5
  N3                           5                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                               cls
clus                             0  1
  DEL PEAK 20(8P23.2) MUTATED   63  5
  DEL PEAK 20(8P23.2) WILD-TYPE 63  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(8P23.2) MUTATED     63    5
  DEL PEAK 20(8P23.2) WILD-TYPE   63    4
   clus
vv  DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE
  0                          63                            63
  1                           5                             4
[1] 2 2
[1] FALSE
D51V7, binary
                               cls
clus                             0  1
  DEL PEAK 20(8P23.2) MUTATED    8 73
  DEL PEAK 20(8P23.2) WILD-TYPE 16 76
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(8P23.2) MUTATED      8   73
  DEL PEAK 20(8P23.2) WILD-TYPE   16   76
        clus
vv       DEL PEAK 20(8P23.2) MUTATED DEL PEAK 20(8P23.2) WILD-TYPE
  FEMALE                           8                            16
  MALE                            73                            76
[1] 2 2
[1] FALSE
D51V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(8P23.2) MUTATED      22                         2    47
  DEL PEAK 20(8P23.2) WILD-TYPE    19                         0    64
D51V9, multiclass
                           clus
vv                          DEL PEAK 20(8P23.2) MUTATED
  ASIAN                                              22
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              47
                           clus
vv                          DEL PEAK 20(8P23.2) WILD-TYPE
  ASIAN                                                19
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V10, binary
                               cls
clus                             0  1
  DEL PEAK 20(8P23.2) MUTATED    1 39
  DEL PEAK 20(8P23.2) WILD-TYPE  2 42
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(8P23.2) MUTATED      1   39
  DEL PEAK 20(8P23.2) WILD-TYPE    2   42
                        clus
vv                       DEL PEAK 20(8P23.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          39
                        clus
vv                       DEL PEAK 20(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            42
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 21(8P12) MUTATION ANALYSIS
D52V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 21(8P12) MUTATED   39 28
  DEL PEAK 21(8P12) WILD-TYPE 61 43
  DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE 
                         67                         104 
  DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE 
                         28                          43 
$`DEL PEAK 21(8P12) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IC-A6RE 
       25.78        31.27         5.92        13.94         4.21         7.69 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 
        0.85         2.63        20.12        18.64         0.53         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FH 
       23.41         9.96        14.50        44.75        60.39        42.77 
TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OH 
       25.41        23.18        25.22         4.31        24.00        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OX TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE 
       21.01         3.32         7.43         7.40         3.95        55.50 
TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
        2.66        13.48         5.49         8.71        13.41        27.12 
TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 
       10.45        12.43        13.15        13.25        12.46        12.49 
TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       22.39        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A7HW TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6XG TCGA-R6-A8WC TCGA-RE-A7BO 
       12.00         7.82         8.02        29.59         1.45         7.00 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8Q7 
        5.29         3.42         4.80        18.31        28.11        42.87 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JE TCGA-Z6-AAPN 
       15.06        11.24         9.17        15.91         2.10         2.66 
TCGA-ZR-A9CJ 
       19.73 

$`DEL PEAK 21(8P12) WILD-TYPE`
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR 
       14.30        58.55         7.63         8.94        16.24        32.45 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT 
        6.21        33.27        20.09        20.78         3.88         9.30 
TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
       17.03        12.82        14.86         4.67        12.16       122.10 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F 
       68.02         3.68        41.52        21.70        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OF 
        6.28         3.16        30.25         0.30         8.94         3.68 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
        4.70        19.99        47.93        18.35         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S 
        3.16        58.59         4.90        29.00         7.13         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NG 
        8.71         2.60        25.12         0.36         3.02        35.97 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ 
       12.92        16.47        13.55        13.22         7.76        21.37 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M 
       83.24        52.57        46.09        10.36         5.92        12.66 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A1 
       13.41         0.10        15.35         0.10         0.10        12.59 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.76        12.59         0.10        15.52        25.25        10.52 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU 
       12.23        12.03        13.18         0.13        33.11         5.16 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.59         5.06        14.70         7.04         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW 
        9.30        15.78         2.89        12.69        20.02        20.38 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         4.44        18.81        19.96        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D 
       12.43         1.55         8.12        30.71        18.18        46.19 
TCGA-X8-AAAR TCGA-Z6-A8JD 
       10.16         3.42 

  DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE 
                       0.53                        0.10 
  DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE 
                      60.39                      122.10 
  DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE 
                     12.430                      12.675 
[1] "0.5 - 60.4 (12.4)"  "0.1 - 122.1 (12.7)"
[1] "hr=" "1.2"
D52V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 21(8P12) MUTATED         3        0        2        0        11
  DEL PEAK 21(8P12) WILD-TYPE       5        5        5        1        28
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 21(8P12) MUTATED          18         9          8          3
  DEL PEAK 21(8P12) WILD-TYPE        11        16          4          7
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 21(8P12) MUTATED            3        3         2
  DEL PEAK 21(8P12) WILD-TYPE          4        2         2
D52V3, multiclass
            clus
vv           DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE
  STAGE I                            3                           5
  STAGE IA                           0                           5
  STAGE IB                           2                           5
  STAGE II                           0                           1
  STAGE IIA                         11                          28
  STAGE IIB                         18                          11
  STAGE III                          9                          16
  STAGE IIIA                         8                           4
  STAGE IIIB                         3                           7
  STAGE IIIC                         3                           4
  STAGE IV                           3                           2
  STAGE IVA                          2                           2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  DEL PEAK 21(8P12) MUTATED      13 15 34  2
  DEL PEAK 21(8P12) WILD-TYPE    18 21 51  3
D52V4, multiclass
       clus
vv      DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE
  T0+T1                        13                          18
  T2                           15                          21
  T3                           34                          51
  T4                            2                           3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2 N3
  DEL PEAK 21(8P12) MUTATED   22 33  4  4
  DEL PEAK 21(8P12) WILD-TYPE 49 31  8  4
D52V5, multiclass
    clus
vv   DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE
  N0                        22                          49
  N1                        33                          31
  N2                         4                           8
  N3                         4                           4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                             cls
clus                           0  1
  DEL PEAK 21(8P12) MUTATED   55  5
  DEL PEAK 21(8P12) WILD-TYPE 71  4
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 21(8P12) MUTATED     55    5
  DEL PEAK 21(8P12) WILD-TYPE   71    4
   clus
vv  DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE
  0                        55                          71
  1                         5                           4
[1] 2 2
[1] FALSE
D52V7, binary
                             cls
clus                           0  1
  DEL PEAK 21(8P12) MUTATED    7 61
  DEL PEAK 21(8P12) WILD-TYPE 17 88
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 21(8P12) MUTATED      7   61
  DEL PEAK 21(8P12) WILD-TYPE   17   88
        clus
vv       DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE
  FEMALE                         7                          17
  MALE                          61                          88
[1] 2 2
[1] FALSE
D52V8, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(8P12) MUTATED      18                         1    40
  DEL PEAK 21(8P12) WILD-TYPE    23                         1    71
D52V9, multiclass
                           clus
vv                          DEL PEAK 21(8P12) MUTATED
  ASIAN                                            18
  BLACK OR AFRICAN AMERICAN                         1
  WHITE                                            40
                           clus
vv                          DEL PEAK 21(8P12) WILD-TYPE
  ASIAN                                              23
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V10, binary
                             cls
clus                           0  1
  DEL PEAK 21(8P12) MUTATED    1 33
  DEL PEAK 21(8P12) WILD-TYPE  2 48
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 21(8P12) MUTATED      1   33
  DEL PEAK 21(8P12) WILD-TYPE    2   48
                        clus
vv                       DEL PEAK 21(8P12) MUTATED DEL PEAK 21(8P12) WILD-TYPE
  HISPANIC OR LATINO                             1                           2
  NOT HISPANIC OR LATINO                        33                          48
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 22(9P23) MUTATION ANALYSIS
D53V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 22(9P23) MUTATED   60 40
  DEL PEAK 22(9P23) WILD-TYPE 40 31
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                        100                          71 
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                         40                          31 
$`DEL PEAK 22(9P23) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27        14.30         7.63         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        4.21        32.45         7.69        20.12        18.64         3.88 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
        0.53         0.79        23.41         4.67        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A938 TCGA-JY-A93D TCGA-JY-A93E 
       44.75        60.39        68.02        25.41        31.56        25.22 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4ON 
        3.16         0.30         8.94         3.68        32.61        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX 
        3.32         7.17         3.16        58.59         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        6.94         2.60         3.95        55.50         2.66        35.97 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.48        16.47        13.22         8.71        13.41        83.24 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X 
       10.45        12.66         0.10        15.35        13.25         0.10 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.46        12.59        12.49        12.76        22.39         0.10 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       15.52        12.33        13.22        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU 
       12.00        12.23        12.03         0.13        33.11         5.16 
TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC 
        5.06        29.59         6.35         9.30        15.78         1.45 
TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69        20.02        20.38         5.29         3.42         4.80 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         4.44        18.81        19.96        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4D 
        1.55        18.31         8.12        28.11        42.87        46.19 
TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       10.16         3.42         2.66        19.73 

$`DEL PEAK 22(9P23) WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
       58.55         5.92        13.94         6.21        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 
        0.85        20.78         2.63         9.30        17.03        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
        9.96        14.86       122.10         3.68        41.52        42.77 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43J 
       21.70        23.18        24.03         6.28        30.25         4.31 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OQ 
       24.00         4.70        19.99        21.01        47.93         1.38 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
        4.90        29.00         8.71        25.12         0.36         7.40 
TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
        3.02        12.92        13.55         7.76         5.49        21.37 
TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N 
       27.12        52.57        46.09        10.36         5.92        12.43 
TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A4A4 TCGA-LN-A4A9 TCGA-LN-A5U5 
       13.41        13.15         0.10        12.59        11.54         4.47 
TCGA-LN-A7HZ TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       13.18         7.82         8.02         7.59        14.70         7.04 
TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-V5-AASV TCGA-VR-A8EY TCGA-VR-A8EZ 
       53.95         2.89         7.00        15.35        30.71        18.18 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JE 
       15.06        11.24         9.17        15.91         2.10 

  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                        0.1                         0.1 
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                      83.24                      122.10 
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                     12.445                      12.920 
[1] "0.1 - 83.2 (12.4)"  "0.1 - 122.1 (12.9)"
[1] "hr=" "1"  
D53V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 22(9P23) MUTATED         2        2        5        1        24
  DEL PEAK 22(9P23) WILD-TYPE       6        3        2        0        15
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 22(9P23) MUTATED          16        19          5          6
  DEL PEAK 22(9P23) WILD-TYPE        13         6          7          4
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 22(9P23) MUTATED            3        1         4
  DEL PEAK 22(9P23) WILD-TYPE          4        4         0
D53V3, multiclass
            clus
vv           DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  STAGE I                            2                           6
  STAGE IA                           2                           3
  STAGE IB                           5                           2
  STAGE II                           1                           0
  STAGE IIA                         24                          15
  STAGE IIB                         16                          13
  STAGE III                         19                           6
  STAGE IIIA                         5                           7
  STAGE IIIB                         6                           4
  STAGE IIIC                         3                           4
  STAGE IV                           1                           4
  STAGE IVA                          4                           0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  DEL PEAK 22(9P23) MUTATED      15 24 52  1
  DEL PEAK 22(9P23) WILD-TYPE    16 12 33  4
D53V4, multiclass
       clus
vv      DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  T0+T1                        15                          16
  T2                           24                          12
  T3                           52                          33
  T4                            1                           4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2 N3
  DEL PEAK 22(9P23) MUTATED   38 44  6  3
  DEL PEAK 22(9P23) WILD-TYPE 33 20  6  5
D53V5, multiclass
    clus
vv   DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  N0                        38                          33
  N1                        44                          20
  N2                         6                           6
  N3                         3                           5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                             cls
clus                           0  1
  DEL PEAK 22(9P23) MUTATED   75  5
  DEL PEAK 22(9P23) WILD-TYPE 51  4
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 22(9P23) MUTATED     75    5
  DEL PEAK 22(9P23) WILD-TYPE   51    4
   clus
vv  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  0                        75                          51
  1                         5                           4
[1] 2 2
[1] FALSE
D53V7, binary
                             cls
clus                           0  1
  DEL PEAK 22(9P23) MUTATED    8 94
  DEL PEAK 22(9P23) WILD-TYPE 16 55
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 22(9P23) MUTATED      8   94
  DEL PEAK 22(9P23) WILD-TYPE   16   55
        clus
vv       DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  FEMALE                         8                          16
  MALE                          94                          55
[1] 2 2
[1] FALSE
D53V8, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(9P23) MUTATED      30                         1    56
  DEL PEAK 22(9P23) WILD-TYPE    11                         1    55
D53V9, multiclass
                           clus
vv                          DEL PEAK 22(9P23) MUTATED
  ASIAN                                            30
  BLACK OR AFRICAN AMERICAN                         1
  WHITE                                            56
                           clus
vv                          DEL PEAK 22(9P23) WILD-TYPE
  ASIAN                                              11
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V10, binary
                             cls
clus                           0  1
  DEL PEAK 22(9P23) MUTATED    3 49
  DEL PEAK 22(9P23) WILD-TYPE  0 32
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 22(9P23) MUTATED      3   49
  DEL PEAK 22(9P23) WILD-TYPE    0   32
                        clus
vv                       DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  HISPANIC OR LATINO                             3                           0
  NOT HISPANIC OR LATINO                        49                          32
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 23(9P21.3) MUTATION ANALYSIS
D54V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 23(9P21.3) MUTATED   78 51
  DEL PEAK 23(9P21.3) WILD-TYPE 22 20
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                          129                            42 
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                           51                            20 
$`DEL PEAK 23(9P21.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27        14.30         7.63         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21        32.45         7.69        33.27         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12        18.64         3.88         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        23.41        12.82         9.96         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93E 
       12.16        44.75        60.39        25.41        23.18        25.22 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH 
        3.16         0.30         4.31         8.94         3.68        32.61 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OT 
       47.93        18.35         3.32         7.17        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y 
       29.00         7.13         7.43         6.94         2.60         0.36 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        3.95         3.02        55.50         2.66        35.97        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       13.41        83.24        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
       12.43        13.41         0.10        13.15        15.35        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39         0.10        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.03        13.18         0.13        33.11         5.16         7.82 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 
        5.06        14.70        29.59         6.35         9.30        15.78 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        1.45        12.69        20.02        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER 
        4.80         9.27         4.44        18.81        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA4D 
        1.55        18.31         8.12        28.11        18.18        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD 
       15.06        11.24         9.17        15.91        10.16         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.10         2.66        19.73 

$`DEL PEAK 23(9P21.3) WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A4QT 
       58.55         5.92        13.94         6.21        20.09         9.30 
TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       14.86       122.10        68.02         3.68        41.52        42.77 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A4OE 
       21.70        31.56        24.03         6.28        30.25        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A88T 
        4.70        19.99        21.01         1.38         3.16         8.71 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NT TCGA-L5-A8NV 
       25.12         7.40        13.48         7.76        27.12        52.57 
TCGA-L5-A8NW TCGA-LN-A49V TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6Y0 
       46.09         0.10         8.02         7.59         7.04        53.95 
TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EY TCGA-VR-A8Q7 
        2.89         7.00        15.35        19.96        30.71        42.87 

  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                          0.1                           0.1 
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                        83.24                        122.10 
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                       12.430                        17.655 
[1] "0.1 - 83.2 (12.4)"  "0.1 - 122.1 (17.7)"
[1] "hr=" "1.3"
D54V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 23(9P21.3) MUTATED         3        2        5        1        32
  DEL PEAK 23(9P21.3) WILD-TYPE       5        3        2        0         7
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 23(9P21.3) MUTATED          20        21          9          8
  DEL PEAK 23(9P21.3) WILD-TYPE         9         4          3          2
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 23(9P21.3) MUTATED            5        5         4
  DEL PEAK 23(9P21.3) WILD-TYPE          2        0         0
D54V3, multiclass
            clus
vv           DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  STAGE I                              3                             5
  STAGE IA                             2                             3
  STAGE IB                             5                             2
  STAGE II                             1                             0
  STAGE IIA                           32                             7
  STAGE IIB                           20                             9
  STAGE III                           21                             4
  STAGE IIIA                           9                             3
  STAGE IIIB                           8                             2
  STAGE IIIC                           5                             2
  STAGE IV                             5                             0
  STAGE IVA                            4                             0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 23(9P21.3) MUTATED      19 29 68  4
  DEL PEAK 23(9P21.3) WILD-TYPE    12  7 17  1
D54V4, multiclass
       clus
vv      DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  T0+T1                          19                            12
  T2                             29                             7
  T3                             68                            17
  T4                              4                             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                            N0 N1 N2 N3
  DEL PEAK 23(9P21.3) MUTATED   53 51  9  6
  DEL PEAK 23(9P21.3) WILD-TYPE 18 13  3  2
D54V5, multiclass
    clus
vv   DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  N0                          53                            18
  N1                          51                            13
  N2                           9                             3
  N3                           6                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                               cls
clus                             0  1
  DEL PEAK 23(9P21.3) MUTATED   96  9
  DEL PEAK 23(9P21.3) WILD-TYPE 30  0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(9P21.3) MUTATED     96    9
  DEL PEAK 23(9P21.3) WILD-TYPE   30    0
   clus
vv  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  0                          96                            30
  1                           9                             0
[1] 2 2
[1] FALSE
D54V7, binary
                               cls
clus                              0   1
  DEL PEAK 23(9P21.3) MUTATED    13 118
  DEL PEAK 23(9P21.3) WILD-TYPE  11  31
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(9P21.3) MUTATED     13  118
  DEL PEAK 23(9P21.3) WILD-TYPE   11   31
        clus
vv       DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  FEMALE                          13                            11
  MALE                           118                            31
[1] 2 2
[1] FALSE
D54V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(9P21.3) MUTATED      39                         1    75
  DEL PEAK 23(9P21.3) WILD-TYPE     2                         1    36
D54V9, multiclass
                           clus
vv                          DEL PEAK 23(9P21.3) MUTATED
  ASIAN                                              39
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              75
                           clus
vv                          DEL PEAK 23(9P21.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V10, binary
                               cls
clus                             0  1
  DEL PEAK 23(9P21.3) MUTATED    3 68
  DEL PEAK 23(9P21.3) WILD-TYPE  0 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(9P21.3) MUTATED      3   68
  DEL PEAK 23(9P21.3) WILD-TYPE    0   13
                        clus
vv                       DEL PEAK 23(9P21.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          68
                        clus
vv                       DEL PEAK 23(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            13
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 24(10P15.3) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 24(10P15.3) MUTATED   26 21
  DEL PEAK 24(10P15.3) WILD-TYPE 74 50
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                            47                            124 
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                            21                             50 
$`DEL PEAK 24(10P15.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3Y9 
       25.78        14.30         5.92         4.21        33.27         0.85 
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A93C 
       18.64         0.53         0.79        23.41        14.50        23.18 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OO 
        0.30         4.31         8.94        24.00         4.70         3.32 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A88V TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
        3.16         4.90         2.60        13.41        27.12        83.24 
TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49W TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        5.92        13.41        13.25        22.39        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO 
       13.22         4.47        25.25        12.03        13.18         0.13 
TCGA-Q9-A6FW TCGA-R6-A6Y0 TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EW 
        7.82        53.95         5.29         3.42         4.80         8.12 
TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B TCGA-Z6-A8JD TCGA-Z6-AAPN 
       18.18        15.06        11.24         3.42         2.66 

$`DEL PEAK 24(10P15.3) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB 
       32.45         7.69         6.21        20.09        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS 
       20.12         3.88         9.30        17.03        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
       14.86         4.67        12.16       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       68.02         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        3.68        32.61        19.99        21.01        47.93        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        7.17         1.38        58.59        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 
        6.94         8.71        25.12         0.36         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        3.02        55.50         2.66        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
        8.71        52.57        46.09        10.36        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
       12.43         0.10        13.15        15.35         0.10         0.10 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
       12.46        12.59        12.49        12.76        12.59         0.10 
TCGA-LN-A4A8 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-M9-A5M8 
       15.52        12.33        10.52        12.00        12.23        33.11 
TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        5.16         8.02         7.59         5.06        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
       29.59         6.35         9.30        15.78         2.89         1.45 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-AASV TCGA-V5-AASW 
       12.69         7.00        20.02        20.38        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        4.44        18.81        19.96        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7D 
       18.31        28.11        30.71        42.87        46.19         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       15.91        10.16         2.10        19.73 

  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                          0.13                           0.10 
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                         83.24                         122.10 
  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE 
                        11.240                         12.725 
[1] "0.1 - 83.2 (11.2)"  "0.1 - 122.1 (12.7)"
[1] "hr=" "1.5"
D55V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 24(10P15.3) MUTATED         1        1        2        0        12
  DEL PEAK 24(10P15.3) WILD-TYPE       7        4        5        1        27
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 24(10P15.3) MUTATED           7         9          3          4
  DEL PEAK 24(10P15.3) WILD-TYPE        22        16          9          6
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 24(10P15.3) MUTATED            2        3         0
  DEL PEAK 24(10P15.3) WILD-TYPE          5        2         4
D55V3, multiclass
            clus
vv           DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  STAGE I                               1                              7
  STAGE IA                              1                              4
  STAGE IB                              2                              5
  STAGE II                              0                              1
  STAGE IIA                            12                             27
  STAGE IIB                             7                             22
  STAGE III                             9                             16
  STAGE IIIA                            3                              9
  STAGE IIIB                            4                              6
  STAGE IIIC                            2                              5
  STAGE IV                              3                              2
  STAGE IVA                             0                              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 24(10P15.3) MUTATED       4 10 31  1
  DEL PEAK 24(10P15.3) WILD-TYPE    27 26 54  4
D55V4, multiclass
       clus
vv      DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  T0+T1                            4                             27
  T2                              10                             26
  T3                              31                             54
  T4                               1                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 24(10P15.3) MUTATED   21 15  6  3
  DEL PEAK 24(10P15.3) WILD-TYPE 50 49  6  5
D55V5, multiclass
    clus
vv   DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  N0                           21                             50
  N1                           15                             49
  N2                            6                              6
  N3                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V6, binary
                                cls
clus                              0  1
  DEL PEAK 24(10P15.3) MUTATED   37  3
  DEL PEAK 24(10P15.3) WILD-TYPE 89  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10P15.3) MUTATED     37    3
  DEL PEAK 24(10P15.3) WILD-TYPE   89    6
   clus
vv  DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  0                           37                             89
  1                            3                              6
[1] 2 2
[1] FALSE
D55V7, binary
                                cls
clus                               0   1
  DEL PEAK 24(10P15.3) MUTATED     6  42
  DEL PEAK 24(10P15.3) WILD-TYPE  18 107
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10P15.3) MUTATED      6   42
  DEL PEAK 24(10P15.3) WILD-TYPE   18  107
        clus
vv       DEL PEAK 24(10P15.3) MUTATED DEL PEAK 24(10P15.3) WILD-TYPE
  FEMALE                            6                             18
  MALE                             42                            107
[1] 2 2
[1] FALSE
D55V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(10P15.3) MUTATED      17                         1    24
  DEL PEAK 24(10P15.3) WILD-TYPE    24                         1    87
D55V9, multiclass
                           clus
vv                          DEL PEAK 24(10P15.3) MUTATED
  ASIAN                                               17
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               24
                           clus
vv                          DEL PEAK 24(10P15.3) WILD-TYPE
  ASIAN                                                 24
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V10, binary
                                cls
clus                              0  1
  DEL PEAK 24(10P15.3) MUTATED    1 25
  DEL PEAK 24(10P15.3) WILD-TYPE  2 56
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10P15.3) MUTATED      1   25
  DEL PEAK 24(10P15.3) WILD-TYPE    2   56
                        clus
vv                       DEL PEAK 24(10P15.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           25
                        clus
vv                       DEL PEAK 24(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             56
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 25(10P11.21) MUTATION ANALYSIS
D56V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 25(10P11.21) MUTATED   23 21
  DEL PEAK 25(10P11.21) WILD-TYPE 77 50
  DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE 
                             44                             127 
  DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE 
                             21                              50 
$`DEL PEAK 25(10P11.21) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YC 
       14.30         5.92        13.94        33.27         0.85        20.12 
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FA 
       18.64         0.53         0.79        23.41        14.50        44.75 
TCGA-JY-A6FE TCGA-JY-A93C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG 
        3.68        23.18         0.30         4.31        24.00         4.70 
TCGA-L5-A4OT TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NT TCGA-L5-A8NU TCGA-LN-A49O 
        4.90        13.48        13.55        27.12        83.24        13.41 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4A9 
       13.15         0.10        13.25        12.59        22.39        11.54 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HZ TCGA-LN-A9FO 
       13.22         4.47        25.25        10.52        13.18         0.13 
TCGA-V5-A7RC TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B 
        3.42         8.12        28.11        18.18        15.06        11.24 
TCGA-Z6-A8JD TCGA-Z6-AAPN 
        3.42         2.66 

$`DEL PEAK 25(10P11.21) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27        58.55         7.63         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3YA 
        4.21        32.45         7.69         6.21        20.09        20.78 
TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS 
        2.63         3.88         9.30        17.03        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD 
       14.86         4.67        12.16       122.10        60.39        68.02 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E 
       41.52        42.77        25.41        21.70        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         8.94         3.68 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       32.61        19.99        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         1.38         3.16        58.59        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
        7.43         6.94         8.71         2.60        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        7.40         3.95         3.02        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       12.92        16.47        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
        8.71        13.41        52.57        46.09        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49X 
       10.45        12.66        12.43         0.10        15.35         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.46        12.49        12.76        12.59         0.10        15.52 
TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-M9-A5M8 
       12.33        12.33        12.00        12.23        12.03        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
        5.16         7.82         8.02         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        29.59         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
        2.89         1.45        12.69         7.00        20.02        20.38 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        5.29         4.80        15.35         9.27         4.44        18.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY 
       19.96        22.82        12.43         1.55        18.31        30.71 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JE 
       42.87        46.19         9.17        15.91        10.16         2.10 
TCGA-ZR-A9CJ 
       19.73 

  DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE 
                            0.1                             0.1 
  DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE 
                          83.24                          122.10 
  DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE 
                          13.20                           12.43 
[1] "0.1 - 83.2 (13.2)"  "0.1 - 122.1 (12.4)"
[1] "hr=" "1.4"
D56V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 25(10P11.21) MUTATED         1        0        1        0        16
  DEL PEAK 25(10P11.21) WILD-TYPE       7        5        6        1        23
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 25(10P11.21) MUTATED           8         6          4          3
  DEL PEAK 25(10P11.21) WILD-TYPE        21        19          8          7
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 25(10P11.21) MUTATED            1        3         1
  DEL PEAK 25(10P11.21) WILD-TYPE          6        2         3
D56V3, multiclass
            clus
vv           DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE
  STAGE I                                1                               7
  STAGE IA                               0                               5
  STAGE IB                               1                               6
  STAGE II                               0                               1
  STAGE IIA                             16                              23
  STAGE IIB                              8                              21
  STAGE III                              6                              19
  STAGE IIIA                             4                               8
  STAGE IIIB                             3                               7
  STAGE IIIC                             1                               6
  STAGE IV                               3                               2
  STAGE IVA                              1                               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3 T4
  DEL PEAK 25(10P11.21) MUTATED       3 12 28  1
  DEL PEAK 25(10P11.21) WILD-TYPE    28 24 57  4
D56V4, multiclass
       clus
vv      DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE
  T0+T1                             3                              28
  T2                               12                              24
  T3                               28                              57
  T4                                1                               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  DEL PEAK 25(10P11.21) MUTATED   22 15  4  2
  DEL PEAK 25(10P11.21) WILD-TYPE 49 49  8  6
D56V5, multiclass
    clus
vv   DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE
  N0                            22                              49
  N1                            15                              49
  N2                             4                               8
  N3                             2                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                                 cls
clus                               0  1
  DEL PEAK 25(10P11.21) MUTATED   38  4
  DEL PEAK 25(10P11.21) WILD-TYPE 88  5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10P11.21) MUTATED     38    4
  DEL PEAK 25(10P11.21) WILD-TYPE   88    5
   clus
vv  DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE
  0                            38                              88
  1                             4                               5
[1] 2 2
[1] FALSE
D56V7, binary
                                 cls
clus                                0   1
  DEL PEAK 25(10P11.21) MUTATED     6  39
  DEL PEAK 25(10P11.21) WILD-TYPE  18 110
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10P11.21) MUTATED      6   39
  DEL PEAK 25(10P11.21) WILD-TYPE   18  110
        clus
vv       DEL PEAK 25(10P11.21) MUTATED DEL PEAK 25(10P11.21) WILD-TYPE
  FEMALE                             6                              18
  MALE                              39                             110
[1] 2 2
[1] FALSE
D56V8, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(10P11.21) MUTATED      19                         1    21
  DEL PEAK 25(10P11.21) WILD-TYPE    22                         1    90
D56V9, multiclass
                           clus
vv                          DEL PEAK 25(10P11.21) MUTATED
  ASIAN                                                19
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                21
                           clus
vv                          DEL PEAK 25(10P11.21) WILD-TYPE
  ASIAN                                                  22
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                  90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V10, binary
                                 cls
clus                               0  1
  DEL PEAK 25(10P11.21) MUTATED    0 24
  DEL PEAK 25(10P11.21) WILD-TYPE  3 57
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10P11.21) MUTATED      0   24
  DEL PEAK 25(10P11.21) WILD-TYPE    3   57
                        clus
vv                       DEL PEAK 25(10P11.21) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            24
                        clus
vv                       DEL PEAK 25(10P11.21) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                              57
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 26(10Q21.1) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 26(10Q21.1) MUTATED   26 13
  DEL PEAK 26(10Q21.1) WILD-TYPE 74 58
  DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE 
                            39                            132 
  DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE 
                            13                             58 
$`DEL PEAK 26(10Q21.1) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GM TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A50L TCGA-IG-A5S3 
       14.30        13.94        33.27         0.85         0.53        23.41 
TCGA-IG-A97H TCGA-JY-A6FD TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OE 
       14.50        68.02        23.18         3.16         0.30        24.00 
TCGA-L5-A4OG TCGA-L5-A4OJ TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A8NK 
        4.70        21.01         1.38         3.16         4.90        13.55 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       27.12        83.24         0.10        12.46        12.59        12.49 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
       22.39         0.10        12.33        13.22        12.33        25.25 
TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-V5-A7RC 
       12.00        12.03        13.18        53.95        15.78         3.42 
TCGA-V5-A7RE TCGA-VR-A8EX TCGA-Z6-A8JE 
        4.80        28.11         2.10 

$`DEL PEAK 26(10Q21.1) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        31.27        58.55         7.63         5.92         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69         6.21        20.09 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03         0.79        12.82         9.96        14.86         4.67 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        60.39         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       42.77        25.41        21.70        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28        30.25         4.31         8.94         3.68        32.61 
TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS 
       19.99        47.93        18.35         3.32         7.17        58.59 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
       29.00         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       25.12         0.36         7.40         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL 
        2.66        35.97        12.92        13.48        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV 
        7.76         5.49        21.37         8.71        13.41        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.41        13.15        15.35         0.10        13.25         0.10 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HV 
       12.76        12.59        15.52        11.54         4.47        10.52 
TCGA-LN-A7HX TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.23         0.13        33.11         5.16         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        14.70         7.04        29.59         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
        9.30         2.89         1.45        12.69         7.00        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
       20.38         5.29        15.35         9.27         4.44        18.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       19.96        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       30.71        18.18        42.87        46.19        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        9.17        15.91        10.16         3.42         2.66        19.73 

  DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE 
                           0.1                            0.1 
  DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE 
                         83.24                         122.10 
  DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE 
                         12.59                          12.51 
[1] "0.1 - 83.2 (12.6)"  "0.1 - 122.1 (12.5)"
[1] "hr=" "1.3"
D57V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 26(10Q21.1) MUTATED         2        1        1        1        13
  DEL PEAK 26(10Q21.1) WILD-TYPE       6        4        6        0        26
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 26(10Q21.1) MUTATED           5         5          4          2
  DEL PEAK 26(10Q21.1) WILD-TYPE        24        20          8          8
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 26(10Q21.1) MUTATED            0        1         2
  DEL PEAK 26(10Q21.1) WILD-TYPE          7        4         2
D57V3, multiclass
            clus
vv           DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE
  STAGE I                               2                              6
  STAGE IA                              1                              4
  STAGE IB                              1                              6
  STAGE II                              1                              0
  STAGE IIA                            13                             26
  STAGE IIB                             5                             24
  STAGE III                             5                             20
  STAGE IIIA                            4                              8
  STAGE IIIB                            2                              8
  STAGE IIIC                            0                              7
  STAGE IV                              1                              4
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 26(10Q21.1) MUTATED       6 10 20  1
  DEL PEAK 26(10Q21.1) WILD-TYPE    25 26 65  4
D57V4, multiclass
       clus
vv      DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE
  T0+T1                            6                             25
  T2                              10                             26
  T3                              20                             65
  T4                               1                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 26(10Q21.1) MUTATED   20 13  3  0
  DEL PEAK 26(10Q21.1) WILD-TYPE 51 51  9  8
D57V5, multiclass
    clus
vv   DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE
  N0                           20                             51
  N1                           13                             51
  N2                            3                              9
  N3                            0                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V6, binary
                                cls
clus                              0  1
  DEL PEAK 26(10Q21.1) MUTATED   31  3
  DEL PEAK 26(10Q21.1) WILD-TYPE 95  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10Q21.1) MUTATED     31    3
  DEL PEAK 26(10Q21.1) WILD-TYPE   95    6
   clus
vv  DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE
  0                           31                             95
  1                            3                              6
[1] 2 2
[1] FALSE
D57V7, binary
                                cls
clus                               0   1
  DEL PEAK 26(10Q21.1) MUTATED     6  34
  DEL PEAK 26(10Q21.1) WILD-TYPE  18 115
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10Q21.1) MUTATED      6   34
  DEL PEAK 26(10Q21.1) WILD-TYPE   18  115
        clus
vv       DEL PEAK 26(10Q21.1) MUTATED DEL PEAK 26(10Q21.1) WILD-TYPE
  FEMALE                            6                             18
  MALE                             34                            115
[1] 2 2
[1] FALSE
D57V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(10Q21.1) MUTATED      18                         1    18
  DEL PEAK 26(10Q21.1) WILD-TYPE    23                         1    93
D57V9, multiclass
                           clus
vv                          DEL PEAK 26(10Q21.1) MUTATED
  ASIAN                                               18
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               18
                           clus
vv                          DEL PEAK 26(10Q21.1) WILD-TYPE
  ASIAN                                                 23
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V10, binary
                                cls
clus                              0  1
  DEL PEAK 26(10Q21.1) MUTATED    0 24
  DEL PEAK 26(10Q21.1) WILD-TYPE  3 57
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10Q21.1) MUTATED      0   24
  DEL PEAK 26(10Q21.1) WILD-TYPE    3   57
                        clus
vv                       DEL PEAK 26(10Q21.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           24
                        clus
vv                       DEL PEAK 26(10Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                             57
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 27(10Q23.31) MUTATION ANALYSIS
D58V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 27(10Q23.31) MUTATED   34 24
  DEL PEAK 27(10Q23.31) WILD-TYPE 66 47
  DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE 
                             58                             113 
  DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE 
                             24                              47 
$`DEL PEAK 27(10Q23.31) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        14.30         5.92        13.94        16.24         4.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A50L TCGA-IG-A5S3 
       33.27        20.09         0.85         2.63         0.53        23.41 
TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J 
       14.50        44.75        23.18         3.16         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO 
        8.94        24.00         4.70        32.61        21.01         3.32 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A8NE TCGA-L5-A8NI 
        3.16        58.59         4.90         7.13        55.50        13.48 
TCGA-L5-A8NK TCGA-L5-A8NT TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R 
       13.55        27.12        83.24        10.45        12.66         0.10 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ 
       12.46        12.59        12.49        22.39         0.10        12.33 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY 
       13.22        12.33        25.25        10.52        12.00        12.03 
TCGA-Q9-A6FU TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-V5-A7RC 
        5.16         7.59         5.06        53.95         2.89         3.42 
TCGA-V5-A7RE TCGA-VR-A8EP TCGA-VR-A8EX TCGA-Z6-A8JE 
        4.80        19.96        28.11         2.10 

$`DEL PEAK 27(10Q23.31) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IC-A6RE 
       31.27        58.55         7.63         8.94        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
        6.21        20.78        20.12        18.64         3.88         9.30 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03         0.79        12.82         9.96        14.86         4.67 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        60.39        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       42.77        25.41        21.70        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON 
        6.28        30.25         3.68        19.99        47.93        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        7.17         1.38        29.00         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        2.60        25.12         0.36         7.40         3.95         3.02 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        35.97        12.92        16.47        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49        21.37         8.71        13.41        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U 
       10.36         5.92        12.43        13.41        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 
        0.10        13.25         0.10        12.76        12.59        15.52 
TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 
       11.54         4.47        12.23        13.18         0.13        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.82         8.02        14.70         7.04        29.59         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
        9.30        15.78         1.45        12.69         7.00        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
       20.38         5.29        15.35         9.27         4.44        18.81 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
       22.82        12.43         1.55        18.31         8.12        30.71 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        42.87        46.19        15.06        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       15.91        10.16         3.42         2.66        19.73 

  DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE 
                            0.1                             0.1 
  DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE 
                          83.24                          122.10 
  DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE 
                         12.395                          12.760 
[1] "0.1 - 83.2 (12.4)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "1"  
D58V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 27(10Q23.31) MUTATED         3        1        1        1        14
  DEL PEAK 27(10Q23.31) WILD-TYPE       5        4        6        0        25
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 27(10Q23.31) MUTATED          11         9          4          4
  DEL PEAK 27(10Q23.31) WILD-TYPE        18        16          8          6
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 27(10Q23.31) MUTATED            1        1         2
  DEL PEAK 27(10Q23.31) WILD-TYPE          6        4         2
D58V3, multiclass
            clus
vv           DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE
  STAGE I                                3                               5
  STAGE IA                               1                               4
  STAGE IB                               1                               6
  STAGE II                               1                               0
  STAGE IIA                             14                              25
  STAGE IIB                             11                              18
  STAGE III                              9                              16
  STAGE IIIA                             4                               8
  STAGE IIIB                             4                               6
  STAGE IIIC                             1                               6
  STAGE IV                               1                               4
  STAGE IVA                              2                               2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3 T4
  DEL PEAK 27(10Q23.31) MUTATED       7 15 30  1
  DEL PEAK 27(10Q23.31) WILD-TYPE    24 21 55  4
D58V4, multiclass
       clus
vv      DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE
  T0+T1                             7                              24
  T2                               15                              21
  T3                               30                              55
  T4                                1                               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  DEL PEAK 27(10Q23.31) MUTATED   24 22  5  1
  DEL PEAK 27(10Q23.31) WILD-TYPE 47 42  7  7
D58V5, multiclass
    clus
vv   DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE
  N0                            24                              47
  N1                            22                              42
  N2                             5                               7
  N3                             1                               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V6, binary
                                 cls
clus                               0  1
  DEL PEAK 27(10Q23.31) MUTATED   46  3
  DEL PEAK 27(10Q23.31) WILD-TYPE 80  6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(10Q23.31) MUTATED     46    3
  DEL PEAK 27(10Q23.31) WILD-TYPE   80    6
   clus
vv  DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE
  0                            46                              80
  1                             3                               6
[1] 2 2
[1] FALSE
D58V7, binary
                                 cls
clus                                0   1
  DEL PEAK 27(10Q23.31) MUTATED    10  49
  DEL PEAK 27(10Q23.31) WILD-TYPE  14 100
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(10Q23.31) MUTATED     10   49
  DEL PEAK 27(10Q23.31) WILD-TYPE   14  100
        clus
vv       DEL PEAK 27(10Q23.31) MUTATED DEL PEAK 27(10Q23.31) WILD-TYPE
  FEMALE                            10                              14
  MALE                              49                             100
[1] 2 2
[1] FALSE
D58V8, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(10Q23.31) MUTATED      20                         1    29
  DEL PEAK 27(10Q23.31) WILD-TYPE    21                         1    82
D58V9, multiclass
                           clus
vv                          DEL PEAK 27(10Q23.31) MUTATED
  ASIAN                                                20
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                29
                           clus
vv                          DEL PEAK 27(10Q23.31) WILD-TYPE
  ASIAN                                                  21
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                  82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V10, binary
                                 cls
clus                               0  1
  DEL PEAK 27(10Q23.31) MUTATED    0 31
  DEL PEAK 27(10Q23.31) WILD-TYPE  3 50
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(10Q23.31) MUTATED      0   31
  DEL PEAK 27(10Q23.31) WILD-TYPE    3   50
                        clus
vv                       DEL PEAK 27(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            31
                        clus
vv                       DEL PEAK 27(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                              50
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 28(11P15.4) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 28(11P15.4) MUTATED   51 21
  DEL PEAK 28(11P15.4) WILD-TYPE 49 50
  DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE 
                            72                             99 
  DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE 
                            21                             50 
$`DEL PEAK 28(11P15.4) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       31.27        14.30         5.92         4.21        32.45         7.69 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A50L TCGA-JY-A938 TCGA-JY-A93E TCGA-L5-A43C 
        0.85         2.63         0.53        25.41        25.22         3.16 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        0.30         4.31         8.94         3.68         4.70        32.61 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A88S TCGA-L5-A88V 
        3.32         7.17         1.38         3.16         6.94         2.60 
TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NJ TCGA-L5-A8NK 
        0.36         3.95         3.02        55.50        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       13.22        13.41        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X 
       12.43        13.41         0.10        13.15        15.35         0.10 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        12.49        12.76         0.10        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A9FO 
        4.47        12.33        25.25        12.00        12.03         0.13 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV 
       29.59        53.95        15.78         1.45        12.69        20.02 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8ER 
        3.42         4.80         9.27         4.44        19.96        12.43 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA7B TCGA-VR-AA7I TCGA-Z6-A8JE 
        8.12        28.11        18.18        11.24        15.91         2.10 

$`DEL PEAK 28(11P15.4) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        58.55         7.63        13.94         8.94        16.24 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 
        6.21        33.27        20.09        20.78        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         9.30        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       44.75        60.39        68.02         3.68        41.52        42.77 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E 
       21.70        23.18        31.56        24.03         6.28        30.25 
TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OS 
       24.00        19.99        21.01        47.93        18.35        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W 
        4.90        29.00         7.13         7.43         8.71        25.12 
TCGA-L5-A88Z TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NM 
        7.40         2.66        35.97        12.92        13.48         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A5 
       46.09         0.10        13.25        12.46        12.59        22.39 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-M9-A5M8 
       15.52        11.54        10.52        12.23        13.18        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
        5.16         7.82         8.02         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-S8-A6BW 
        7.04         6.35         9.30         2.89         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU 
        5.29        15.35        18.81        22.82         1.55        18.31 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR 
       30.71        42.87        46.19        15.06         9.17        10.16 
TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        3.42         2.66        19.73 

  DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE 
                           0.1                            0.1 
  DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE 
                          55.5                          122.1 
  DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE 
                        10.845                         14.700 
[1] "0.1 - 55.5 (10.8)"  "0.1 - 122.1 (14.7)"
[1] "hr=" "1"  
D59V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 28(11P15.4) MUTATED         3        2        2        1        16
  DEL PEAK 28(11P15.4) WILD-TYPE       5        3        5        0        23
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 28(11P15.4) MUTATED          10        13          7          2
  DEL PEAK 28(11P15.4) WILD-TYPE        19        12          5          8
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 28(11P15.4) MUTATED            3        2         2
  DEL PEAK 28(11P15.4) WILD-TYPE          4        3         2
D59V3, multiclass
            clus
vv           DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE
  STAGE I                               3                              5
  STAGE IA                              2                              3
  STAGE IB                              2                              5
  STAGE II                              1                              0
  STAGE IIA                            16                             23
  STAGE IIB                            10                             19
  STAGE III                            13                             12
  STAGE IIIA                            7                              5
  STAGE IIIB                            2                              8
  STAGE IIIC                            3                              4
  STAGE IV                              2                              3
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 28(11P15.4) MUTATED      11 12 40  3
  DEL PEAK 28(11P15.4) WILD-TYPE    20 24 45  2
D59V4, multiclass
       clus
vv      DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE
  T0+T1                           11                             20
  T2                              12                             24
  T3                              40                             45
  T4                               3                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 28(11P15.4) MUTATED   30 28  4  4
  DEL PEAK 28(11P15.4) WILD-TYPE 41 36  8  4
D59V5, multiclass
    clus
vv   DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE
  N0                           30                             41
  N1                           28                             36
  N2                            4                              8
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V6, binary
                                cls
clus                              0  1
  DEL PEAK 28(11P15.4) MUTATED   51  4
  DEL PEAK 28(11P15.4) WILD-TYPE 75  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(11P15.4) MUTATED     51    4
  DEL PEAK 28(11P15.4) WILD-TYPE   75    5
   clus
vv  DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE
  0                           51                             75
  1                            4                              5
[1] 2 2
[1] FALSE
D59V7, binary
                                cls
clus                              0  1
  DEL PEAK 28(11P15.4) MUTATED    6 68
  DEL PEAK 28(11P15.4) WILD-TYPE 18 81
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(11P15.4) MUTATED      6   68
  DEL PEAK 28(11P15.4) WILD-TYPE   18   81
        clus
vv       DEL PEAK 28(11P15.4) MUTATED DEL PEAK 28(11P15.4) WILD-TYPE
  FEMALE                            6                             18
  MALE                             68                             81
[1] 2 2
[1] FALSE
D59V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(11P15.4) MUTATED      25                         1    40
  DEL PEAK 28(11P15.4) WILD-TYPE    16                         1    71
D59V9, multiclass
                           clus
vv                          DEL PEAK 28(11P15.4) MUTATED
  ASIAN                                               25
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               40
                           clus
vv                          DEL PEAK 28(11P15.4) WILD-TYPE
  ASIAN                                                 16
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V10, binary
                                cls
clus                              0  1
  DEL PEAK 28(11P15.4) MUTATED    1 38
  DEL PEAK 28(11P15.4) WILD-TYPE  2 43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(11P15.4) MUTATED      1   38
  DEL PEAK 28(11P15.4) WILD-TYPE    2   43
                        clus
vv                       DEL PEAK 28(11P15.4) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           38
                        clus
vv                       DEL PEAK 28(11P15.4) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             43
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 29(11Q25) MUTATION ANALYSIS
D60V1, survival
                              sevent
clus2                           0  1
  DEL PEAK 29(11Q25) MUTATED   43 30
  DEL PEAK 29(11Q25) WILD-TYPE 57 41
  DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE 
                          73                           98 
  DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE 
                          30                           41 
$`DEL PEAK 29(11Q25) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       14.30         7.63         5.92        20.12        18.64         3.88 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FH 
       17.03        23.41         9.96        14.50        12.16        42.77 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP 
        3.16         0.30         3.68        47.93         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 
        3.16        29.00         6.94         2.60         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NT 
       55.50         2.66        12.92        13.55        13.22        27.12 
TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       52.57        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.10         0.10        13.25        12.59        12.49        12.76 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
       22.39         0.10        15.52        12.33        13.22        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-Q9-A6FW 
       25.25        12.00        12.23         0.13         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A8W8 TCGA-R6-A8WC 
        8.02         7.59         5.06         6.35         2.89         1.45 
TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8EU 
       12.69        20.02         3.42        18.81        12.43        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
        8.12        28.11        18.18        11.24         9.17        15.91 
TCGA-Z6-A8JE 
        2.10 

$`DEL PEAK 29(11Q25) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27        58.55        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
        4.21        32.45         7.69         6.21        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 
        0.85        20.78         2.63         9.30         0.53         0.79 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
       12.82        14.86         4.67       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        25.41        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43J 
       31.56        25.22        24.03         6.28        30.25         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        8.94        24.00         4.70        32.61        19.99        21.01 
TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
       18.35         1.38        58.59         4.90         7.13         7.43 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NG TCGA-L5-A8NI 
        8.71        25.12         0.36         7.40        35.97        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X 
       83.24        46.09        13.41        13.15        15.35         0.10 
TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HY 
       12.46        12.59        11.54         4.47        10.52        12.03 
TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 
       13.18        33.11        14.70         7.04        29.59        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
        9.30        15.78         7.00        20.38         5.29         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET 
       15.35         9.27         4.44        19.96        22.82         1.55 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-X8-AAAR TCGA-Z6-A8JD 
       30.71        42.87        46.19        15.06        10.16         3.42 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

  DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE 
                         0.1                          0.1 
  DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE 
                        55.5                        122.1 
  DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE 
                       12.16                        13.71 
[1] "0.1 - 55.5 (12.2)"  "0.1 - 122.1 (13.7)"
[1] "hr=" "1.5"
D60V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 29(11Q25) MUTATED         1        3        1        1        18
  DEL PEAK 29(11Q25) WILD-TYPE       7        2        6        0        21
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 29(11Q25) MUTATED          10        12          3          5
  DEL PEAK 29(11Q25) WILD-TYPE        19        13          9          5
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 29(11Q25) MUTATED            4        3         2
  DEL PEAK 29(11Q25) WILD-TYPE          3        2         2
D60V3, multiclass
            clus
vv           DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE
  STAGE I                             1                            7
  STAGE IA                            3                            2
  STAGE IB                            1                            6
  STAGE II                            1                            0
  STAGE IIA                          18                           21
  STAGE IIB                          10                           19
  STAGE III                          12                           13
  STAGE IIIA                          3                            9
  STAGE IIIB                          5                            5
  STAGE IIIC                          4                            3
  STAGE IV                            3                            2
  STAGE IVA                           2                            2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3 T4
  DEL PEAK 29(11Q25) MUTATED      10 17 35  2
  DEL PEAK 29(11Q25) WILD-TYPE    21 19 50  3
D60V4, multiclass
       clus
vv      DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE
  T0+T1                         10                           21
  T2                            17                           19
  T3                            35                           50
  T4                             2                            3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2 N3
  DEL PEAK 29(11Q25) MUTATED   29 25  4  5
  DEL PEAK 29(11Q25) WILD-TYPE 42 39  8  3
D60V5, multiclass
    clus
vv   DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE
  N0                         29                           42
  N1                         25                           39
  N2                          4                            8
  N3                          5                            3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V6, binary
                              cls
clus                            0  1
  DEL PEAK 29(11Q25) MUTATED   51  5
  DEL PEAK 29(11Q25) WILD-TYPE 75  4
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 29(11Q25) MUTATED     51    5
  DEL PEAK 29(11Q25) WILD-TYPE   75    4
   clus
vv  DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE
  0                         51                           75
  1                          5                            4
[1] 2 2
[1] FALSE
D60V7, binary
                              cls
clus                            0  1
  DEL PEAK 29(11Q25) MUTATED    8 65
  DEL PEAK 29(11Q25) WILD-TYPE 16 84
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 29(11Q25) MUTATED      8   65
  DEL PEAK 29(11Q25) WILD-TYPE   16   84
        clus
vv       DEL PEAK 29(11Q25) MUTATED DEL PEAK 29(11Q25) WILD-TYPE
  FEMALE                          8                           16
  MALE                           65                           84
[1] 2 2
[1] FALSE
D60V8, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(11Q25) MUTATED      22                         1    44
  DEL PEAK 29(11Q25) WILD-TYPE    19                         1    67
D60V9, multiclass
                           clus
vv                          DEL PEAK 29(11Q25) MUTATED
  ASIAN                                             22
  BLACK OR AFRICAN AMERICAN                          1
  WHITE                                             44
                           clus
vv                          DEL PEAK 29(11Q25) WILD-TYPE
  ASIAN                                               19
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V10, binary
                              cls
clus                            0  1
  DEL PEAK 29(11Q25) MUTATED    1 39
  DEL PEAK 29(11Q25) WILD-TYPE  2 42
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 29(11Q25) MUTATED      1   39
  DEL PEAK 29(11Q25) WILD-TYPE    2   42
                        clus
vv                       DEL PEAK 29(11Q25) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         39
                        clus
vv                       DEL PEAK 29(11Q25) WILD-TYPE
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           42
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 30(12Q23.1) MUTATION ANALYSIS
D61V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 30(12Q23.1) MUTATED   32 15
  DEL PEAK 30(12Q23.1) WILD-TYPE 68 56
  DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE 
                            47                            124 
  DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE 
                            15                             56 
$`DEL PEAK 30(12Q23.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IG-A3I8 
       25.78        31.27        14.30        13.94        32.45        33.27 
TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FD 
        2.63        18.64         0.79        23.41        14.50        68.02 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OH 
       42.77        25.41        25.22        30.25         8.94        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88V 
       21.01         3.32         7.17        58.59         7.13         2.60 
TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        0.36         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NS TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A4A1 TCGA-LN-A5U6 TCGA-Q9-A6FW 
       13.41        12.66        13.41        12.59        12.33         7.82 
TCGA-R6-A6KZ TCGA-R6-A8W8 TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASX 
        5.06         2.89        20.02        20.38         3.42         4.44 
TCGA-VR-A8ET TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-X8-AAAR TCGA-Z6-AAPN 
        1.55        42.87        11.24        10.16         2.66 

$`DEL PEAK 30(12Q23.1) WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       58.55         7.63         5.92         8.94        16.24         4.21 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC 
        7.69         6.21        20.09         0.85        20.78        20.12 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS 
        3.88         9.30         0.53        17.03        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
       14.86         4.67        12.16       122.10        44.75        60.39 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F 
        3.68        41.52        21.70        23.18        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF 
        6.28         3.16         0.30         4.31        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR 
        4.70        19.99        47.93        18.35         1.38         3.16 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W 
        4.90        29.00         7.43         6.94         8.71        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        7.40         3.95        35.97        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        27.12        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N 
       52.57        46.09        10.36         5.92        10.45        12.43 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
        0.10        13.15        15.35         0.10        13.25         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.46        12.49        12.76        12.59        22.39         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 
       15.52        11.54        12.33        13.22         4.47        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO 
       10.52        12.00        12.23        12.03        13.18         0.13 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       33.11         5.16         8.02         7.59        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC 
       29.59         6.35        53.95         9.30        15.78         1.45 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       12.69         7.00         5.29         4.80        15.35         9.27 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW 
       18.81        19.96        22.82        12.43        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D 
       28.11        30.71        18.18        46.19        15.06         9.17 
TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       15.91         3.42         2.10        19.73 

  DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE 
                          0.36                           0.10 
  DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE 
                         68.02                         122.10 
  DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE 
                         13.41                          12.43 
[1] "0.4 - 68.0 (13.4)"  "0.1 - 122.1 (12.4)"
[1] "hr=" "1.5"
D61V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 30(12Q23.1) MUTATED         4        1        2        0         9
  DEL PEAK 30(12Q23.1) WILD-TYPE       4        4        5        1        30
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 30(12Q23.1) MUTATED          11         4          4          1
  DEL PEAK 30(12Q23.1) WILD-TYPE        18        21          8          9
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 30(12Q23.1) MUTATED            1        2         1
  DEL PEAK 30(12Q23.1) WILD-TYPE          6        3         3
D61V3, multiclass
            clus
vv           DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              1                              4
  STAGE IB                              2                              5
  STAGE II                              0                              1
  STAGE IIA                             9                             30
  STAGE IIB                            11                             18
  STAGE III                             4                             21
  STAGE IIIA                            4                              8
  STAGE IIIB                            1                              9
  STAGE IIIC                            1                              6
  STAGE IV                              2                              3
  STAGE IVA                             1                              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 30(12Q23.1) MUTATED      11  9 23  0
  DEL PEAK 30(12Q23.1) WILD-TYPE    20 27 62  5
D61V4, multiclass
       clus
vv      DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE
  T0+T1                           11                             20
  T2                               9                             27
  T3                              23                             62
  T4                               0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 30(12Q23.1) MUTATED   21 17  2  2
  DEL PEAK 30(12Q23.1) WILD-TYPE 50 47 10  6
D61V5, multiclass
    clus
vv   DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE
  N0                           21                             50
  N1                           17                             47
  N2                            2                             10
  N3                            2                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V6, binary
                                cls
clus                              0  1
  DEL PEAK 30(12Q23.1) MUTATED   33  3
  DEL PEAK 30(12Q23.1) WILD-TYPE 93  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(12Q23.1) MUTATED     33    3
  DEL PEAK 30(12Q23.1) WILD-TYPE   93    6
   clus
vv  DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE
  0                           33                             93
  1                            3                              6
[1] 2 2
[1] FALSE
D61V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(12Q23.1) MUTATED    10  37
  DEL PEAK 30(12Q23.1) WILD-TYPE  14 112
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(12Q23.1) MUTATED     10   37
  DEL PEAK 30(12Q23.1) WILD-TYPE   14  112
        clus
vv       DEL PEAK 30(12Q23.1) MUTATED DEL PEAK 30(12Q23.1) WILD-TYPE
  FEMALE                           10                             14
  MALE                             37                            112
[1] 2 2
[1] FALSE
D61V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(12Q23.1) MUTATED       6                         1    33
  DEL PEAK 30(12Q23.1) WILD-TYPE    35                         1    78
D61V9, multiclass
                           clus
vv                          DEL PEAK 30(12Q23.1) MUTATED
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               33
                           clus
vv                          DEL PEAK 30(12Q23.1) WILD-TYPE
  ASIAN                                                 35
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V10, binary
                                cls
clus                              0  1
  DEL PEAK 30(12Q23.1) MUTATED    0 19
  DEL PEAK 30(12Q23.1) WILD-TYPE  3 62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(12Q23.1) MUTATED      0   19
  DEL PEAK 30(12Q23.1) WILD-TYPE    3   62
                        clus
vv                       DEL PEAK 30(12Q23.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           19
                        clus
vv                       DEL PEAK 30(12Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                             62
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 31(13Q12.11) MUTATION ANALYSIS
D62V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 31(13Q12.11) MUTATED   42 28
  DEL PEAK 31(13Q12.11) WILD-TYPE 58 43
  DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE 
                             70                             101 
  DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE 
                             28                              43 
$`DEL PEAK 31(13Q12.11) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IG-A3QL 
       25.78        58.55         7.63         8.94        32.45        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A51D TCGA-IG-A5B8 
        0.85        20.78         2.63         3.88        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A93C 
       23.41         9.96         4.67        60.39        68.02        23.18 
TCGA-JY-A93E TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OT 
       25.22         8.94         3.68        47.93         3.16         4.90 
TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NU TCGA-L5-A8NW 
       29.00         6.94        13.22         5.49        83.24        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.10        13.15        15.35        13.25        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A7HV 
       12.59        22.39         0.10        11.54        12.33        10.52 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6XG 
       12.23        12.03         0.13         5.16         5.06        29.59 
TCGA-R6-A6XQ TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EO 
        6.35         1.45        12.69         4.80        15.35        18.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       19.96        22.82        18.31        28.11        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7I TCGA-Z6-A8JE 
       42.87        11.24        15.91         2.10 

$`DEL PEAK 31(13Q12.11) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       31.27        14.30         5.92        13.94        16.24         4.21 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
        7.69         6.21        33.27        20.12        18.64         9.30 
TCGA-IG-A50L TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        0.53        12.82        14.86        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       44.75         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       31.56        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        4.31        24.00         4.70        32.61        19.99        21.01 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW 
       18.35         3.32         7.17         1.38        58.59         7.13 
TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
        7.43         8.71         2.60        25.12         0.36         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        3.95         3.02        55.50         2.66        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.48        16.47        13.55         7.76        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y 
       13.41        27.12        52.57         0.10         0.10        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 
       12.59        15.52        12.33        13.22         4.47        25.25 
TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.00        13.18        33.11         7.82         8.02         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       14.70         7.04        53.95         9.30        15.78         2.89 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW 
        7.00        20.02        20.38         5.29         3.42         9.27 
TCGA-V5-AASX TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-AA4D TCGA-VR-AA4G 
        4.44        12.43         1.55         8.12        46.19        15.06 
TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        9.17        10.16         3.42         2.66        19.73 

  DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE 
                            0.1                             0.1 
  DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE 
                          83.24                          122.10 
  DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE 
                         12.625                          12.460 
[1] "0.1 - 83.2 (12.6)"  "0.1 - 122.1 (12.5)"
[1] "hr=" "1.1"
D62V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 31(13Q12.11) MUTATED         2        2        4        1        17
  DEL PEAK 31(13Q12.11) WILD-TYPE       6        3        3        0        22
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 31(13Q12.11) MUTATED           9        12          6          6
  DEL PEAK 31(13Q12.11) WILD-TYPE        20        13          6          4
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 31(13Q12.11) MUTATED            2        3         1
  DEL PEAK 31(13Q12.11) WILD-TYPE          5        2         3
D62V3, multiclass
            clus
vv           DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE
  STAGE I                                2                               6
  STAGE IA                               2                               3
  STAGE IB                               4                               3
  STAGE II                               1                               0
  STAGE IIA                             17                              22
  STAGE IIB                              9                              20
  STAGE III                             12                              13
  STAGE IIIA                             6                               6
  STAGE IIIB                             6                               4
  STAGE IIIC                             2                               5
  STAGE IV                               3                               2
  STAGE IVA                              1                               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3 T4
  DEL PEAK 31(13Q12.11) MUTATED       9 14 40  3
  DEL PEAK 31(13Q12.11) WILD-TYPE    22 22 45  2
D62V4, multiclass
       clus
vv      DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE
  T0+T1                             9                              22
  T2                               14                              22
  T3                               40                              45
  T4                                3                               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  DEL PEAK 31(13Q12.11) MUTATED   32 25  6  3
  DEL PEAK 31(13Q12.11) WILD-TYPE 39 39  6  5
D62V5, multiclass
    clus
vv   DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE
  N0                            32                              39
  N1                            25                              39
  N2                             6                               6
  N3                             3                               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V6, binary
                                 cls
clus                               0  1
  DEL PEAK 31(13Q12.11) MUTATED   55  4
  DEL PEAK 31(13Q12.11) WILD-TYPE 71  5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 31(13Q12.11) MUTATED     55    4
  DEL PEAK 31(13Q12.11) WILD-TYPE   71    5
   clus
vv  DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE
  0                            55                              71
  1                             4                               5
[1] 2 2
[1] FALSE
D62V7, binary
                                 cls
clus                               0  1
  DEL PEAK 31(13Q12.11) MUTATED    7 64
  DEL PEAK 31(13Q12.11) WILD-TYPE 17 85
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 31(13Q12.11) MUTATED      7   64
  DEL PEAK 31(13Q12.11) WILD-TYPE   17   85
        clus
vv       DEL PEAK 31(13Q12.11) MUTATED DEL PEAK 31(13Q12.11) WILD-TYPE
  FEMALE                             7                              17
  MALE                              64                              85
[1] 2 2
[1] FALSE
D62V8, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(13Q12.11) MUTATED      24                         1    39
  DEL PEAK 31(13Q12.11) WILD-TYPE    17                         1    72
D62V9, multiclass
                           clus
vv                          DEL PEAK 31(13Q12.11) MUTATED
  ASIAN                                                24
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                39
                           clus
vv                          DEL PEAK 31(13Q12.11) WILD-TYPE
  ASIAN                                                  17
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                  72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V10, binary
                                 cls
clus                               0  1
  DEL PEAK 31(13Q12.11) MUTATED    1 39
  DEL PEAK 31(13Q12.11) WILD-TYPE  2 42
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 31(13Q12.11) MUTATED      1   39
  DEL PEAK 31(13Q12.11) WILD-TYPE    2   42
                        clus
vv                       DEL PEAK 31(13Q12.11) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            39
                        clus
vv                       DEL PEAK 31(13Q12.11) WILD-TYPE
  HISPANIC OR LATINO                                   2
  NOT HISPANIC OR LATINO                              42
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK 32(13Q14.2) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 32(13Q14.2) MUTATED   41 27
  DEL PEAK 32(13Q14.2) WILD-TYPE 59 44
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                            68                            103 
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                            27                             44 
$`DEL PEAK 32(13Q14.2) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-IG-A3QL TCGA-IG-A3Y9 
       25.78        58.55         7.63         8.94        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
       20.78         2.63         3.88         0.53        17.03        23.41 
TCGA-IG-A6QS TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A93E 
        9.96        44.75        60.39        68.02         3.68        25.22 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OU 
       24.00         3.68        21.01        47.93         3.16        29.00 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NU 
        3.95         3.02        13.48        13.22         5.49        83.24 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41         0.10        13.15        15.35         0.10        13.25 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 
       12.49        12.76        12.59        22.39         0.10        11.54 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A9FO 
       13.22        12.33        10.52        12.23        12.03         0.13 
TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A8WG TCGA-V5-A7RE TCGA-VR-A8EO 
        5.06        29.59         6.35        12.69         4.80        18.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       19.96        22.82        18.31        28.11        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA7I 
       42.87        15.91 

$`DEL PEAK 32(13Q14.2) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       31.27        14.30         5.92        13.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3YC TCGA-IG-A4P3 
       32.45         7.69         6.21        33.27        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
        9.30         0.79        12.82        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       12.16       122.10        41.52        42.77        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       23.18        31.56        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        0.30         4.31         8.94         4.70        32.61        19.99 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         3.32         7.17         1.38        58.59         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        0.36         7.40        55.50         2.66        35.97        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.55         7.76        21.37         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NV TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A8 
       27.12        52.57         0.10        12.46        12.59        15.52 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-M9-A5M8 
       12.33         4.47        25.25        12.00        13.18        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
        5.16         7.82         8.02         7.59        14.70         7.04 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
       53.95         9.30        15.78         2.89         1.45         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW 
       20.02        20.38         5.29         3.42        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-AA4D TCGA-VR-AA4G 
        4.44        12.43         1.55         8.12        46.19        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
       11.24         9.17        10.16         3.42         2.10         2.66 
TCGA-ZR-A9CJ 
       19.73 

  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                           0.1                            0.1 
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                         83.24                         122.10 
  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE 
                        12.955                         12.160 
[1] "0.1 - 83.2 (13.0)"  "0.1 - 122.1 (12.2)"
[1] "hr=" "1.2"
D63V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 32(13Q14.2) MUTATED         4        2        2        1        18
  DEL PEAK 32(13Q14.2) WILD-TYPE       4        3        5        0        21
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 32(13Q14.2) MUTATED           9        14          6          4
  DEL PEAK 32(13Q14.2) WILD-TYPE        20        11          6          6
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 32(13Q14.2) MUTATED            2        1         1
  DEL PEAK 32(13Q14.2) WILD-TYPE          5        4         3
D63V3, multiclass
            clus
vv           DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              2                              3
  STAGE IB                              2                              5
  STAGE II                              1                              0
  STAGE IIA                            18                             21
  STAGE IIB                             9                             20
  STAGE III                            14                             11
  STAGE IIIA                            6                              6
  STAGE IIIB                            4                              6
  STAGE IIIC                            2                              5
  STAGE IV                              1                              4
  STAGE IVA                             1                              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 32(13Q14.2) MUTATED      11 16 35  3
  DEL PEAK 32(13Q14.2) WILD-TYPE    20 20 50  2
D63V4, multiclass
       clus
vv      DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE
  T0+T1                           11                             20
  T2                              16                             20
  T3                              35                             50
  T4                               3                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 32(13Q14.2) MUTATED   32 28  3  2
  DEL PEAK 32(13Q14.2) WILD-TYPE 39 36  9  6
D63V5, multiclass
    clus
vv   DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE
  N0                           32                             39
  N1                           28                             36
  N2                            3                              9
  N3                            2                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V6, binary
                                cls
clus                              0  1
  DEL PEAK 32(13Q14.2) MUTATED   58  2
  DEL PEAK 32(13Q14.2) WILD-TYPE 68  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(13Q14.2) MUTATED     58    2
  DEL PEAK 32(13Q14.2) WILD-TYPE   68    7
   clus
vv  DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE
  0                           58                             68
  1                            2                              7
[1] 2 2
[1] FALSE
D63V7, binary
                                cls
clus                              0  1
  DEL PEAK 32(13Q14.2) MUTATED    6 63
  DEL PEAK 32(13Q14.2) WILD-TYPE 18 86
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(13Q14.2) MUTATED      6   63
  DEL PEAK 32(13Q14.2) WILD-TYPE   18   86
        clus
vv       DEL PEAK 32(13Q14.2) MUTATED DEL PEAK 32(13Q14.2) WILD-TYPE
  FEMALE                            6                             18
  MALE                             63                             86
[1] 2 2
[1] FALSE
D63V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(13Q14.2) MUTATED      26                         0    38
  DEL PEAK 32(13Q14.2) WILD-TYPE    15                         2    73
D63V9, multiclass
                           clus
vv                          DEL PEAK 32(13Q14.2) MUTATED
  ASIAN                                               26
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               38
                           clus
vv                          DEL PEAK 32(13Q14.2) WILD-TYPE
  ASIAN                                                 15
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V10, binary
                                cls
clus                              0  1
  DEL PEAK 32(13Q14.2) MUTATED    1 36
  DEL PEAK 32(13Q14.2) WILD-TYPE  2 45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(13Q14.2) MUTATED      1   36
  DEL PEAK 32(13Q14.2) WILD-TYPE    2   45
                        clus
vv                       DEL PEAK 32(13Q14.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           36
                        clus
vv                       DEL PEAK 32(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             45
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK 33(13Q21.31) MUTATION ANALYSIS
D64V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 33(13Q21.31) MUTATED   36 27
  DEL PEAK 33(13Q21.31) WILD-TYPE 64 44
  DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE 
                             63                             108 
  DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE 
                             27                              44 
$`DEL PEAK 33(13Q21.31) MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3Y9 
       58.55         7.63         8.94        32.45        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
       20.78         2.63         3.88         0.53        17.03        23.41 
TCGA-IG-A6QS TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A93E TCGA-L5-A4OE 
        9.96        44.75        60.39        68.02        25.22        24.00 
TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A88V 
        3.68        21.01        47.93         3.16        29.00         2.60 
TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ 
       13.48        13.22         5.49        83.24        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
        5.92        10.45        12.43        13.41         0.10        13.15 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 
       15.35        13.25        12.46        12.49        12.76        22.39 
TCGA-LN-A4A6 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY 
        0.10        13.22        12.33        10.52        12.23        12.03 
TCGA-LN-A9FO TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8WG 
        0.13         7.59         5.06         6.35         9.30        12.69 
TCGA-V5-A7RE TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8EU TCGA-VR-A8EX 
        4.80        18.81        19.96        22.82        18.31        28.11 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7I 
       18.18        42.87        15.91 

$`DEL PEAK 33(13Q21.31) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO 
       25.78        31.27        14.30         5.92        13.94        16.24 
TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3YC TCGA-IG-A4P3 
        4.21         7.69         6.21        33.27        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
        9.30         0.79        12.82        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       12.16       122.10         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        31.56        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OH 
       30.25         0.30         4.31         8.94         4.70        32.61 
TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       19.99        18.35         3.32         7.17         1.38        58.59 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W 
        4.90         7.13         7.43         6.94         8.71        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        0.36         7.40         3.95         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ 
       35.97        12.92        16.47        13.55         7.76        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-LN-A49M TCGA-LN-A49V 
        8.71        13.41        27.12        52.57        12.66         0.10 
TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        0.10        12.59        12.59        15.52        11.54        12.33 
TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU 
        4.47        25.25        12.00        13.18        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 
        7.82         8.02        14.70         7.04        29.59        53.95 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
       15.78         2.89         1.45         7.00        20.02        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8ER 
        5.29         3.42        15.35         9.27         4.44        12.43 
TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
        1.55         8.12        30.71        46.19        15.06        11.24 
TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        9.17        10.16         3.42         2.10         2.66        19.73 

  DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE 
                            0.1                             0.1 
  DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE 
                          83.24                          122.10 
  DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE 
                         13.150                          12.245 
[1] "0.1 - 83.2 (13.2)"  "0.1 - 122.1 (12.2)"
[1] "hr=" "1.1"
D64V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 33(13Q21.31) MUTATED         3        2        2        1        16
  DEL PEAK 33(13Q21.31) WILD-TYPE       5        3        5        0        23
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 33(13Q21.31) MUTATED           9        12          6          4
  DEL PEAK 33(13Q21.31) WILD-TYPE        20        13          6          6
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 33(13Q21.31) MUTATED            2        1         1
  DEL PEAK 33(13Q21.31) WILD-TYPE          5        4         3
D64V3, multiclass
            clus
vv           DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE
  STAGE I                                3                               5
  STAGE IA                               2                               3
  STAGE IB                               2                               5
  STAGE II                               1                               0
  STAGE IIA                             16                              23
  STAGE IIB                              9                              20
  STAGE III                             12                              13
  STAGE IIIA                             6                               6
  STAGE IIIB                             4                               6
  STAGE IIIC                             2                               5
  STAGE IV                               1                               4
  STAGE IVA                              1                               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3 T4
  DEL PEAK 33(13Q21.31) MUTATED      10 14 32  3
  DEL PEAK 33(13Q21.31) WILD-TYPE    21 22 53  2
D64V4, multiclass
       clus
vv      DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE
  T0+T1                            10                              21
  T2                               14                              22
  T3                               32                              53
  T4                                3                               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  DEL PEAK 33(13Q21.31) MUTATED   29 25  3  2
  DEL PEAK 33(13Q21.31) WILD-TYPE 42 39  9  6
D64V5, multiclass
    clus
vv   DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE
  N0                            29                              42
  N1                            25                              39
  N2                             3                               9
  N3                             2                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V6, binary
                                 cls
clus                               0  1
  DEL PEAK 33(13Q21.31) MUTATED   51  2
  DEL PEAK 33(13Q21.31) WILD-TYPE 75  7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q21.31) MUTATED     51    2
  DEL PEAK 33(13Q21.31) WILD-TYPE   75    7
   clus
vv  DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE
  0                            51                              75
  1                             2                               7
[1] 2 2
[1] FALSE
D64V7, binary
                                 cls
clus                               0  1
  DEL PEAK 33(13Q21.31) MUTATED    5 59
  DEL PEAK 33(13Q21.31) WILD-TYPE 19 90
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q21.31) MUTATED      5   59
  DEL PEAK 33(13Q21.31) WILD-TYPE   19   90
        clus
vv       DEL PEAK 33(13Q21.31) MUTATED DEL PEAK 33(13Q21.31) WILD-TYPE
  FEMALE                             5                              19
  MALE                              59                              90
[1] 2 2
[1] FALSE
D64V8, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(13Q21.31) MUTATED      23                         0    36
  DEL PEAK 33(13Q21.31) WILD-TYPE    18                         2    75
D64V9, multiclass
                           clus
vv                          DEL PEAK 33(13Q21.31) MUTATED
  ASIAN                                                23
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                36
                           clus
vv                          DEL PEAK 33(13Q21.31) WILD-TYPE
  ASIAN                                                  18
  BLACK OR AFRICAN AMERICAN                               2
  WHITE                                                  75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V10, binary
                                 cls
clus                               0  1
  DEL PEAK 33(13Q21.31) MUTATED    2 33
  DEL PEAK 33(13Q21.31) WILD-TYPE  1 48
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q21.31) MUTATED      2   33
  DEL PEAK 33(13Q21.31) WILD-TYPE    1   48
                        clus
vv                       DEL PEAK 33(13Q21.31) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            33
                        clus
vv                       DEL PEAK 33(13Q21.31) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                              48
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK 34(14Q23.3) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 34(14Q23.3) MUTATED   26 23
  DEL PEAK 34(14Q23.3) WILD-TYPE 74 48
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                            49                            122 
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                            23                             48 
$`DEL PEAK 34(14Q23.3) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3QL 
       31.27         7.63         8.94        16.24         4.21        20.09 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FB 
       23.41        12.82         4.67        14.50       122.10        60.39 
TCGA-JY-A6FH TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
       42.77        25.22         0.30         8.94        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88Y 
        4.70         3.16        29.00         7.13         6.94         0.36 
TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L7-A6VZ TCGA-LN-A49L 
        3.95        55.50         2.66        16.47        10.36        10.45 
TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-M9-A5M8 TCGA-R6-A6DQ 
       13.25        12.59        10.52        12.03        33.11         7.59 
TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-VR-A8EO 
        5.06         6.35         9.30        15.78         7.00        18.81 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-Z6-AAPN 
       22.82        12.43        18.31        42.87        15.06         2.66 
TCGA-ZR-A9CJ 
       19.73 

$`DEL PEAK 34(14Q23.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GR 
       25.78        14.30        58.55         5.92        13.94        32.45 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69         6.21        33.27         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
        0.79         9.96        14.86        12.16        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        25.41        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OH 
       24.03         6.28         3.16        30.25         4.31        32.61 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       19.99        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V 
        1.38        58.59         4.90         7.43         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
       25.12         7.40         3.02        35.97        12.92        13.48 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K 
       13.41        27.12        83.24        52.57        46.09         5.92 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.66        12.43        13.41         0.10        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10         0.10        12.46        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39         0.10        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ 
        4.47        12.33        25.25        12.00        12.23        13.18 
TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 
        0.13         5.16         7.82         8.02        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV 
       29.59        53.95         2.89         1.45        12.69        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42         4.80        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
        4.44        19.96         1.55         8.12        28.11        30.71 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       18.18        46.19        11.24         9.17        15.91        10.16 
TCGA-Z6-A8JD TCGA-Z6-A8JE 
        3.42         2.10 

  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                           0.3                            0.1 
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                        122.10                          83.24 
  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE 
                        12.430                         12.625 
[1] "0.3 - 122.1 (12.4)" "0.1 - 83.2 (12.6)" 
[1] "hr=" "1.2"
D65V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 34(14Q23.3) MUTATED         3        1        1        0         7
  DEL PEAK 34(14Q23.3) WILD-TYPE       5        4        6        1        32
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 34(14Q23.3) MUTATED           8         9          3          4
  DEL PEAK 34(14Q23.3) WILD-TYPE        21        16          9          6
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 34(14Q23.3) MUTATED            2        1         3
  DEL PEAK 34(14Q23.3) WILD-TYPE          5        4         1
D65V3, multiclass
            clus
vv           DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  STAGE I                               3                              5
  STAGE IA                              1                              4
  STAGE IB                              1                              6
  STAGE II                              0                              1
  STAGE IIA                             7                             32
  STAGE IIB                             8                             21
  STAGE III                             9                             16
  STAGE IIIA                            3                              9
  STAGE IIIB                            4                              6
  STAGE IIIC                            2                              5
  STAGE IV                              1                              4
  STAGE IVA                             3                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 34(14Q23.3) MUTATED      10  6 28  1
  DEL PEAK 34(14Q23.3) WILD-TYPE    21 30 57  4
D65V4, multiclass
       clus
vv      DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  T0+T1                           10                             21
  T2                               6                             30
  T3                              28                             57
  T4                               1                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 34(14Q23.3) MUTATED   16 21  5  2
  DEL PEAK 34(14Q23.3) WILD-TYPE 55 43  7  6
D65V5, multiclass
    clus
vv   DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  N0                           16                             55
  N1                           21                             43
  N2                            5                              7
  N3                            2                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V6, binary
                                cls
clus                              0  1
  DEL PEAK 34(14Q23.3) MUTATED   33  4
  DEL PEAK 34(14Q23.3) WILD-TYPE 93  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q23.3) MUTATED     33    4
  DEL PEAK 34(14Q23.3) WILD-TYPE   93    5
   clus
vv  DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  0                           33                             93
  1                            4                              5
[1] 2 2
[1] FALSE
D65V7, binary
                                cls
clus                               0   1
  DEL PEAK 34(14Q23.3) MUTATED     7  42
  DEL PEAK 34(14Q23.3) WILD-TYPE  17 107
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q23.3) MUTATED      7   42
  DEL PEAK 34(14Q23.3) WILD-TYPE   17  107
        clus
vv       DEL PEAK 34(14Q23.3) MUTATED DEL PEAK 34(14Q23.3) WILD-TYPE
  FEMALE                            7                             17
  MALE                             42                            107
[1] 2 2
[1] FALSE
D65V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(14Q23.3) MUTATED       8                         0    32
  DEL PEAK 34(14Q23.3) WILD-TYPE    33                         2    79
D65V9, multiclass
                           clus
vv                          DEL PEAK 34(14Q23.3) MUTATED
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               32
                           clus
vv                          DEL PEAK 34(14Q23.3) WILD-TYPE
  ASIAN                                                 33
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V10, binary
                                cls
clus                              0  1
  DEL PEAK 34(14Q23.3) MUTATED    1 17
  DEL PEAK 34(14Q23.3) WILD-TYPE  2 64
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q23.3) MUTATED      1   17
  DEL PEAK 34(14Q23.3) WILD-TYPE    2   64
                        clus
vv                       DEL PEAK 34(14Q23.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           17
                        clus
vv                       DEL PEAK 34(14Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             64
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK 35(15Q11.2) MUTATION ANALYSIS
D66V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 35(15Q11.2) MUTATED   34 24
  DEL PEAK 35(15Q11.2) WILD-TYPE 66 47
  DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE 
                            58                            113 
  DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE 
                            24                             47 
$`DEL PEAK 35(15Q11.2) MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL 
        7.63         5.92        16.24        32.45         7.69        20.09 
TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A625 TCGA-IG-A97H TCGA-JY-A938 TCGA-JY-A93C 
       20.12         3.88        12.82        14.50        25.41        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       31.56        25.22         0.30         8.94        24.00         4.70 
TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A893 TCGA-L5-A8NE 
       32.61        47.93         4.90        29.00         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
        2.66        12.92         5.49         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4A8 
       83.24        10.45         0.10        12.59        22.39        15.52 
TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HY TCGA-LN-A9FO TCGA-Q9-A6FU 
       12.33        12.33        25.25        12.03         0.13         5.16 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-RE-A7BO 
        7.59         5.06        14.70        29.59         9.30         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EO TCGA-VR-A8EX 
       20.02        20.38         3.42         4.80        18.81        28.11 
TCGA-VR-A8EZ TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.18        10.16         3.42         2.10 

$`DEL PEAK 35(15Q11.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        31.27        14.30        58.55        13.94         8.94 
TCGA-2H-A9GQ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        4.21         6.21        33.27         0.85        20.78         2.63 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       18.64         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86         4.67        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       60.39        68.02         3.68        41.52        42.77        21.70 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         4.31         3.68 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       19.99        21.01        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        3.16        58.59         7.13         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NG 
        2.60        25.12         0.36         7.40         3.95        35.97 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ 
       13.48        16.47        13.55        13.22         7.76        21.37 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       52.57        46.09        10.36         5.92        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.41        13.15        15.35         0.10        13.25         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 
       12.46        12.49        12.76        12.59         0.10        11.54 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ 
       13.22         4.47        10.52        12.00        12.23        13.18 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 
       33.11         7.82         8.02         7.04         6.35        53.95 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RB TCGA-V5-AASV 
       15.78         2.89         1.45        12.69         5.29        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         4.44        19.96        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       18.31         8.12        30.71        42.87        46.19        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       11.24         9.17        15.91         2.66        19.73 

  DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE 
                           0.1                            0.1 
  DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE 
                         83.24                         122.10 
  DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE 
                        12.705                         12.490 
[1] "0.1 - 83.2 (12.7)"  "0.1 - 122.1 (12.5)"
[1] "hr=" "1"  
D66V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 35(15Q11.2) MUTATED         3        1        2        0        10
  DEL PEAK 35(15Q11.2) WILD-TYPE       5        4        5        1        29
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 35(15Q11.2) MUTATED          10         8          4          6
  DEL PEAK 35(15Q11.2) WILD-TYPE        19        17          8          4
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 35(15Q11.2) MUTATED            2        2         3
  DEL PEAK 35(15Q11.2) WILD-TYPE          5        3         1
D66V3, multiclass
            clus
vv           DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE
  STAGE I                               3                              5
  STAGE IA                              1                              4
  STAGE IB                              2                              5
  STAGE II                              0                              1
  STAGE IIA                            10                             29
  STAGE IIB                            10                             19
  STAGE III                             8                             17
  STAGE IIIA                            4                              8
  STAGE IIIB                            6                              4
  STAGE IIIC                            2                              5
  STAGE IV                              2                              3
  STAGE IVA                             3                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 35(15Q11.2) MUTATED      11 11 31  0
  DEL PEAK 35(15Q11.2) WILD-TYPE    20 25 54  5
D66V4, multiclass
       clus
vv      DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE
  T0+T1                           11                             20
  T2                              11                             25
  T3                              31                             54
  T4                               0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 35(15Q11.2) MUTATED   23 21  6  2
  DEL PEAK 35(15Q11.2) WILD-TYPE 48 43  6  6
D66V5, multiclass
    clus
vv   DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE
  N0                           23                             48
  N1                           21                             43
  N2                            6                              6
  N3                            2                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V6, binary
                                cls
clus                              0  1
  DEL PEAK 35(15Q11.2) MUTATED   42  5
  DEL PEAK 35(15Q11.2) WILD-TYPE 84  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(15Q11.2) MUTATED     42    5
  DEL PEAK 35(15Q11.2) WILD-TYPE   84    4
   clus
vv  DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE
  0                           42                             84
  1                            5                              4
[1] 2 2
[1] FALSE
D66V7, binary
                                cls
clus                              0  1
  DEL PEAK 35(15Q11.2) MUTATED    8 51
  DEL PEAK 35(15Q11.2) WILD-TYPE 16 98
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(15Q11.2) MUTATED      8   51
  DEL PEAK 35(15Q11.2) WILD-TYPE   16   98
        clus
vv       DEL PEAK 35(15Q11.2) MUTATED DEL PEAK 35(15Q11.2) WILD-TYPE
  FEMALE                            8                             16
  MALE                             51                             98
[1] 2 2
[1] FALSE
D66V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(15Q11.2) MUTATED      14                         1    37
  DEL PEAK 35(15Q11.2) WILD-TYPE    27                         1    74
D66V9, multiclass
                           clus
vv                          DEL PEAK 35(15Q11.2) MUTATED
  ASIAN                                               14
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               37
                           clus
vv                          DEL PEAK 35(15Q11.2) WILD-TYPE
  ASIAN                                                 27
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V10, binary
                                cls
clus                              0  1
  DEL PEAK 35(15Q11.2) MUTATED    1 30
  DEL PEAK 35(15Q11.2) WILD-TYPE  2 51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(15Q11.2) MUTATED      1   30
  DEL PEAK 35(15Q11.2) WILD-TYPE    2   51
                        clus
vv                       DEL PEAK 35(15Q11.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           30
                        clus
vv                       DEL PEAK 35(15Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             51
[1] 2 2
[1] FALSE

Clustering(67) Variable = DEL PEAK 36(16P13.3) MUTATION ANALYSIS
D67V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 36(16P13.3) MUTATED   31 31
  DEL PEAK 36(16P13.3) WILD-TYPE 69 40
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                            62                            109 
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                            31                             40 
$`DEL PEAK 36(16P13.3) MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ 
       58.55         7.63         5.92        13.94         8.94         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3YC TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C 
       32.45         7.69        20.12        42.77        25.41        23.18 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH 
       25.22         3.16         8.94        24.00         4.70        32.61 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 
        1.38         3.16        58.59         0.36         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NN TCGA-L5-A8NT TCGA-L5-A8NV 
        3.02        12.92        13.48         5.49        27.12        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49V TCGA-LN-A4A5 
       46.09        10.36        10.45        12.43         0.10        22.39 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A7HW TCGA-LN-A7HY TCGA-Q9-A6FU TCGA-R6-A6DN 
       12.33         4.47        12.00        12.03         5.16         8.02 
TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        5.06        29.59         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89         1.45        12.69         7.00         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8Q7 
        4.80         9.27        19.96        22.82        12.43        42.87 
TCGA-VR-AA7I TCGA-Z6-A8JE 
       15.91         2.10 

$`DEL PEAK 36(16P13.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GO TCGA-IC-A6RF TCGA-IG-A3I8 
       25.78        31.27        14.30        16.24         6.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS 
       20.09         0.85        20.78         2.63        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
       44.75        60.39        68.02         3.68        41.52        21.70 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       31.56        24.03         6.28        30.25         0.30         4.31 
TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        3.68        19.99        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        7.17         4.90        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        8.71         2.60        25.12        55.50         2.66        35.97 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         7.76        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R 
       13.41        83.24         5.92        12.66        13.41         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        15.35        13.25         0.10        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.76        12.59         0.10        15.52        11.54 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ 
       13.22        12.33        25.25        10.52        12.23        13.18 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
        0.13        33.11         7.82         7.59        14.70         7.04 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ET 
       20.02        20.38        15.35         4.44        18.81         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D 
       18.31         8.12        28.11        30.71        18.18        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN 
       15.06        11.24         9.17        10.16         3.42         2.66 
TCGA-ZR-A9CJ 
       19.73 

  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                           0.1                            0.1 
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                         58.59                         122.10 
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                        10.405                         13.180 
[1] "0.1 - 58.6 (10.4)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.5"
D67V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 36(16P13.3) MUTATED         4        1        2        0         7
  DEL PEAK 36(16P13.3) WILD-TYPE       4        4        5        1        32
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 36(16P13.3) MUTATED           9        11          5          4
  DEL PEAK 36(16P13.3) WILD-TYPE        20        14          7          6
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 36(16P13.3) MUTATED            1        2         1
  DEL PEAK 36(16P13.3) WILD-TYPE          6        3         3
D67V3, multiclass
            clus
vv           DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              1                              4
  STAGE IB                              2                              5
  STAGE II                              0                              1
  STAGE IIA                             7                             32
  STAGE IIB                             9                             20
  STAGE III                            11                             14
  STAGE IIIA                            5                              7
  STAGE IIIB                            4                              6
  STAGE IIIC                            1                              6
  STAGE IV                              2                              3
  STAGE IVA                             1                              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 36(16P13.3) MUTATED      13  9 27  2
  DEL PEAK 36(16P13.3) WILD-TYPE    18 27 58  3
D67V4, multiclass
       clus
vv      DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  T0+T1                           13                             18
  T2                               9                             27
  T3                              27                             58
  T4                               2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 36(16P13.3) MUTATED   17 27  6  1
  DEL PEAK 36(16P13.3) WILD-TYPE 54 37  6  7
D67V5, multiclass
    clus
vv   DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  N0                           17                             54
  N1                           27                             37
  N2                            6                              6
  N3                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V6, binary
                                cls
clus                              0  1
  DEL PEAK 36(16P13.3) MUTATED   41  3
  DEL PEAK 36(16P13.3) WILD-TYPE 85  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16P13.3) MUTATED     41    3
  DEL PEAK 36(16P13.3) WILD-TYPE   85    6
   clus
vv  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  0                           41                             85
  1                            3                              6
[1] 2 2
[1] FALSE
D67V7, binary
                                cls
clus                              0  1
  DEL PEAK 36(16P13.3) MUTATED    7 56
  DEL PEAK 36(16P13.3) WILD-TYPE 17 93
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16P13.3) MUTATED      7   56
  DEL PEAK 36(16P13.3) WILD-TYPE   17   93
        clus
vv       DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  FEMALE                            7                             17
  MALE                             56                             93
[1] 2 2
[1] FALSE
D67V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(16P13.3) MUTATED      10                         1    42
  DEL PEAK 36(16P13.3) WILD-TYPE    31                         1    69
D67V9, multiclass
                           clus
vv                          DEL PEAK 36(16P13.3) MUTATED
  ASIAN                                               10
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               42
                           clus
vv                          DEL PEAK 36(16P13.3) WILD-TYPE
  ASIAN                                                 31
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V10, binary
                                cls
clus                              0  1
  DEL PEAK 36(16P13.3) MUTATED    3 26
  DEL PEAK 36(16P13.3) WILD-TYPE  0 55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16P13.3) MUTATED      3   26
  DEL PEAK 36(16P13.3) WILD-TYPE    0   55
                        clus
vv                       DEL PEAK 36(16P13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           26
                        clus
vv                       DEL PEAK 36(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  0
  NOT HISPANIC OR LATINO                             55
[1] 2 2
[1] FALSE

Clustering(68) Variable = DEL PEAK 37(16Q23.1) MUTATION ANALYSIS
D68V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 37(16Q23.1) MUTATED   48 32
  DEL PEAK 37(16Q23.1) WILD-TYPE 52 39
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            80                             91 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            32                             39 
$`DEL PEAK 37(16Q23.1) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-IG-A3QL TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A97H 
        4.21        20.09        20.12         3.88         0.53        14.50 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93D 
      122.10        60.39        42.77        25.41        23.18        31.56 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OJ 
       25.22         3.16         8.94        24.00         3.68        21.01 
TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
       18.35         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        7.43         2.60         0.36         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
        2.66        35.97        16.47        13.22         7.76         5.49 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ 
        8.71        13.41        27.12        83.24        46.09        10.36 
TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4MQ 
       10.45        13.41         0.10        13.25        12.59        12.33 
TCGA-LN-A4MR TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-R6-A6DN 
       13.22        10.52        12.00        12.03        13.18         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.59         5.06        14.70         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB 
       15.78         2.89         1.45        12.69         7.00         5.29 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-Z6-A8JD 
        4.80         9.27        18.81        19.96        22.82         3.42 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

$`DEL PEAK 37(16Q23.1) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
       25.78        14.30        58.55        32.45         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QT 
       33.27         0.85        20.78         2.63        18.64         9.30 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        4.67        12.16        44.75        68.02         3.68        41.52 
TCGA-JY-A939 TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       21.70        24.03         6.28        30.25         0.30         4.31 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP 
        4.70        32.61        19.99        47.93         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NH 
        1.38         6.94         8.71        25.12         7.40        12.92 
TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49M 
       13.48        13.55        21.37        52.57         5.92        12.66 
TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y 
       12.43         0.10        13.15        15.35         0.10        12.46 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39         0.10        15.52 
TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HX TCGA-LN-A9FO 
       11.54         4.47        12.33        25.25        12.23         0.13 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-S8-A6BV 
       33.11         5.16         7.82         7.04        29.59        20.02 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8ER TCGA-VR-A8ET 
       20.38         3.42        15.35         4.44        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        30.71        18.18        42.87 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        15.06        11.24         9.17        15.91        10.16 
TCGA-Z6-A8JE 
        2.10 

  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                           0.1                            0.1 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                        122.10                          68.02 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                         12.18                          12.66 
[1] "0.1 - 122.1 (12.2)" "0.1 - 68.0 (12.7)" 
[1] "hr=" "1.1"
D68V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 37(16Q23.1) MUTATED         4        1        2        0        12
  DEL PEAK 37(16Q23.1) WILD-TYPE       4        4        5        1        27
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 37(16Q23.1) MUTATED          16        14          3          5
  DEL PEAK 37(16Q23.1) WILD-TYPE        13        11          9          5
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 37(16Q23.1) MUTATED            3        1         3
  DEL PEAK 37(16Q23.1) WILD-TYPE          4        4         1
D68V3, multiclass
            clus
vv           DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              1                              4
  STAGE IB                              2                              5
  STAGE II                              0                              1
  STAGE IIA                            12                             27
  STAGE IIB                            16                             13
  STAGE III                            14                             11
  STAGE IIIA                            3                              9
  STAGE IIIB                            5                              5
  STAGE IIIC                            3                              4
  STAGE IV                              1                              4
  STAGE IVA                             3                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 37(16Q23.1) MUTATED      14 14 40  0
  DEL PEAK 37(16Q23.1) WILD-TYPE    17 22 45  5
D68V4, multiclass
       clus
vv      DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  T0+T1                           14                             17
  T2                              14                             22
  T3                              40                             45
  T4                               0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 37(16Q23.1) MUTATED   25 34  5  3
  DEL PEAK 37(16Q23.1) WILD-TYPE 46 30  7  5
D68V5, multiclass
    clus
vv   DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  N0                           25                             46
  N1                           34                             30
  N2                            5                              7
  N3                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V6, binary
                                cls
clus                              0  1
  DEL PEAK 37(16Q23.1) MUTATED   54  4
  DEL PEAK 37(16Q23.1) WILD-TYPE 72  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.1) MUTATED     54    4
  DEL PEAK 37(16Q23.1) WILD-TYPE   72    5
   clus
vv  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  0                           54                             72
  1                            4                              5
[1] 2 2
[1] FALSE
D68V7, binary
                                cls
clus                              0  1
  DEL PEAK 37(16Q23.1) MUTATED    9 71
  DEL PEAK 37(16Q23.1) WILD-TYPE 15 78
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.1) MUTATED      9   71
  DEL PEAK 37(16Q23.1) WILD-TYPE   15   78
        clus
vv       DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  FEMALE                            9                             15
  MALE                             71                             78
[1] 2 2
[1] FALSE
D68V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 37(16Q23.1) MUTATED      14                         0    55
  DEL PEAK 37(16Q23.1) WILD-TYPE    27                         2    56
D68V9, multiclass
                           clus
vv                          DEL PEAK 37(16Q23.1) MUTATED
  ASIAN                                               14
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               55
                           clus
vv                          DEL PEAK 37(16Q23.1) WILD-TYPE
  ASIAN                                                 27
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V10, binary
                                cls
clus                              0  1
  DEL PEAK 37(16Q23.1) MUTATED    3 31
  DEL PEAK 37(16Q23.1) WILD-TYPE  0 50
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.1) MUTATED      3   31
  DEL PEAK 37(16Q23.1) WILD-TYPE    0   50
                        clus
vv                       DEL PEAK 37(16Q23.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           31
                        clus
vv                       DEL PEAK 37(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  0
  NOT HISPANIC OR LATINO                             50
[1] 2 2
[1] FALSE

Clustering(69) Variable = DEL PEAK 38(17P12) MUTATION ANALYSIS
D69V1, survival
                              sevent
clus2                           0  1
  DEL PEAK 38(17P12) MUTATED   46 35
  DEL PEAK 38(17P12) WILD-TYPE 54 36
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                          81                           90 
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                          35                           36 
$`DEL PEAK 38(17P12) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ 
       25.78         7.63         5.92        13.94         8.94         4.21 
TCGA-2H-A9GR TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H 
       32.45        18.64         3.88         0.79        23.41        14.50 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93D TCGA-JY-A93E 
      122.10        60.39        42.77        25.41        31.56        25.22 
TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OO 
       30.25        24.00         3.68         4.70        32.61         3.32 
TCGA-L5-A4OP TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V 
        7.17         4.90        29.00         7.13         7.43         2.60 
TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ 
        0.36         3.95        55.50        35.97        13.48        16.47 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
       13.22         5.49         8.71        13.41        27.12        83.24 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
        5.92        10.45        12.66        13.15        15.35        13.25 
TCGA-LN-A4A1 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU 
       12.59        12.33        10.52        13.18        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y2 
        7.82         7.59         5.06         7.04        29.59         9.30 
TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
       15.78         1.45        12.69         7.00        20.02        20.38 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        4.80         9.27         4.44        19.96        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7B 
        1.55        18.31         8.12        18.18        46.19        11.24 
TCGA-X8-AAAR TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       10.16         2.66        19.73 

$`DEL PEAK 38(17P12) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IC-A6RF 
       31.27        14.30        58.55        16.24         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        9.30         0.53        17.03        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        4.67        12.16        44.75        68.02         3.68        41.52 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       21.70        23.18        24.03         6.28         3.16         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        4.31         8.94        19.99        21.01        47.93        18.35 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W 
        1.38         3.16        58.59         6.94         8.71        25.12 
TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NM 
        7.40         3.02         2.66        12.92        13.55         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49N TCGA-LN-A49O 
       21.37        52.57        46.09        10.36        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.10         0.10         0.10        12.46        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39         0.10        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       13.22         4.47        25.25        12.00        12.23        12.03 
TCGA-LN-A9FO TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 
        0.13         8.02        14.70         6.35        53.95         2.89 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EX TCGA-VR-A8EY 
        5.29         3.42        15.35        18.81        28.11        30.71 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE 
       42.87        15.06         9.17        15.91         3.42         2.10 

  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                        0.36                         0.10 
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                      122.10                        68.02 
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                      12.660                       12.475 
[1] "0.4 - 122.1 (12.7)" "0.1 - 68.0 (12.5)" 
[1] "hr=" "1"  
D69V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 38(17P12) MUTATED         5        1        4        0        15
  DEL PEAK 38(17P12) WILD-TYPE       3        4        3        1        24
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 38(17P12) MUTATED          13        15          2          6
  DEL PEAK 38(17P12) WILD-TYPE        16        10         10          4
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 38(17P12) MUTATED            4        3         1
  DEL PEAK 38(17P12) WILD-TYPE          3        2         3
D69V3, multiclass
            clus
vv           DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  STAGE I                             5                            3
  STAGE IA                            1                            4
  STAGE IB                            4                            3
  STAGE II                            0                            1
  STAGE IIA                          15                           24
  STAGE IIB                          13                           16
  STAGE III                          15                           10
  STAGE IIIA                          2                           10
  STAGE IIIB                          6                            4
  STAGE IIIC                          4                            3
  STAGE IV                            3                            2
  STAGE IVA                           1                            3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3 T4
  DEL PEAK 38(17P12) MUTATED      14 14 43  1
  DEL PEAK 38(17P12) WILD-TYPE    17 22 42  4
D69V4, multiclass
       clus
vv      DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  T0+T1                         14                           17
  T2                            14                           22
  T3                            43                           42
  T4                             1                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2 N3
  DEL PEAK 38(17P12) MUTATED   28 32  6  5
  DEL PEAK 38(17P12) WILD-TYPE 43 32  6  3
D69V5, multiclass
    clus
vv   DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  N0                         28                           43
  N1                         32                           32
  N2                          6                            6
  N3                          5                            3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V6, binary
                              cls
clus                            0  1
  DEL PEAK 38(17P12) MUTATED   59  4
  DEL PEAK 38(17P12) WILD-TYPE 67  5
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 38(17P12) MUTATED     59    4
  DEL PEAK 38(17P12) WILD-TYPE   67    5
   clus
vv  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  0                         59                           67
  1                          4                            5
[1] 2 2
[1] FALSE
D69V7, binary
                              cls
clus                            0  1
  DEL PEAK 38(17P12) MUTATED    9 72
  DEL PEAK 38(17P12) WILD-TYPE 15 77
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 38(17P12) MUTATED      9   72
  DEL PEAK 38(17P12) WILD-TYPE   15   77
        clus
vv       DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  FEMALE                          9                           15
  MALE                           72                           77
[1] 2 2
[1] FALSE
D69V8, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 38(17P12) MUTATED      12                         0    58
  DEL PEAK 38(17P12) WILD-TYPE    29                         2    53
D69V9, multiclass
                           clus
vv                          DEL PEAK 38(17P12) MUTATED
  ASIAN                                             12
  BLACK OR AFRICAN AMERICAN                          0
  WHITE                                             58
                           clus
vv                          DEL PEAK 38(17P12) WILD-TYPE
  ASIAN                                               29
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V10, binary
                              cls
clus                            0  1
  DEL PEAK 38(17P12) MUTATED    2 31
  DEL PEAK 38(17P12) WILD-TYPE  1 50
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 38(17P12) MUTATED      2   31
  DEL PEAK 38(17P12) WILD-TYPE    1   50
                        clus
vv                       DEL PEAK 38(17P12) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         31
                        clus
vv                       DEL PEAK 38(17P12) WILD-TYPE
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           50
[1] 2 2
[1] FALSE

Clustering(70) Variable = DEL PEAK 39(17Q25.3) MUTATION ANALYSIS
D70V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 39(17Q25.3) MUTATED   32  8
  DEL PEAK 39(17Q25.3) WILD-TYPE 68 63
  DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE 
                            40                            131 
  DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE 
                             8                             63 
$`DEL PEAK 39(17Q25.3) MUTATED`
TCGA-2H-A9GN TCGA-IC-A6RE TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H 
        8.94         7.69        18.64         0.79        23.41        14.50 
TCGA-JY-A938 TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OR TCGA-L5-A4OU 
       25.41         4.70        32.61        21.01         3.16        29.00 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NR 
        0.36         7.40         3.95        55.50        35.97         8.71 
TCGA-LN-A49M TCGA-LN-A49S TCGA-LN-A49Y TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A5U6 
       12.66        13.15        12.46         0.10        12.33        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A9FO 
       25.25        10.52        12.00        12.23        12.03         0.13 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-V5-A7RE TCGA-V5-AASV 
        5.16         7.82         9.30        15.78         4.80        15.35 
TCGA-V5-AASX TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-X8-AAAR 
        4.44        28.11        42.87        10.16 

$`DEL PEAK 39(17Q25.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RF TCGA-IG-A3I8 
       13.94        16.24         4.21        32.45         6.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS 
       20.09         0.85        20.78         2.63        20.12         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        9.30         0.53        17.03        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        4.67        12.16       122.10        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        42.77        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OM 
        4.31         8.94        24.00         3.68        19.99        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         3.32         7.17         1.38        58.59         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.02         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT 
       13.22         7.76         5.49        21.37        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       83.24        52.57        46.09        10.36         5.92        10.45 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.43        13.41         0.10        15.35         0.10        13.25 
TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HZ TCGA-M9-A5M8 
       15.52        11.54        13.22         4.47        13.18        33.11 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        6.35        53.95         2.89         1.45        12.69         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EO 
       20.02        20.38         5.29         3.42         9.27        18.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       19.96        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       30.71        18.18        46.19        15.06        11.24         9.17 
TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       15.91         3.42         2.10         2.66        19.73 

  DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE 
                           0.1                            0.1 
  DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE 
                          55.5                          122.1 
  DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE 
                         12.13                          12.82 
[1] "0.1 - 55.5 (12.1)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "2"  
D70V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 39(17Q25.3) MUTATED         3        1        2        1        11
  DEL PEAK 39(17Q25.3) WILD-TYPE       5        4        5        0        28
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 39(17Q25.3) MUTATED           7         5          1          2
  DEL PEAK 39(17Q25.3) WILD-TYPE        22        20         11          8
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 39(17Q25.3) MUTATED            0        0         2
  DEL PEAK 39(17Q25.3) WILD-TYPE          7        5         2
D70V3, multiclass
            clus
vv           DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE
  STAGE I                               3                              5
  STAGE IA                              1                              4
  STAGE IB                              2                              5
  STAGE II                              1                              0
  STAGE IIA                            11                             28
  STAGE IIB                             7                             22
  STAGE III                             5                             20
  STAGE IIIA                            1                             11
  STAGE IIIB                            2                              8
  STAGE IIIC                            0                              7
  STAGE IV                              0                              5
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 39(17Q25.3) MUTATED      10 10 18  0
  DEL PEAK 39(17Q25.3) WILD-TYPE    21 26 67  5
D70V4, multiclass
       clus
vv      DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE
  T0+T1                           10                             21
  T2                              10                             26
  T3                              18                             67
  T4                               0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 39(17Q25.3) MUTATED   20 15  2  0
  DEL PEAK 39(17Q25.3) WILD-TYPE 51 49 10  8
D70V5, multiclass
    clus
vv   DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE
  N0                           20                             51
  N1                           15                             49
  N2                            2                             10
  N3                            0                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V6, binary
                                cls
clus                              0  1
  DEL PEAK 39(17Q25.3) MUTATED   32  2
  DEL PEAK 39(17Q25.3) WILD-TYPE 94  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17Q25.3) MUTATED     32    2
  DEL PEAK 39(17Q25.3) WILD-TYPE   94    7
   clus
vv  DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE
  0                           32                             94
  1                            2                              7
[1] 2 2
[1] FALSE
D70V7, binary
                                cls
clus                               0   1
  DEL PEAK 39(17Q25.3) MUTATED     6  34
  DEL PEAK 39(17Q25.3) WILD-TYPE  18 115
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17Q25.3) MUTATED      6   34
  DEL PEAK 39(17Q25.3) WILD-TYPE   18  115
        clus
vv       DEL PEAK 39(17Q25.3) MUTATED DEL PEAK 39(17Q25.3) WILD-TYPE
  FEMALE                            6                             18
  MALE                             34                            115
[1] 2 2
[1] FALSE
D70V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 39(17Q25.3) MUTATED      13                         1    23
  DEL PEAK 39(17Q25.3) WILD-TYPE    28                         1    88
D70V9, multiclass
                           clus
vv                          DEL PEAK 39(17Q25.3) MUTATED
  ASIAN                                               13
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               23
                           clus
vv                          DEL PEAK 39(17Q25.3) WILD-TYPE
  ASIAN                                                 28
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V10, binary
                                cls
clus                              0  1
  DEL PEAK 39(17Q25.3) MUTATED    1 24
  DEL PEAK 39(17Q25.3) WILD-TYPE  2 57
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17Q25.3) MUTATED      1   24
  DEL PEAK 39(17Q25.3) WILD-TYPE    2   57
                        clus
vv                       DEL PEAK 39(17Q25.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           24
                        clus
vv                       DEL PEAK 39(17Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             57
[1] 2 2
[1] FALSE

Clustering(71) Variable = DEL PEAK 40(18P11.23) MUTATION ANALYSIS
D71V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 40(18P11.23) MUTATED   32 24
  DEL PEAK 40(18P11.23) WILD-TYPE 68 47
  DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE 
                             56                             115 
  DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE 
                             24                              47 
$`DEL PEAK 40(18P11.23) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A3I8 
       25.78        14.30         5.92         8.94        16.24        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FA 
        0.85         2.63         0.79        23.41        14.50        44.75 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43E TCGA-L5-A43H 
       23.18        31.56        25.22        24.03        30.25         0.30 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OP TCGA-L5-A88S 
       24.00         3.68         4.70        32.61         7.17         6.94 
TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ 
        3.95        55.50         2.66        35.97        12.92        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49L 
       13.55        13.22         8.71        52.57         5.92        10.45 
TCGA-LN-A49N TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A7HY TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.43        12.46        12.59        12.03         5.16         7.82 
TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-RE-A7BO 
        7.59        29.59         6.35         9.30         1.45         7.00 
TCGA-S8-A6BV TCGA-V5-AASW TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8EW TCGA-X8-AAAR 
       20.02         9.27        19.96        22.82         8.12        10.16 
TCGA-Z6-A8JD TCGA-ZR-A9CJ 
        3.42        19.73 

$`DEL PEAK 40(18P11.23) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-2H-A9GR 
       31.27        58.55         7.63        13.94         4.21        32.45 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 
        7.69         6.21        20.09        20.78        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS 
        3.88         9.30         0.53        17.03        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD 
       14.86         4.67        12.16       122.10        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-KH-A6WC 
        3.68        41.52        42.77        25.41        21.70         6.28 
TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16         4.31         8.94        19.99        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         3.32         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN 
        0.36         7.40         3.02        13.48         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ 
       21.37        13.41        27.12        83.24        46.09        10.36 
TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.66        13.41         0.10        13.15        15.35         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       13.25         0.10        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
        0.10        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ 
       12.33        25.25        10.52        12.00        12.23        13.18 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        0.13        33.11         8.02         5.06        14.70         7.04 
TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB 
       53.95        15.78         2.89        12.69        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ER 
        3.42         4.80        15.35         4.44        18.81        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
        1.55        18.31        28.11        30.71        18.18        42.87 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JE 
       46.19        15.06        11.24         9.17        15.91         2.10 
TCGA-Z6-AAPN 
        2.66 

  DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE 
                            0.3                             0.1 
  DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE 
                           55.5                           122.1 
  DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE 
                         12.445                          12.660 
[1] "0.3 - 55.5 (12.4)"  "0.1 - 122.1 (12.7)"
[1] "hr=" "1.1"
D71V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 40(18P11.23) MUTATED         3        1        3        0         8
  DEL PEAK 40(18P11.23) WILD-TYPE       5        4        4        1        31
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 40(18P11.23) MUTATED           7        11          4          6
  DEL PEAK 40(18P11.23) WILD-TYPE        22        14          8          4
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 40(18P11.23) MUTATED            2        1         2
  DEL PEAK 40(18P11.23) WILD-TYPE          5        4         2
D71V3, multiclass
            clus
vv           DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE
  STAGE I                                3                               5
  STAGE IA                               1                               4
  STAGE IB                               3                               4
  STAGE II                               0                               1
  STAGE IIA                              8                              31
  STAGE IIB                              7                              22
  STAGE III                             11                              14
  STAGE IIIA                             4                               8
  STAGE IIIB                             6                               4
  STAGE IIIC                             2                               5
  STAGE IV                               1                               4
  STAGE IVA                              2                               2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3 T4
  DEL PEAK 40(18P11.23) MUTATED       9  6 34  1
  DEL PEAK 40(18P11.23) WILD-TYPE    22 30 51  4
D71V4, multiclass
       clus
vv      DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE
  T0+T1                             9                              22
  T2                                6                              30
  T3                               34                              51
  T4                                1                               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  DEL PEAK 40(18P11.23) MUTATED   19 22  6  2
  DEL PEAK 40(18P11.23) WILD-TYPE 52 42  6  6
D71V5, multiclass
    clus
vv   DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE
  N0                            19                              52
  N1                            22                              42
  N2                             6                               6
  N3                             2                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V6, binary
                                 cls
clus                               0  1
  DEL PEAK 40(18P11.23) MUTATED   40  3
  DEL PEAK 40(18P11.23) WILD-TYPE 86  6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(18P11.23) MUTATED     40    3
  DEL PEAK 40(18P11.23) WILD-TYPE   86    6
   clus
vv  DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE
  0                            40                              86
  1                             3                               6
[1] 2 2
[1] FALSE
D71V7, binary
                                 cls
clus                                0   1
  DEL PEAK 40(18P11.23) MUTATED    10  46
  DEL PEAK 40(18P11.23) WILD-TYPE  14 103
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(18P11.23) MUTATED     10   46
  DEL PEAK 40(18P11.23) WILD-TYPE   14  103
        clus
vv       DEL PEAK 40(18P11.23) MUTATED DEL PEAK 40(18P11.23) WILD-TYPE
  FEMALE                            10                              14
  MALE                              46                             103
[1] 2 2
[1] FALSE
D71V8, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 40(18P11.23) MUTATED      10                         0    40
  DEL PEAK 40(18P11.23) WILD-TYPE    31                         2    71
D71V9, multiclass
                           clus
vv                          DEL PEAK 40(18P11.23) MUTATED
  ASIAN                                                10
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                40
                           clus
vv                          DEL PEAK 40(18P11.23) WILD-TYPE
  ASIAN                                                  31
  BLACK OR AFRICAN AMERICAN                               2
  WHITE                                                  71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V10, binary
                                 cls
clus                               0  1
  DEL PEAK 40(18P11.23) MUTATED    1 24
  DEL PEAK 40(18P11.23) WILD-TYPE  2 57
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(18P11.23) MUTATED      1   24
  DEL PEAK 40(18P11.23) WILD-TYPE    2   57
                        clus
vv                       DEL PEAK 40(18P11.23) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            24
                        clus
vv                       DEL PEAK 40(18P11.23) WILD-TYPE
  HISPANIC OR LATINO                                   2
  NOT HISPANIC OR LATINO                              57
[1] 2 2
[1] FALSE

Clustering(72) Variable = DEL PEAK 41(18Q12.2) MUTATION ANALYSIS
D72V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 41(18Q12.2) MUTATED   56 46
  DEL PEAK 41(18Q12.2) WILD-TYPE 44 25
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                           102                             69 
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                            46                             25 
$`DEL PEAK 41(18Q12.2) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        31.27        58.55         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L 
       32.45         7.69         0.85         2.63         3.88         0.53 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FD 
        0.79        23.41         9.96        14.50        12.16        68.02 
TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
        3.68        42.77        25.41        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
       24.03         3.16         0.30         8.94        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OT 
        4.70        32.61         3.32         7.17         3.16         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 
       29.00         7.13         7.43         6.94         2.60         3.95 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        3.02        55.50         2.66        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.55        13.22        21.37         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       27.12        83.24        52.57        10.36        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A4A1 
       12.43        13.41         0.10        15.35        13.25        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HX 
       22.39         0.10        12.33        13.22         4.47        12.23 
TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       13.18        33.11         5.16         7.82         8.02         7.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        6.35        53.95         2.89         1.45        12.69         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EP TCGA-VR-A8EQ 
       20.02         5.29         3.42         9.27        19.96        22.82 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G 
       12.43        18.31         8.12        18.18        46.19        15.06 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        9.17        15.91        10.16         3.42         2.66        19.73 

$`DEL PEAK 41(18Q12.2) WILD-TYPE`
TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IC-A6RF TCGA-IG-A3I8 
       14.30         7.63         5.92        13.94         6.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D 
       20.09        20.78        20.12        18.64         9.30        17.03 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
       12.82        14.86         4.67       122.10        44.75        60.39 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OI 
       41.52        21.70         6.28        30.25         4.31        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A88T 
       21.01        47.93        18.35         1.38        58.59         8.71 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NW 
       25.12         0.36         7.40         7.76         5.49        46.09 
TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
        5.92        13.15         0.10         0.10        12.46        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A5U7 
       12.76        12.59        15.52        11.54        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A9FO TCGA-R6-A6KZ TCGA-R6-A6L4 
       10.52        12.00        12.03         0.13         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-S8-A6BW TCGA-V5-A7RE 
        7.04        29.59         9.30        15.78        20.38         4.80 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EY 
       15.35         4.44        18.81         1.55        28.11        30.71 
TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-Z6-A8JE 
       42.87        11.24         2.10 

  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                           0.1                            0.1 
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                         83.24                         122.10 
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                         12.38                          12.82 
[1] "0.1 - 83.2 (12.4)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "1.4"
D72V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 41(18Q12.2) MUTATED         4        2        4        1        21
  DEL PEAK 41(18Q12.2) WILD-TYPE       4        3        3        0        18
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 41(18Q12.2) MUTATED          15        17          6          7
  DEL PEAK 41(18Q12.2) WILD-TYPE        14         8          6          3
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 41(18Q12.2) MUTATED            6        4         2
  DEL PEAK 41(18Q12.2) WILD-TYPE          1        1         2
D72V3, multiclass
            clus
vv           DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              2                              3
  STAGE IB                              4                              3
  STAGE II                              1                              0
  STAGE IIA                            21                             18
  STAGE IIB                            15                             14
  STAGE III                            17                              8
  STAGE IIIA                            6                              6
  STAGE IIIB                            7                              3
  STAGE IIIC                            6                              1
  STAGE IV                              4                              1
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 41(18Q12.2) MUTATED      16 19 55  3
  DEL PEAK 41(18Q12.2) WILD-TYPE    15 17 30  2
D72V4, multiclass
       clus
vv      DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  T0+T1                           16                             15
  T2                              19                             17
  T3                              55                             30
  T4                               3                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 41(18Q12.2) MUTATED   39 38  9  6
  DEL PEAK 41(18Q12.2) WILD-TYPE 32 26  3  2
D72V5, multiclass
    clus
vv   DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  N0                           39                             32
  N1                           38                             26
  N2                            9                              3
  N3                            6                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V6, binary
                                cls
clus                              0  1
  DEL PEAK 41(18Q12.2) MUTATED   75  6
  DEL PEAK 41(18Q12.2) WILD-TYPE 51  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q12.2) MUTATED     75    6
  DEL PEAK 41(18Q12.2) WILD-TYPE   51    3
   clus
vv  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  0                           75                             51
  1                            6                              3
[1] 2 2
[1] FALSE
D72V7, binary
                                cls
clus                              0  1
  DEL PEAK 41(18Q12.2) MUTATED   14 89
  DEL PEAK 41(18Q12.2) WILD-TYPE 10 60
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q12.2) MUTATED     14   89
  DEL PEAK 41(18Q12.2) WILD-TYPE   10   60
        clus
vv       DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  FEMALE                           14                             10
  MALE                             89                             60
[1] 2 2
[1] FALSE
D72V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 41(18Q12.2) MUTATED      21                         1    67
  DEL PEAK 41(18Q12.2) WILD-TYPE    20                         1    44
D72V9, multiclass
                           clus
vv                          DEL PEAK 41(18Q12.2) MUTATED
  ASIAN                                               21
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               67
                           clus
vv                          DEL PEAK 41(18Q12.2) WILD-TYPE
  ASIAN                                                 20
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V10, binary
                                cls
clus                              0  1
  DEL PEAK 41(18Q12.2) MUTATED    2 42
  DEL PEAK 41(18Q12.2) WILD-TYPE  1 39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q12.2) MUTATED      2   42
  DEL PEAK 41(18Q12.2) WILD-TYPE    1   39
                        clus
vv                       DEL PEAK 41(18Q12.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           42
                        clus
vv                       DEL PEAK 41(18Q12.2) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                             39
[1] 2 2
[1] FALSE

Clustering(73) Variable = DEL PEAK 42(18Q21.2) MUTATION ANALYSIS
D73V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 42(18Q21.2) MUTATED   61 47
  DEL PEAK 42(18Q21.2) WILD-TYPE 39 24
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                           108                             63 
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                            47                             24 
$`DEL PEAK 42(18Q21.2) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YB 
        8.94        16.24        32.45         7.69         0.85         2.63 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS 
       18.64         3.88         0.53         0.79        23.41         9.96 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A938 
       14.50        12.16        68.02         3.68        42.77        25.41 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43H 
       23.18        31.56        25.22        24.03         3.16         0.30 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ 
        8.94        24.00         3.68         4.70        32.61        21.01 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX 
        3.32         7.17         3.16         4.90        29.00         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        6.94         2.60         3.95         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       35.97        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
       21.37         8.71        13.41        27.12        83.24        52.57 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       10.36        10.45        12.66        12.43        13.41         0.10 
TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ 
       13.25        12.46        12.59        22.39         0.10        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HX TCGA-M9-A5M8 
       13.22         4.47        12.33        25.25        12.23        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-R6-A6XQ 
        5.16         7.82         8.02         7.59        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95         9.30         2.89         1.45        12.69         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP 
       20.02         5.29         4.80         9.27        18.81        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA4D TCGA-VR-AA4G 
       22.82        12.43        18.31         8.12        46.19        15.06 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        9.17        15.91        10.16         3.42         2.66        19.73 

$`DEL PEAK 42(18Q21.2) WILD-TYPE`
TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA 
        5.92         4.21         6.21        33.27        20.09        20.78 
TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 
       20.12         9.30        17.03        12.82        14.86         4.67 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FG TCGA-JY-A939 TCGA-KH-A6WC 
      122.10        44.75        60.39        41.52        21.70         6.28 
TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ 
       30.25         4.31        19.99        47.93        18.35         1.38 
TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
       58.59         7.13         8.71        25.12         0.36         7.40 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49U 
        7.76         5.49        46.09         5.92        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 
        0.10         0.10        12.49        12.76        12.59        15.52 
TCGA-LN-A4A9 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO 
       11.54        10.52        12.00        12.03        13.18         0.13 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-S8-A6BW TCGA-V5-A7RC 
        5.06        14.70         7.04        15.78        20.38         3.42 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       15.35         4.44         1.55        28.11        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-Z6-A8JE 
       42.87        11.24         2.10 

  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                           0.1                            0.1 
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                         83.24                         122.10 
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                        12.445                         12.760 
[1] "0.1 - 83.2 (12.4)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "1.2"
D73V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 42(18Q21.2) MUTATED         5        2        5        1        21
  DEL PEAK 42(18Q21.2) WILD-TYPE       3        3        2        0        18
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 42(18Q21.2) MUTATED          18        18          6          8
  DEL PEAK 42(18Q21.2) WILD-TYPE        11         7          6          2
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 42(18Q21.2) MUTATED            5        4         2
  DEL PEAK 42(18Q21.2) WILD-TYPE          2        1         2
D73V3, multiclass
            clus
vv           DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  STAGE I                               5                              3
  STAGE IA                              2                              3
  STAGE IB                              5                              2
  STAGE II                              1                              0
  STAGE IIA                            21                             18
  STAGE IIB                            18                             11
  STAGE III                            18                              7
  STAGE IIIA                            6                              6
  STAGE IIIB                            8                              2
  STAGE IIIC                            5                              2
  STAGE IV                              4                              1
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 42(18Q21.2) MUTATED      19 21 56  3
  DEL PEAK 42(18Q21.2) WILD-TYPE    12 15 29  2
D73V4, multiclass
       clus
vv      DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  T0+T1                           19                             12
  T2                              21                             15
  T3                              56                             29
  T4                               3                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 42(18Q21.2) MUTATED   42 42  9  5
  DEL PEAK 42(18Q21.2) WILD-TYPE 29 22  3  3
D73V5, multiclass
    clus
vv   DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  N0                           42                             29
  N1                           42                             22
  N2                            9                              3
  N3                            5                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V6, binary
                                cls
clus                              0  1
  DEL PEAK 42(18Q21.2) MUTATED   81  6
  DEL PEAK 42(18Q21.2) WILD-TYPE 45  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q21.2) MUTATED     81    6
  DEL PEAK 42(18Q21.2) WILD-TYPE   45    3
   clus
vv  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  0                           81                             45
  1                            6                              3
[1] 2 2
[1] FALSE
D73V7, binary
                                cls
clus                              0  1
  DEL PEAK 42(18Q21.2) MUTATED   14 96
  DEL PEAK 42(18Q21.2) WILD-TYPE 10 53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q21.2) MUTATED     14   96
  DEL PEAK 42(18Q21.2) WILD-TYPE   10   53
        clus
vv       DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  FEMALE                           14                             10
  MALE                             96                             53
[1] 2 2
[1] FALSE
D73V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 42(18Q21.2) MUTATED      23                         0    72
  DEL PEAK 42(18Q21.2) WILD-TYPE    18                         2    39
D73V9, multiclass
                           clus
vv                          DEL PEAK 42(18Q21.2) MUTATED
  ASIAN                                               23
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               72
                           clus
vv                          DEL PEAK 42(18Q21.2) WILD-TYPE
  ASIAN                                                 18
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V10, binary
                                cls
clus                              0  1
  DEL PEAK 42(18Q21.2) MUTATED    3 46
  DEL PEAK 42(18Q21.2) WILD-TYPE  0 35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q21.2) MUTATED      3   46
  DEL PEAK 42(18Q21.2) WILD-TYPE    0   35
                        clus
vv                       DEL PEAK 42(18Q21.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           46
                        clus
vv                       DEL PEAK 42(18Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                  0
  NOT HISPANIC OR LATINO                             35
[1] 2 2
[1] FALSE

Clustering(74) Variable = DEL PEAK 43(18Q22.3) MUTATION ANALYSIS
D74V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 43(18Q22.3) MUTATED   60 41
  DEL PEAK 43(18Q22.3) WILD-TYPE 40 30
  DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE 
                           101                             70 
  DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE 
                            41                             30 
$`DEL PEAK 43(18Q22.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27        14.30         7.63         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4P3 
       32.45         7.69        33.27         0.85         2.63        18.64 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I 
        0.53         0.79        23.41         9.96        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C 
       44.75        68.02         3.68        42.77        25.41        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43M 
       31.56        25.22        24.03         3.16         0.30         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO 
       24.00         3.68         4.70        32.61        21.01         3.32 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        3.16         4.90        29.00         7.43         6.94         2.60 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        3.95         3.02        55.50         2.66        35.97        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.55        13.22        21.37         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49M TCGA-LN-A49N 
       27.12        83.24        52.57        10.36        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A6 
       13.41         0.10        13.25        12.46        12.59         0.10 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HX TCGA-M9-A5M8 
       12.33        13.22         4.47        12.33        12.23        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-R6-A6XQ 
        5.16         7.82         8.02         7.59        29.59         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        9.30         1.45        12.69         7.00        20.02         5.29 
TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU 
        9.27        18.81        19.96        22.82        12.43        18.31 
TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D 
        8.12        30.71        42.87        46.19        15.06         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       15.91        10.16         3.42         2.10        19.73 

$`DEL PEAK 43(18Q22.3) WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IC-A6RF TCGA-IG-A3QL 
       58.55         5.92        13.94         4.21         6.21        20.09 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 
       20.78        20.12         3.88         9.30        17.03        12.82 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FG TCGA-JY-A939 
       14.86         4.67       122.10        60.39        41.52        21.70 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON 
        6.28        30.25         4.31        19.99        47.93        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88T TCGA-L5-A88W 
        7.17         1.38        58.59         7.13         8.71        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NW 
        0.36         7.40        13.48         7.76         5.49        46.09 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
        5.92        10.45        13.15        15.35         0.10         0.10 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.76        12.59        22.39        15.52        11.54 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO 
       25.25        10.52        12.00        12.03        13.18         0.13 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 
        5.06        14.70         7.04        53.95        15.78         2.89 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8ET 
       20.38         3.42         4.80        15.35         4.44         1.55 
TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA7B TCGA-Z6-AAPN 
       28.11        18.18        11.24         2.66 

  DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE 
                           0.1                            0.1 
  DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE 
                         83.24                         122.10 
  DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE 
                         12.59                          12.54 
[1] "0.1 - 83.2 (12.6)"  "0.1 - 122.1 (12.5)"
[1] "hr=" "1.1"
D74V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 43(18Q22.3) MUTATED         4        1        4        1        19
  DEL PEAK 43(18Q22.3) WILD-TYPE       4        4        3        0        20
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 43(18Q22.3) MUTATED          18        17          8          7
  DEL PEAK 43(18Q22.3) WILD-TYPE        11         8          4          3
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 43(18Q22.3) MUTATED            5        4         2
  DEL PEAK 43(18Q22.3) WILD-TYPE          2        1         2
D74V3, multiclass
            clus
vv           DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              1                              4
  STAGE IB                              4                              3
  STAGE II                              1                              0
  STAGE IIA                            19                             20
  STAGE IIB                            18                             11
  STAGE III                            17                              8
  STAGE IIIA                            8                              4
  STAGE IIIB                            7                              3
  STAGE IIIC                            5                              2
  STAGE IV                              4                              1
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 43(18Q22.3) MUTATED      15 19 57  3
  DEL PEAK 43(18Q22.3) WILD-TYPE    16 17 28  2
D74V4, multiclass
       clus
vv      DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE
  T0+T1                           15                             16
  T2                              19                             17
  T3                              57                             28
  T4                               3                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 43(18Q22.3) MUTATED   37 43  8  5
  DEL PEAK 43(18Q22.3) WILD-TYPE 34 21  4  3
D74V5, multiclass
    clus
vv   DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE
  N0                           37                             34
  N1                           43                             21
  N2                            8                              4
  N3                            5                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V6, binary
                                cls
clus                              0  1
  DEL PEAK 43(18Q22.3) MUTATED   77  6
  DEL PEAK 43(18Q22.3) WILD-TYPE 49  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(18Q22.3) MUTATED     77    6
  DEL PEAK 43(18Q22.3) WILD-TYPE   49    3
   clus
vv  DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE
  0                           77                             49
  1                            6                              3
[1] 2 2
[1] FALSE
D74V7, binary
                                cls
clus                              0  1
  DEL PEAK 43(18Q22.3) MUTATED   15 88
  DEL PEAK 43(18Q22.3) WILD-TYPE  9 61
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(18Q22.3) MUTATED     15   88
  DEL PEAK 43(18Q22.3) WILD-TYPE    9   61
        clus
vv       DEL PEAK 43(18Q22.3) MUTATED DEL PEAK 43(18Q22.3) WILD-TYPE
  FEMALE                           15                              9
  MALE                             88                             61
[1] 2 2
[1] FALSE
D74V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 43(18Q22.3) MUTATED      21                         0    69
  DEL PEAK 43(18Q22.3) WILD-TYPE    20                         2    42
D74V9, multiclass
                           clus
vv                          DEL PEAK 43(18Q22.3) MUTATED
  ASIAN                                               21
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               69
                           clus
vv                          DEL PEAK 43(18Q22.3) WILD-TYPE
  ASIAN                                                 20
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V10, binary
                                cls
clus                              0  1
  DEL PEAK 43(18Q22.3) MUTATED    3 40
  DEL PEAK 43(18Q22.3) WILD-TYPE  0 41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(18Q22.3) MUTATED      3   40
  DEL PEAK 43(18Q22.3) WILD-TYPE    0   41
                        clus
vv                       DEL PEAK 43(18Q22.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           40
                        clus
vv                       DEL PEAK 43(18Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                  0
  NOT HISPANIC OR LATINO                             41
[1] 2 2
[1] FALSE

Clustering(75) Variable = DEL PEAK 44(19P13.3) MUTATION ANALYSIS
D75V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 44(19P13.3) MUTATED   52 35
  DEL PEAK 44(19P13.3) WILD-TYPE 48 36
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                            87                             84 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                            35                             36 
$`DEL PEAK 44(19P13.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS 
        8.94        16.24         4.21         2.63        18.64         3.88 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H 
        0.53        17.03         0.79        23.41         4.67        14.50 
TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93E 
      122.10        68.02        42.77        25.41        23.18        25.22 
TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM 
       30.25         8.94        24.00         3.68        32.61        47.93 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y 
        3.32         7.17        58.59         7.43         2.60         0.36 
TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.95         2.66        35.97        12.92        16.47        13.55 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
        5.49         8.71        13.41        52.57        46.09        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
       10.45        12.66         0.10        13.15        15.35        13.25 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A5U5 
       12.46        12.49        12.76         0.10        12.33         4.47 
TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-R6-A6DN 
       12.33        10.52        12.23        13.18         0.13         8.02 
TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        5.06         7.04        29.59        15.78         2.89         1.45 
TCGA-R6-A8WG TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP 
       12.69         3.42         4.80         9.27        18.81        19.96 
TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7D TCGA-VR-AA7I 
       12.43         8.12        42.87        46.19         9.17        15.91 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.10         2.66        19.73 

$`DEL PEAK 44(19P13.3) WILD-TYPE`
TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
        5.92        32.45         7.69         6.21        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A6QS 
        0.85        20.78        20.12         9.30        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG 
       14.86        12.16        44.75        60.39         3.68        41.52 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       21.70        31.56        24.03         6.28         3.16         0.30 
TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OQ 
        4.31         4.70        19.99        21.01        18.35         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T 
        3.16         4.90        29.00         7.13         6.94         8.71 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NL 
       25.12         7.40         3.02        55.50        13.48        13.22 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NT TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49N 
        7.76        21.37        27.12        83.24         5.92        12.43 
TCGA-LN-A49O TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A5 
       13.41         0.10         0.10        12.59        12.59        22.39 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HY 
       15.52        11.54        13.22        25.25        12.00        12.03 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6XQ 
       33.11         5.16         7.82         7.59        14.70         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
       53.95         9.30         7.00        20.02        20.38         5.29 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX 
       15.35         4.44        22.82         1.55        18.31        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B TCGA-X8-AAAR TCGA-Z6-A8JD 
       30.71        18.18        15.06        11.24        10.16         3.42 

  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                           0.1                            0.1 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                        122.10                          83.24 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                         12.49                          12.59 
[1] "0.1 - 122.1 (12.5)" "0.1 - 83.2 (12.6)" 
[1] "hr=" "1.1"
D75V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 44(19P13.3) MUTATED         4        2        4        1        15
  DEL PEAK 44(19P13.3) WILD-TYPE       4        3        3        0        24
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 44(19P13.3) MUTATED          13        16          5          7
  DEL PEAK 44(19P13.3) WILD-TYPE        16         9          7          3
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 44(19P13.3) MUTATED            4        2         3
  DEL PEAK 44(19P13.3) WILD-TYPE          3        3         1
D75V3, multiclass
            clus
vv           DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  STAGE I                               4                              4
  STAGE IA                              2                              3
  STAGE IB                              4                              3
  STAGE II                              1                              0
  STAGE IIA                            15                             24
  STAGE IIB                            13                             16
  STAGE III                            16                              9
  STAGE IIIA                            5                              7
  STAGE IIIB                            7                              3
  STAGE IIIC                            4                              3
  STAGE IV                              2                              3
  STAGE IVA                             3                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 44(19P13.3) MUTATED      15 14 48  2
  DEL PEAK 44(19P13.3) WILD-TYPE    16 22 37  3
D75V4, multiclass
       clus
vv      DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  T0+T1                           15                             16
  T2                              14                             22
  T3                              48                             37
  T4                               2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 44(19P13.3) MUTATED   31 36  7  4
  DEL PEAK 44(19P13.3) WILD-TYPE 40 28  5  4
D75V5, multiclass
    clus
vv   DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  N0                           31                             40
  N1                           36                             28
  N2                            7                              5
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V6, binary
                                cls
clus                              0  1
  DEL PEAK 44(19P13.3) MUTATED   65  5
  DEL PEAK 44(19P13.3) WILD-TYPE 61  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED     65    5
  DEL PEAK 44(19P13.3) WILD-TYPE   61    4
   clus
vv  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  0                           65                             61
  1                            5                              4
[1] 2 2
[1] FALSE
D75V7, binary
                                cls
clus                              0  1
  DEL PEAK 44(19P13.3) MUTATED    8 80
  DEL PEAK 44(19P13.3) WILD-TYPE 16 69
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED      8   80
  DEL PEAK 44(19P13.3) WILD-TYPE   16   69
        clus
vv       DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  FEMALE                            8                             16
  MALE                             80                             69
[1] 2 2
[1] FALSE
D75V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 44(19P13.3) MUTATED      24                         1    50
  DEL PEAK 44(19P13.3) WILD-TYPE    17                         1    61
D75V9, multiclass
                           clus
vv                          DEL PEAK 44(19P13.3) MUTATED
  ASIAN                                               24
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               50
                           clus
vv                          DEL PEAK 44(19P13.3) WILD-TYPE
  ASIAN                                                 17
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V10, binary
                                cls
clus                              0  1
  DEL PEAK 44(19P13.3) MUTATED    1 40
  DEL PEAK 44(19P13.3) WILD-TYPE  2 41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED      1   40
  DEL PEAK 44(19P13.3) WILD-TYPE    2   41
                        clus
vv                       DEL PEAK 44(19P13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           40
                        clus
vv                       DEL PEAK 44(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             41
[1] 2 2
[1] FALSE

Clustering(76) Variable = DEL PEAK 45(19Q11) MUTATION ANALYSIS
D76V1, survival
                              sevent
clus2                           0  1
  DEL PEAK 45(19Q11) MUTATED   26 20
  DEL PEAK 45(19Q11) WILD-TYPE 74 51
  DEL PEAK 45(19Q11) MUTATED DEL PEAK 45(19Q11) WILD-TYPE 
                          46                          125 
  DEL PEAK 45(19Q11) MUTATED DEL PEAK 45(19Q11) WILD-TYPE 
                          20                           51 
$`DEL PEAK 45(19Q11) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3YB TCGA-IG-A6QS 
       25.78        14.30        16.24         4.21         2.63         9.96 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OM 
       68.02         3.68        42.77        30.25         4.31        47.93 
TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L5-A8NL 
        7.17        58.59         7.43         2.66        16.47        13.22 
TCGA-L5-A8NN TCGA-L5-A8NW TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V 
        5.49        46.09        12.66         0.10        13.15         0.10 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.46        12.59        12.49        12.76         4.47        12.33 
TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-R6-A6DN TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A8WC 
       12.23        13.18         8.02         7.04        53.95         1.45 
TCGA-V5-A7RB TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-A8Q7 
        5.29         9.27        18.81         8.12        18.18        42.87 
TCGA-VR-AA4D TCGA-VR-AA7D TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       46.19         9.17         2.66        19.73 

$`DEL PEAK 45(19Q11) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       32.45         7.69         6.21        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
       20.78        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03         0.79        23.41        12.82        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FG 
       14.50        12.16       122.10        44.75        60.39        41.52 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       25.41        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
        6.28         3.16         0.30         8.94        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO 
        4.70        32.61        19.99        21.01        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S 
        1.38         3.16         4.90        29.00         7.13         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 
        8.71         2.60        25.12         0.36         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK 
        3.02        55.50        35.97        12.92        13.48        13.55 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
        7.76        21.37         8.71        13.41        27.12        83.24 
TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O 
       52.57        10.36         5.92        10.45        12.43        13.41 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       15.35        13.25         0.10        12.59        22.39         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HV 
       15.52        11.54        12.33        13.22        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.00        12.03         0.13        33.11         5.16         7.82 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 
        7.59         5.06        14.70        29.59         6.35         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
       15.78         2.89        12.69         7.00        20.02        20.38 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ 
        3.42         4.80        15.35         4.44        19.96        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-AA4G 
       12.43         1.55        18.31        28.11        30.71        15.06 
TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE 
       11.24        15.91        10.16         3.42         2.10 

  DEL PEAK 45(19Q11) MUTATED DEL PEAK 45(19Q11) WILD-TYPE 
                         0.1                          0.1 
  DEL PEAK 45(19Q11) MUTATED DEL PEAK 45(19Q11) WILD-TYPE 
                       68.02                       122.10 
  DEL PEAK 45(19Q11) MUTATED DEL PEAK 45(19Q11) WILD-TYPE 
                      12.475                       12.690 
[1] "0.1 - 68.0 (12.5)"  "0.1 - 122.1 (12.7)"
[1] "hr=" "1"  
D76V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 45(19Q11) MUTATED         1        2        2        0        10
  DEL PEAK 45(19Q11) WILD-TYPE       7        3        5        1        29
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 45(19Q11) MUTATED           6         9          2          2
  DEL PEAK 45(19Q11) WILD-TYPE        23        16         10          8
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 45(19Q11) MUTATED            3        1         2
  DEL PEAK 45(19Q11) WILD-TYPE          4        4         2
D76V3, multiclass
            clus
vv           DEL PEAK 45(19Q11) MUTATED DEL PEAK 45(19Q11) WILD-TYPE
  STAGE I                             1                            7
  STAGE IA                            2                            3
  STAGE IB                            2                            5
  STAGE II                            0                            1
  STAGE IIA                          10                           29
  STAGE IIB                           6                           23
  STAGE III                           9                           16
  STAGE IIIA                          2                           10
  STAGE IIIB                          2                            8
  STAGE IIIC                          3                            4
  STAGE IV                            1                            4
  STAGE IVA                           2                            2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1 T2 T3 T4
  DEL PEAK 45(19Q11) MUTATED       6  9 26  0
  DEL PEAK 45(19Q11) WILD-TYPE    25 27 59  5
D76V4, multiclass
       clus
vv      DEL PEAK 45(19Q11) MUTATED DEL PEAK 45(19Q11) WILD-TYPE
  T0+T1                          6                           25
  T2                             9                           27
  T3                            26                           59
  T4                             0                            5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2 N3
  DEL PEAK 45(19Q11) MUTATED   16 21  1  3
  DEL PEAK 45(19Q11) WILD-TYPE 55 43 11  5
D76V5, multiclass
    clus
vv   DEL PEAK 45(19Q11) MUTATED DEL PEAK 45(19Q11) WILD-TYPE
  N0                         16                           55
  N1                         21                           43
  N2                          1                           11
  N3                          3                            5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V6, binary
                              cls
clus                            0  1
  DEL PEAK 45(19Q11) MUTATED   33  3
  DEL PEAK 45(19Q11) WILD-TYPE 93  6
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 45(19Q11) MUTATED     33    3
  DEL PEAK 45(19Q11) WILD-TYPE   93    6
   clus
vv  DEL PEAK 45(19Q11) MUTATED DEL PEAK 45(19Q11) WILD-TYPE
  0                         33                           93
  1                          3                            6
[1] 2 2
[1] FALSE
D76V7, binary
                              cls
clus                             0   1
  DEL PEAK 45(19Q11) MUTATED     4  42
  DEL PEAK 45(19Q11) WILD-TYPE  20 107
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 45(19Q11) MUTATED      4   42
  DEL PEAK 45(19Q11) WILD-TYPE   20  107
        clus
vv       DEL PEAK 45(19Q11) MUTATED DEL PEAK 45(19Q11) WILD-TYPE
  FEMALE                          4                           20
  MALE                           42                          107
[1] 2 2
[1] FALSE
D76V8, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 45(19Q11) MUTATED      14                         0    26
  DEL PEAK 45(19Q11) WILD-TYPE    27                         2    85
D76V9, multiclass
                           clus
vv                          DEL PEAK 45(19Q11) MUTATED
  ASIAN                                             14
  BLACK OR AFRICAN AMERICAN                          0
  WHITE                                             26
                           clus
vv                          DEL PEAK 45(19Q11) WILD-TYPE
  ASIAN                                               27
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V10, binary
                              cls
clus                            0  1
  DEL PEAK 45(19Q11) MUTATED    1 21
  DEL PEAK 45(19Q11) WILD-TYPE  2 60
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 45(19Q11) MUTATED      1   21
  DEL PEAK 45(19Q11) WILD-TYPE    2   60
                        clus
vv                       DEL PEAK 45(19Q11) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         21
                        clus
vv                       DEL PEAK 45(19Q11) WILD-TYPE
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           60
[1] 2 2
[1] FALSE

Clustering(77) Variable = DEL PEAK 46(20P12.1) MUTATION ANALYSIS
D77V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 46(20P12.1) MUTATED   22 10
  DEL PEAK 46(20P12.1) WILD-TYPE 78 61
  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE 
                            32                            139 
  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE 
                            10                             61 
$`DEL PEAK 46(20P12.1) MUTATED`
TCGA-2H-A9GI TCGA-IG-A4QS TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FH TCGA-JY-A938 
       14.30         3.88        44.75        68.02        42.77        25.41 
TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A8NE TCGA-L5-A8NF 
        8.94         3.68        32.61         3.32        55.50         2.66 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A6VZ 
       16.47        13.22         8.71        13.41        83.24        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49Y TCGA-LN-A7HW TCGA-LN-A7HY 
       10.45        12.66        13.41        12.46        12.00        12.03 
TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-VR-A8EQ 
        5.06        29.59        53.95        12.69        20.38        22.82 
TCGA-VR-A8Q7 TCGA-ZR-A9CJ 
       42.87        19.73 

$`DEL PEAK 46(20P12.1) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
        8.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       18.64         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C 
      122.10        60.39         3.68        41.52        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ 
        0.30         4.31        24.00         4.70        19.99        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       47.93        18.35         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        4.90        29.00         7.13         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        2.60        25.12         0.36         7.40         3.95         3.02 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN 
       35.97        12.92        13.48        13.55         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49N 
       21.37        27.12        52.57        46.09         5.92        12.43 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
        0.10        13.15        15.35         0.10        13.25         0.10 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 
       25.25        10.52        12.23        13.18         0.13        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
        5.16         7.82         8.02         7.59        14.70         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
        6.35         9.30        15.78         2.89         1.45         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.02         5.29         3.42         4.80        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        4.44        18.81        19.96        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G 
        8.12        28.11        30.71        18.18        46.19        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE 
       11.24         9.17        15.91        10.16         3.42         2.10 
TCGA-Z6-AAPN 
        2.66 

  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE 
                          2.66                           0.10 
  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE 
                         83.24                         122.10 
  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE 
                         13.41                          12.33 
[1] "2.7 - 83.2 (13.4)"  "0.1 - 122.1 (12.3)"
[1] "hr=" "2.1"
D77V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 46(20P12.1) MUTATED         1        0        1        0         7
  DEL PEAK 46(20P12.1) WILD-TYPE       7        5        6        1        32
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 46(20P12.1) MUTATED           6         6          1          1
  DEL PEAK 46(20P12.1) WILD-TYPE        23        19         11          9
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 46(20P12.1) MUTATED            3        0         1
  DEL PEAK 46(20P12.1) WILD-TYPE          4        5         3
D77V3, multiclass
            clus
vv           DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE
  STAGE I                               1                              7
  STAGE IA                              0                              5
  STAGE IB                              1                              6
  STAGE II                              0                              1
  STAGE IIA                             7                             32
  STAGE IIB                             6                             23
  STAGE III                             6                             19
  STAGE IIIA                            1                             11
  STAGE IIIB                            1                              9
  STAGE IIIC                            3                              4
  STAGE IV                              0                              5
  STAGE IVA                             1                              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 46(20P12.1) MUTATED       3  8 17  0
  DEL PEAK 46(20P12.1) WILD-TYPE    28 28 68  5
D77V4, multiclass
       clus
vv      DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE
  T0+T1                            3                             28
  T2                               8                             28
  T3                              17                             68
  T4                               0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 46(20P12.1) MUTATED   12 11  2  3
  DEL PEAK 46(20P12.1) WILD-TYPE 59 53 10  5
D77V5, multiclass
    clus
vv   DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE
  N0                           12                             59
  N1                           11                             53
  N2                            2                             10
  N3                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V6, binary
                                cls
clus                               0   1
  DEL PEAK 46(20P12.1) MUTATED    22   1
  DEL PEAK 46(20P12.1) WILD-TYPE 104   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(20P12.1) MUTATED     22    1
  DEL PEAK 46(20P12.1) WILD-TYPE  104    8
   clus
vv  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE
  0                           22                            104
  1                            1                              8
[1] 2 2
[1] FALSE
D77V7, binary
                                cls
clus                               0   1
  DEL PEAK 46(20P12.1) MUTATED     3  29
  DEL PEAK 46(20P12.1) WILD-TYPE  21 120
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(20P12.1) MUTATED      3   29
  DEL PEAK 46(20P12.1) WILD-TYPE   21  120
        clus
vv       DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE
  FEMALE                            3                             21
  MALE                             29                            120
[1] 2 2
[1] FALSE
D77V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 46(20P12.1) MUTATED       8                         0    21
  DEL PEAK 46(20P12.1) WILD-TYPE    33                         2    90
D77V9, multiclass
                           clus
vv                          DEL PEAK 46(20P12.1) MUTATED
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               21
                           clus
vv                          DEL PEAK 46(20P12.1) WILD-TYPE
  ASIAN                                                 33
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V10, binary
                                cls
clus                              0  1
  DEL PEAK 46(20P12.1) MUTATED    1 13
  DEL PEAK 46(20P12.1) WILD-TYPE  2 68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(20P12.1) MUTATED      1   13
  DEL PEAK 46(20P12.1) WILD-TYPE    2   68
                        clus
vv                       DEL PEAK 46(20P12.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           13
                        clus
vv                       DEL PEAK 46(20P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             68
[1] 2 2
[1] FALSE

Clustering(78) Variable = DEL PEAK 47(21Q11.2) MUTATION ANALYSIS
D78V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 47(21Q11.2) MUTATED   59 40
  DEL PEAK 47(21Q11.2) WILD-TYPE 41 31
  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE 
                            99                             72 
  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE 
                            40                             31 
$`DEL PEAK 47(21Q11.2) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IG-A3I8 
       25.78         7.63         5.92        13.94        32.45        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
        0.85        20.78        20.12        18.64         3.88         0.53 
TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A93C 
        0.79         9.96        12.16       122.10        68.02        23.18 
TCGA-JY-A93D TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       31.56        24.03         3.16        30.25         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OM 
        8.94        24.00         3.68         4.70        32.61        47.93 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
       18.35         7.17         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 
        7.13         6.94         2.60         0.36         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        3.02         2.66        12.92        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49         8.71        13.41        27.12        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.36         5.92        12.43        13.41         0.10        13.15 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 
       13.25         0.10        12.76        22.39         0.10        11.54 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       13.22         4.47        12.33        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L6 
       13.18        33.11         7.82         8.02         5.06         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       29.59         6.35         9.30         2.89         1.45        12.69 
TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ 
       20.38         4.80         9.27         4.44        18.81        22.82 
TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B 
        1.55         8.12        28.11        42.87        46.19        11.24 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.10         2.66        19.73 

$`DEL PEAK 47(21Q11.2) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       31.27        14.30        58.55         8.94        16.24         4.21 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D 
        7.69         6.21        20.09         2.63         9.30        17.03 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FA 
       23.41        12.82        14.86         4.67        14.50        44.75 
TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       60.39         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OQ 
       25.22         6.28        19.99        21.01         3.32         1.38 
TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NI 
        7.43         8.71        25.12        55.50        35.97        13.48 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49U 
        7.76        21.37        83.24        10.45        12.66        15.35 
TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A8 
        0.10        12.46        12.59        12.49        12.59        15.52 
TCGA-LN-A4MQ TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-R6-A6DQ 
       12.33        25.25        10.52         0.13         5.16         7.59 
TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
       14.70        53.95        15.78         7.00        20.02         5.29 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EY 
        3.42        15.35        19.96        12.43        18.31        30.71 
TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD 
       18.18        15.06         9.17        15.91        10.16         3.42 

  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE 
                           0.1                            0.1 
  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE 
                        122.10                          83.24 
  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE 
                          12.0                           14.4 
[1] "0.1 - 122.1 (12.0)" "0.1 - 83.2 (14.4)" 
[1] "hr=" "1.1"
D78V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 47(21Q11.2) MUTATED         5        3        7        1        21
  DEL PEAK 47(21Q11.2) WILD-TYPE       3        2        0        0        18
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 47(21Q11.2) MUTATED          12        14          6          6
  DEL PEAK 47(21Q11.2) WILD-TYPE        17        11          6          4
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 47(21Q11.2) MUTATED            3        4         2
  DEL PEAK 47(21Q11.2) WILD-TYPE          4        1         2
D78V3, multiclass
            clus
vv           DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE
  STAGE I                               5                              3
  STAGE IA                              3                              2
  STAGE IB                              7                              0
  STAGE II                              1                              0
  STAGE IIA                            21                             18
  STAGE IIB                            12                             17
  STAGE III                            14                             11
  STAGE IIIA                            6                              6
  STAGE IIIB                            6                              4
  STAGE IIIC                            3                              4
  STAGE IV                              4                              1
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 47(21Q11.2) MUTATED      18 19 48  2
  DEL PEAK 47(21Q11.2) WILD-TYPE    13 17 37  3
D78V4, multiclass
       clus
vv      DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE
  T0+T1                           18                             13
  T2                              19                             17
  T3                              48                             37
  T4                               2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 47(21Q11.2) MUTATED   43 34  6  4
  DEL PEAK 47(21Q11.2) WILD-TYPE 28 30  6  4
D78V5, multiclass
    clus
vv   DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE
  N0                           43                             28
  N1                           34                             30
  N2                            6                              6
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V6, binary
                                cls
clus                              0  1
  DEL PEAK 47(21Q11.2) MUTATED   67  6
  DEL PEAK 47(21Q11.2) WILD-TYPE 59  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(21Q11.2) MUTATED     67    6
  DEL PEAK 47(21Q11.2) WILD-TYPE   59    3
   clus
vv  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE
  0                           67                             59
  1                            6                              3
[1] 2 2
[1] FALSE
D78V7, binary
                                cls
clus                              0  1
  DEL PEAK 47(21Q11.2) MUTATED   14 85
  DEL PEAK 47(21Q11.2) WILD-TYPE 10 64
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(21Q11.2) MUTATED     14   85
  DEL PEAK 47(21Q11.2) WILD-TYPE   10   64
        clus
vv       DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE
  FEMALE                           14                             10
  MALE                             85                             64
[1] 2 2
[1] FALSE
D78V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 47(21Q11.2) MUTATED      22                         0    67
  DEL PEAK 47(21Q11.2) WILD-TYPE    19                         2    44
D78V9, multiclass
                           clus
vv                          DEL PEAK 47(21Q11.2) MUTATED
  ASIAN                                               22
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               67
                           clus
vv                          DEL PEAK 47(21Q11.2) WILD-TYPE
  ASIAN                                                 19
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V10, binary
                                cls
clus                              0  1
  DEL PEAK 47(21Q11.2) MUTATED    2 43
  DEL PEAK 47(21Q11.2) WILD-TYPE  1 38
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(21Q11.2) MUTATED      2   43
  DEL PEAK 47(21Q11.2) WILD-TYPE    1   38
                        clus
vv                       DEL PEAK 47(21Q11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           43
                        clus
vv                       DEL PEAK 47(21Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                             38
[1] 2 2
[1] FALSE

Clustering(79) Variable = DEL PEAK 48(21Q21.1) MUTATION ANALYSIS
D79V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 48(21Q21.1) MUTATED   58 42
  DEL PEAK 48(21Q21.1) WILD-TYPE 42 29
  DEL PEAK 48(21Q21.1) MUTATED DEL PEAK 48(21Q21.1) WILD-TYPE 
                           100                             71 
  DEL PEAK 48(21Q21.1) MUTATED DEL PEAK 48(21Q21.1) WILD-TYPE 
                            42                             29 
$`DEL PEAK 48(21Q21.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IG-A3I8 
       25.78         7.63         5.92        13.94        32.45        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
        0.85        20.78        20.12        18.64         3.88         0.53 
TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A93C 
        0.79         9.96        12.16       122.10        68.02        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       31.56        25.22        24.03         3.16        30.25         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        4.31         8.94        24.00         3.68         4.70        32.61 
TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
       47.93         7.17         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z 
        7.13         7.43         6.94         2.60         0.36         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.95         3.02         2.66        12.92        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV 
       13.22         5.49         8.71        13.41        27.12        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       46.09        10.36         5.92        12.43        13.41         0.10 
TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR 
       13.15        13.25        12.76         0.10        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
        4.47        12.33        12.00        12.23        12.03        13.18 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG 
       33.11         7.82         8.02         5.06         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RC 
        6.35         9.30         2.89         1.45        12.69         3.42 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER 
        4.80         9.27         4.44        18.81        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        1.55         8.12        28.11        18.18        42.87        46.19 
TCGA-VR-AA7D TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        9.17         2.10         2.66        19.73 

$`DEL PEAK 48(21Q21.1) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       31.27        14.30        58.55         8.94        16.24         4.21 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D 
        7.69         6.21        20.09         2.63         9.30        17.03 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FA 
       23.41        12.82        14.86         4.67        14.50        44.75 
TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       60.39         3.68        41.52        42.77        25.41        21.70 
TCGA-KH-A6WC TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        6.28        19.99        21.01        18.35         3.32         1.38 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NM 
        8.71        25.12        55.50        35.97        13.48         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49U TCGA-LN-A49V 
       21.37        83.24        10.45        12.66        15.35         0.10 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10        12.46        12.59        12.49        12.59        22.39 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A9FO TCGA-Q9-A6FU 
       15.52        11.54        25.25        10.52         0.13         5.16 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BV 
        7.59        14.70        53.95        15.78         7.00        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EU TCGA-VR-A8EY 
       20.38         5.29        15.35        19.96        18.31        30.71 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD 
       15.06        11.24        15.91        10.16         3.42 

  DEL PEAK 48(21Q21.1) MUTATED DEL PEAK 48(21Q21.1) WILD-TYPE 
                           0.1                            0.1 
  DEL PEAK 48(21Q21.1) MUTATED DEL PEAK 48(21Q21.1) WILD-TYPE 
                        122.10                          83.24 
  DEL PEAK 48(21Q21.1) MUTATED DEL PEAK 48(21Q21.1) WILD-TYPE 
                        12.015                         14.700 
[1] "0.1 - 122.1 (12.0)" "0.1 - 83.2 (14.7)" 
[1] "hr=" "1.2"
D79V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 48(21Q21.1) MUTATED         5        3        6        1        18
  DEL PEAK 48(21Q21.1) WILD-TYPE       3        2        1        0        21
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 48(21Q21.1) MUTATED          13        16          7          6
  DEL PEAK 48(21Q21.1) WILD-TYPE        16         9          5          4
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 48(21Q21.1) MUTATED            5        3         2
  DEL PEAK 48(21Q21.1) WILD-TYPE          2        2         2
D79V3, multiclass
            clus
vv           DEL PEAK 48(21Q21.1) MUTATED DEL PEAK 48(21Q21.1) WILD-TYPE
  STAGE I                               5                              3
  STAGE IA                              3                              2
  STAGE IB                              6                              1
  STAGE II                              1                              0
  STAGE IIA                            18                             21
  STAGE IIB                            13                             16
  STAGE III                            16                              9
  STAGE IIIA                            7                              5
  STAGE IIIB                            6                              4
  STAGE IIIC                            5                              2
  STAGE IV                              3                              2
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 48(21Q21.1) MUTATED      17 18 50  3
  DEL PEAK 48(21Q21.1) WILD-TYPE    14 18 35  2
D79V4, multiclass
       clus
vv      DEL PEAK 48(21Q21.1) MUTATED DEL PEAK 48(21Q21.1) WILD-TYPE
  T0+T1                           17                             14
  T2                              18                             18
  T3                              50                             35
  T4                               3                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 48(21Q21.1) MUTATED   39 38  6  5
  DEL PEAK 48(21Q21.1) WILD-TYPE 32 26  6  3
D79V5, multiclass
    clus
vv   DEL PEAK 48(21Q21.1) MUTATED DEL PEAK 48(21Q21.1) WILD-TYPE
  N0                           39                             32
  N1                           38                             26
  N2                            6                              6
  N3                            5                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V6, binary
                                cls
clus                              0  1
  DEL PEAK 48(21Q21.1) MUTATED   71  5
  DEL PEAK 48(21Q21.1) WILD-TYPE 55  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(21Q21.1) MUTATED     71    5
  DEL PEAK 48(21Q21.1) WILD-TYPE   55    4
   clus
vv  DEL PEAK 48(21Q21.1) MUTATED DEL PEAK 48(21Q21.1) WILD-TYPE
  0                           71                             55
  1                            5                              4
[1] 2 2
[1] FALSE
D79V7, binary
                                cls
clus                              0  1
  DEL PEAK 48(21Q21.1) MUTATED   13 88
  DEL PEAK 48(21Q21.1) WILD-TYPE 11 61
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(21Q21.1) MUTATED     13   88
  DEL PEAK 48(21Q21.1) WILD-TYPE   11   61
        clus
vv       DEL PEAK 48(21Q21.1) MUTATED DEL PEAK 48(21Q21.1) WILD-TYPE
  FEMALE                           13                             11
  MALE                             88                             61
[1] 2 2
[1] FALSE
D79V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 48(21Q21.1) MUTATED      21                         1    67
  DEL PEAK 48(21Q21.1) WILD-TYPE    20                         1    44
D79V9, multiclass
                           clus
vv                          DEL PEAK 48(21Q21.1) MUTATED
  ASIAN                                               21
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               67
                           clus
vv                          DEL PEAK 48(21Q21.1) WILD-TYPE
  ASIAN                                                 20
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V10, binary
                                cls
clus                              0  1
  DEL PEAK 48(21Q21.1) MUTATED    2 42
  DEL PEAK 48(21Q21.1) WILD-TYPE  1 39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(21Q21.1) MUTATED      2   42
  DEL PEAK 48(21Q21.1) WILD-TYPE    1   39
                        clus
vv                       DEL PEAK 48(21Q21.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           42
                        clus
vv                       DEL PEAK 48(21Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                             39
[1] 2 2
[1] FALSE

Clustering(80) Variable = DEL PEAK 49(21Q22.12) MUTATION ANALYSIS
D80V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 49(21Q22.12) MUTATED   56 44
  DEL PEAK 49(21Q22.12) WILD-TYPE 44 27
  DEL PEAK 49(21Q22.12) MUTATED DEL PEAK 49(21Q22.12) WILD-TYPE 
                            100                              71 
  DEL PEAK 49(21Q22.12) MUTATED DEL PEAK 49(21Q22.12) WILD-TYPE 
                             44                              27 
$`DEL PEAK 49(21Q22.12) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GR 
       25.78         7.63         5.92        13.94         8.94        32.45 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       33.27         0.85        20.78        20.12        18.64         3.88 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        0.53         0.79         9.96       122.10        44.75        68.02 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       23.18        31.56        24.03         3.16        30.25         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ 
        4.31         8.94        24.00         4.70        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
       47.93         7.17         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z 
        7.13         7.43         6.94         2.60         0.36         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ 
        3.95         3.02         2.66        35.97        12.92        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV 
       13.55        13.22         8.71        13.41        27.12        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S 
       46.09        10.36         5.92        12.43        13.41        13.15 
TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
        0.10        12.76         0.10        12.33        13.22        12.33 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FW 
       12.00        12.23        12.03        13.18        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         7.59         5.06         7.04        29.59         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RC TCGA-V5-A7RE 
        9.30         2.89         1.45        12.69         3.42         4.80 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         4.44        18.81        22.82        12.43         1.55 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B 
        8.12        28.11        18.18        42.87        46.19        11.24 
TCGA-VR-AA7D TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        9.17         2.10         2.66        19.73 

$`DEL PEAK 49(21Q22.12) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE 
       31.27        14.30        58.55        16.24         4.21         7.69 
TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 
        6.21        20.09         2.63         9.30        17.03        23.41 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FB 
       12.82        14.86         4.67        14.50        12.16        60.39 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93E 
        3.68        41.52        42.77        25.41        21.70        25.22 
TCGA-KH-A6WC TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        6.28         3.68        19.99        18.35         3.32         1.38 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN 
        8.71        25.12        55.50        13.48         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49U 
       21.37        83.24        10.45        12.66         0.10        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 
        0.10        13.25        12.46        12.59        12.49        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV 
       22.39        15.52        11.54         4.47        25.25        10.52 
TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-RE-A7BO 
        0.13         5.16        14.70        53.95        15.78         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EU 
       20.02        20.38         5.29        15.35        19.96        18.31 
TCGA-VR-A8EY TCGA-VR-AA4G TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD 
       30.71        15.06        15.91        10.16         3.42 

  DEL PEAK 49(21Q22.12) MUTATED DEL PEAK 49(21Q22.12) WILD-TYPE 
                            0.1                             0.1 
  DEL PEAK 49(21Q22.12) MUTATED DEL PEAK 49(21Q22.12) WILD-TYPE 
                         122.10                           83.24 
  DEL PEAK 49(21Q22.12) MUTATED DEL PEAK 49(21Q22.12) WILD-TYPE 
                         12.015                          14.300 
[1] "0.1 - 122.1 (12.0)" "0.1 - 83.2 (14.3)" 
[1] "hr=" "1.3"
D80V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 49(21Q22.12) MUTATED         6        3        6        1        18
  DEL PEAK 49(21Q22.12) WILD-TYPE       2        2        1        0        21
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 49(21Q22.12) MUTATED          13        15          6          6
  DEL PEAK 49(21Q22.12) WILD-TYPE        16        10          6          4
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 49(21Q22.12) MUTATED            5        3         2
  DEL PEAK 49(21Q22.12) WILD-TYPE          2        2         2
D80V3, multiclass
            clus
vv           DEL PEAK 49(21Q22.12) MUTATED DEL PEAK 49(21Q22.12) WILD-TYPE
  STAGE I                                6                               2
  STAGE IA                               3                               2
  STAGE IB                               6                               1
  STAGE II                               1                               0
  STAGE IIA                             18                              21
  STAGE IIB                             13                              16
  STAGE III                             15                              10
  STAGE IIIA                             6                               6
  STAGE IIIB                             6                               4
  STAGE IIIC                             5                               2
  STAGE IV                               3                               2
  STAGE IVA                              2                               2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3 T4
  DEL PEAK 49(21Q22.12) MUTATED      17 18 49  3
  DEL PEAK 49(21Q22.12) WILD-TYPE    14 18 36  2
D80V4, multiclass
       clus
vv      DEL PEAK 49(21Q22.12) MUTATED DEL PEAK 49(21Q22.12) WILD-TYPE
  T0+T1                            17                              14
  T2                               18                              18
  T3                               49                              36
  T4                                3                               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  DEL PEAK 49(21Q22.12) MUTATED   40 35  6  6
  DEL PEAK 49(21Q22.12) WILD-TYPE 31 29  6  2
D80V5, multiclass
    clus
vv   DEL PEAK 49(21Q22.12) MUTATED DEL PEAK 49(21Q22.12) WILD-TYPE
  N0                            40                              31
  N1                            35                              29
  N2                             6                               6
  N3                             6                               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V6, binary
                                 cls
clus                               0  1
  DEL PEAK 49(21Q22.12) MUTATED   71  5
  DEL PEAK 49(21Q22.12) WILD-TYPE 55  4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 49(21Q22.12) MUTATED     71    5
  DEL PEAK 49(21Q22.12) WILD-TYPE   55    4
   clus
vv  DEL PEAK 49(21Q22.12) MUTATED DEL PEAK 49(21Q22.12) WILD-TYPE
  0                            71                              55
  1                             5                               4
[1] 2 2
[1] FALSE
D80V7, binary
                                 cls
clus                               0  1
  DEL PEAK 49(21Q22.12) MUTATED   16 85
  DEL PEAK 49(21Q22.12) WILD-TYPE  8 64
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 49(21Q22.12) MUTATED     16   85
  DEL PEAK 49(21Q22.12) WILD-TYPE    8   64
        clus
vv       DEL PEAK 49(21Q22.12) MUTATED DEL PEAK 49(21Q22.12) WILD-TYPE
  FEMALE                            16                               8
  MALE                              85                              64
[1] 2 2
[1] FALSE
D80V8, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 49(21Q22.12) MUTATED      20                         1    67
  DEL PEAK 49(21Q22.12) WILD-TYPE    21                         1    44
D80V9, multiclass
                           clus
vv                          DEL PEAK 49(21Q22.12) MUTATED
  ASIAN                                                20
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                67
                           clus
vv                          DEL PEAK 49(21Q22.12) WILD-TYPE
  ASIAN                                                  21
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                  44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V10, binary
                                 cls
clus                               0  1
  DEL PEAK 49(21Q22.12) MUTATED    2 41
  DEL PEAK 49(21Q22.12) WILD-TYPE  1 40
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 49(21Q22.12) MUTATED      2   41
  DEL PEAK 49(21Q22.12) WILD-TYPE    1   40
                        clus
vv                       DEL PEAK 49(21Q22.12) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            41
                        clus
vv                       DEL PEAK 49(21Q22.12) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                              40
[1] 2 2
[1] FALSE

Clustering(81) Variable = DEL PEAK 50(22Q11.1) MUTATION ANALYSIS
D81V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 50(22Q11.1) MUTATED   39 37
  DEL PEAK 50(22Q11.1) WILD-TYPE 61 34
  DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE 
                            76                             95 
  DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE 
                            37                             34 
$`DEL PEAK 50(22Q11.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3YB 
       13.94         8.94        16.24         4.21        32.45         2.63 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-JY-A6F8 
       18.64         3.88         0.53         0.79        23.41       122.10 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A4OE TCGA-L5-A4OG 
       42.77        25.41        31.56         3.16        24.00         4.70 
TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       32.61        18.35         7.17         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 
       29.00         7.13         2.60         0.36         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NW TCGA-L7-A6VZ 
       13.55        13.22         5.49         8.71        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W 
        5.92        10.45        13.41         0.10        15.35        13.25 
TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-R6-A6DN 
        0.10        12.76        10.52        12.03        13.18         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
        7.59         5.06        15.78         2.89         1.45         7.00 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8EU 
        5.29         4.80         9.27        18.81        22.82        18.31 
TCGA-VR-A8EZ TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       18.18         2.10         2.66        19.73 

$`DEL PEAK 50(22Q11.1) WILD-TYPE`
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        7.69         6.21        33.27        20.09         0.85        20.78 
TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       20.12         9.30        17.03        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        4.67        14.50        12.16        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F 
        3.68        41.52        21.70        23.18        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF 
        6.28        30.25         0.30         4.31         8.94         3.68 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OX 
       19.99        21.01        47.93         3.32         1.38         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A8NG TCGA-L5-A8NM TCGA-L5-A8NQ 
        6.94         8.71        25.12        35.97         7.76        21.37 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49M TCGA-LN-A49N 
       13.41        27.12        83.24        52.57        12.66        12.43 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 
       13.15         0.10        12.46        12.59        12.49        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39         0.10        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A9FO 
        4.47        12.33        25.25        12.00        12.23         0.13 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
       33.11         5.16         7.82        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW 
        6.35        53.95         9.30        12.69        20.02        20.38 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET 
        3.42        15.35         4.44        19.96        12.43         1.55 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
        8.12        28.11        30.71        42.87        46.19        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD 
       11.24         9.17        15.91        10.16         3.42 

  DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE 
                           0.1                            0.1 
  DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE 
                        122.10                          83.24 
  DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE 
                        10.485                         12.660 
[1] "0.1 - 122.1 (10.5)" "0.1 - 83.2 (12.7)" 
[1] "hr=" "1.6"
D81V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 50(22Q11.1) MUTATED         5        2        3        0        12
  DEL PEAK 50(22Q11.1) WILD-TYPE       3        3        4        1        27
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 50(22Q11.1) MUTATED          11        17          3          3
  DEL PEAK 50(22Q11.1) WILD-TYPE        18         8          9          7
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 50(22Q11.1) MUTATED            4        3         3
  DEL PEAK 50(22Q11.1) WILD-TYPE          3        2         1
D81V3, multiclass
            clus
vv           DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE
  STAGE I                               5                              3
  STAGE IA                              2                              3
  STAGE IB                              3                              4
  STAGE II                              0                              1
  STAGE IIA                            12                             27
  STAGE IIB                            11                             18
  STAGE III                            17                              8
  STAGE IIIA                            3                              9
  STAGE IIIB                            3                              7
  STAGE IIIC                            4                              3
  STAGE IV                              3                              2
  STAGE IVA                             3                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 50(22Q11.1) MUTATED      18 10 41  0
  DEL PEAK 50(22Q11.1) WILD-TYPE    13 26 44  5
D81V4, multiclass
       clus
vv      DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE
  T0+T1                           18                             13
  T2                              10                             26
  T3                              41                             44
  T4                               0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 50(22Q11.1) MUTATED   26 37  2  4
  DEL PEAK 50(22Q11.1) WILD-TYPE 45 27 10  4
D81V5, multiclass
    clus
vv   DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE
  N0                           26                             45
  N1                           37                             27
  N2                            2                             10
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V6, binary
                                cls
clus                              0  1
  DEL PEAK 50(22Q11.1) MUTATED   54  6
  DEL PEAK 50(22Q11.1) WILD-TYPE 72  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 50(22Q11.1) MUTATED     54    6
  DEL PEAK 50(22Q11.1) WILD-TYPE   72    3
   clus
vv  DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE
  0                           54                             72
  1                            6                              3
[1] 2 2
[1] FALSE
D81V7, binary
                                cls
clus                              0  1
  DEL PEAK 50(22Q11.1) MUTATED   11 65
  DEL PEAK 50(22Q11.1) WILD-TYPE 13 84
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 50(22Q11.1) MUTATED     11   65
  DEL PEAK 50(22Q11.1) WILD-TYPE   13   84
        clus
vv       DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE
  FEMALE                           11                             13
  MALE                             65                             84
[1] 2 2
[1] FALSE
D81V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 50(22Q11.1) MUTATED      12                         0    50
  DEL PEAK 50(22Q11.1) WILD-TYPE    29                         2    61
D81V9, multiclass
                           clus
vv                          DEL PEAK 50(22Q11.1) MUTATED
  ASIAN                                               12
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               50
                           clus
vv                          DEL PEAK 50(22Q11.1) WILD-TYPE
  ASIAN                                                 29
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V10, binary
                                cls
clus                              0  1
  DEL PEAK 50(22Q11.1) MUTATED    1 29
  DEL PEAK 50(22Q11.1) WILD-TYPE  2 52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 50(22Q11.1) MUTATED      1   29
  DEL PEAK 50(22Q11.1) WILD-TYPE    2   52
                        clus
vv                       DEL PEAK 50(22Q11.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           29
                        clus
vv                       DEL PEAK 50(22Q11.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             52
[1] 2 2
[1] FALSE

Clustering(82) Variable = DEL PEAK 51(XP21.1) MUTATION ANALYSIS
D82V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 51(XP21.1) MUTATED   37 26
  DEL PEAK 51(XP21.1) WILD-TYPE 63 45
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                           63                           108 
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                           26                            45 
$`DEL PEAK 51(XP21.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
       25.78        14.30         4.21        32.45        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
        0.85        20.78         3.88         0.53        17.03        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FH TCGA-JY-A938 
       12.82         9.96         4.67        44.75        42.77        25.41 
TCGA-JY-A93C TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM 
       23.18         4.31        24.00         3.68        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A891 TCGA-L5-A8NJ TCGA-L5-A8NS 
       18.35         7.17         1.38         3.95        16.47        13.41 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
        5.92        12.66         0.10        12.46        12.59        12.49 
TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       22.39        13.22        12.33        25.25        10.52        12.00 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A8W8 
       13.18         0.13        33.11         5.16         8.02         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASW TCGA-V5-AASX 
        1.45        12.69        20.02         5.29         9.27         4.44 
TCGA-VR-A8EO TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7I 
       18.81        18.31         8.12        18.18        42.87        15.91 
TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE 
       10.16         3.42         2.10 

$`DEL PEAK 51(XP21.1) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       16.24         7.69         6.21         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.30         0.79        14.86        14.50        12.16       122.10 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D 
       60.39        68.02         3.68        41.52        21.70        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OO TCGA-L5-A4OR 
        8.94         4.70        32.61        19.99         3.32         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 
        8.71         2.60        25.12         0.36         7.40         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK 
       55.50         2.66        35.97        12.92        13.48        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT 
       13.22         7.76         5.49        21.37         8.71        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49N 
       83.24        52.57        46.09        10.36        10.45        12.43 
TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.41        13.15        15.35         0.10        13.25         0.10 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.76        12.59         0.10        15.52        11.54        12.33 
TCGA-LN-A5U5 TCGA-LN-A7HX TCGA-LN-A7HY TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ 
        4.47        12.23        12.03         7.82         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       14.70         7.04        29.59         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
       15.78         7.00        20.38         3.42         4.80        15.35 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EY 
       19.96        22.82        12.43         1.55        28.11        30.71 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       46.19        15.06        11.24         9.17         2.66        19.73 

  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                          0.1                           0.1 
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                        47.93                        122.10 
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                        12.66                         12.43 
[1] "0.1 - 47.9 (12.7)"  "0.1 - 122.1 (12.4)"
[1] "hr=" "1.2"
D82V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 51(XP21.1) MUTATED         1        2        0        0        16
  DEL PEAK 51(XP21.1) WILD-TYPE       7        3        7        1        23
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 51(XP21.1) MUTATED          14         6          7          8
  DEL PEAK 51(XP21.1) WILD-TYPE        15        19          5          2
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 51(XP21.1) MUTATED            1        1         0
  DEL PEAK 51(XP21.1) WILD-TYPE          6        4         4
D82V3, multiclass
            clus
vv           DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  STAGE I                              1                             7
  STAGE IA                             2                             3
  STAGE IB                             0                             7
  STAGE II                             0                             1
  STAGE IIA                           16                            23
  STAGE IIB                           14                            15
  STAGE III                            6                            19
  STAGE IIIA                           7                             5
  STAGE IIIB                           8                             2
  STAGE IIIC                           1                             6
  STAGE IV                             1                             4
  STAGE IVA                            0                             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 51(XP21.1) MUTATED       9 14 33  3
  DEL PEAK 51(XP21.1) WILD-TYPE    22 22 52  2
D82V4, multiclass
       clus
vv      DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  T0+T1                           9                            22
  T2                             14                            22
  T3                             33                            52
  T4                              3                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 51(XP21.1) MUTATED   29 21  8  1
  DEL PEAK 51(XP21.1) WILD-TYPE 42 43  4  7
D82V5, multiclass
    clus
vv   DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  N0                          29                            42
  N1                          21                            43
  N2                           8                             4
  N3                           1                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V6, binary
                               cls
clus                             0  1
  DEL PEAK 51(XP21.1) MUTATED   48  1
  DEL PEAK 51(XP21.1) WILD-TYPE 78  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XP21.1) MUTATED     48    1
  DEL PEAK 51(XP21.1) WILD-TYPE   78    8
   clus
vv  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  0                          48                            78
  1                           1                             8
[1] 2 2
[1] FALSE
D82V7, binary
                               cls
clus                             0  1
  DEL PEAK 51(XP21.1) MUTATED    6 59
  DEL PEAK 51(XP21.1) WILD-TYPE 18 90
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XP21.1) MUTATED      6   59
  DEL PEAK 51(XP21.1) WILD-TYPE   18   90
        clus
vv       DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  FEMALE                           6                            18
  MALE                            59                            90
[1] 2 2
[1] FALSE
D82V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 51(XP21.1) MUTATED      22                         0    37
  DEL PEAK 51(XP21.1) WILD-TYPE    19                         2    74
D82V9, multiclass
                           clus
vv                          DEL PEAK 51(XP21.1) MUTATED
  ASIAN                                              22
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              37
                           clus
vv                          DEL PEAK 51(XP21.1) WILD-TYPE
  ASIAN                                                19
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V10, binary
                               cls
clus                             0  1
  DEL PEAK 51(XP21.1) MUTATED    2 37
  DEL PEAK 51(XP21.1) WILD-TYPE  1 44
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XP21.1) MUTATED      2   37
  DEL PEAK 51(XP21.1) WILD-TYPE    1   44
                        clus
vv                       DEL PEAK 51(XP21.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          37
                        clus
vv                       DEL PEAK 51(XP21.1) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            44
[1] 2 2
[1] FALSE

Clustering(83) Variable = DEL PEAK 52(XP11.3) MUTATION ANALYSIS
D83V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 52(XP11.3) MUTATED   42 25
  DEL PEAK 52(XP11.3) WILD-TYPE 58 46
  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                           67                           104 
  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                           25                            46 
$`DEL PEAK 52(XP11.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3QL 
       25.78        14.30         8.94         4.21        32.45        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D 
        0.85        20.78        20.12         3.88         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6FA 
        0.79        23.41        12.82         9.96         4.67        44.75 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF 
       42.77        25.41        23.18         4.31        24.00         3.68 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A891 TCGA-L5-A8NJ 
       21.01        47.93        18.35         7.17         3.95        16.47 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49W 
        8.71        13.41         5.92        12.66         0.10        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A9 
        0.10        12.46        12.59        12.49        22.39        11.54 
TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       13.22        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A8W8 TCGA-R6-A8WC 
       13.18         0.13        33.11         5.16         2.89         1.45 
TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       12.69        20.02         9.27         4.44        18.81        19.96 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD 
       18.31         8.12        42.87        15.91        10.16         3.42 
TCGA-Z6-A8JE 
        2.10 

$`DEL PEAK 52(XP11.3) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO 
       31.27        58.55         7.63         5.92        13.94        16.24 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QT 
        7.69         6.21        33.27         2.63        18.64         9.30 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD 
       14.86        14.50        12.16       122.10        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
        3.68        41.52        21.70        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OG 
        6.28         3.16        30.25         0.30         8.94         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       32.61        19.99         3.32         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        4.90        29.00         7.13         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         0.36         7.40         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        35.97        12.92        13.48        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49        21.37        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S 
       46.09        10.36        10.45        12.43        13.41        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 
       15.35         0.10        12.76        12.59         0.10        15.52 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.33         4.47        12.33         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        14.70         7.04        29.59         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        9.30        15.78         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EX 
        4.80        15.35        22.82        12.43         1.55        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       30.71        18.18        46.19        15.06        11.24         9.17 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                          0.1                           0.1 
  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                        47.93                        122.10 
  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                        12.59                         12.51 
[1] "0.1 - 47.9 (12.6)"  "0.1 - 122.1 (12.5)"
[1] "hr=" "1.1"
D83V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 52(XP11.3) MUTATED         1        2        1        0        18
  DEL PEAK 52(XP11.3) WILD-TYPE       7        3        6        1        21
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 52(XP11.3) MUTATED          13        10          7          9
  DEL PEAK 52(XP11.3) WILD-TYPE        16        15          5          1
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 52(XP11.3) MUTATED            0        1         0
  DEL PEAK 52(XP11.3) WILD-TYPE          7        4         4
D83V3, multiclass
            clus
vv           DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  STAGE I                              1                             7
  STAGE IA                             2                             3
  STAGE IB                             1                             6
  STAGE II                             0                             1
  STAGE IIA                           18                            21
  STAGE IIB                           13                            16
  STAGE III                           10                            15
  STAGE IIIA                           7                             5
  STAGE IIIB                           9                             1
  STAGE IIIC                           0                             7
  STAGE IV                             1                             4
  STAGE IVA                            0                             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 52(XP11.3) MUTATED       8 14 39  3
  DEL PEAK 52(XP11.3) WILD-TYPE    23 22 46  2
D83V4, multiclass
       clus
vv      DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  T0+T1                           8                            23
  T2                             14                            22
  T3                             39                            46
  T4                              3                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 52(XP11.3) MUTATED   32 24  8  0
  DEL PEAK 52(XP11.3) WILD-TYPE 39 40  4  8
D83V5, multiclass
    clus
vv   DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  N0                          32                            39
  N1                          24                            40
  N2                           8                             4
  N3                           0                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V6, binary
                               cls
clus                             0  1
  DEL PEAK 52(XP11.3) MUTATED   55  1
  DEL PEAK 52(XP11.3) WILD-TYPE 71  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 52(XP11.3) MUTATED     55    1
  DEL PEAK 52(XP11.3) WILD-TYPE   71    8
   clus
vv  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  0                          55                            71
  1                           1                             8
[1] 2 2
[1] FALSE
D83V7, binary
                               cls
clus                             0  1
  DEL PEAK 52(XP11.3) MUTATED    6 63
  DEL PEAK 52(XP11.3) WILD-TYPE 18 86
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 52(XP11.3) MUTATED      6   63
  DEL PEAK 52(XP11.3) WILD-TYPE   18   86
        clus
vv       DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  FEMALE                           6                            18
  MALE                            63                            86
[1] 2 2
[1] FALSE
D83V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 52(XP11.3) MUTATED      26                         0    36
  DEL PEAK 52(XP11.3) WILD-TYPE    15                         2    75
D83V9, multiclass
                           clus
vv                          DEL PEAK 52(XP11.3) MUTATED
  ASIAN                                              26
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              36
                           clus
vv                          DEL PEAK 52(XP11.3) WILD-TYPE
  ASIAN                                                15
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V10, binary
                               cls
clus                             0  1
  DEL PEAK 52(XP11.3) MUTATED    1 40
  DEL PEAK 52(XP11.3) WILD-TYPE  2 41
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 52(XP11.3) MUTATED      1   40
  DEL PEAK 52(XP11.3) WILD-TYPE    2   41
                        clus
vv                       DEL PEAK 52(XP11.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          40
                        clus
vv                       DEL PEAK 52(XP11.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            41
[1] 2 2
[1] FALSE

Clustering(84) Variable = DEL PEAK 53(XQ11.2) MUTATION ANALYSIS
D84V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 53(XQ11.2) MUTATED   28 12
  DEL PEAK 53(XQ11.2) WILD-TYPE 72 59
  DEL PEAK 53(XQ11.2) MUTATED DEL PEAK 53(XQ11.2) WILD-TYPE 
                           40                           131 
  DEL PEAK 53(XQ11.2) MUTATED DEL PEAK 53(XQ11.2) WILD-TYPE 
                           12                            59 
$`DEL PEAK 53(XQ11.2) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GQ TCGA-IG-A3YC TCGA-IG-A6QS TCGA-JY-A6FA TCGA-JY-A6FH 
       25.78         4.21        20.12         9.96        44.75        42.77 
TCGA-JY-A938 TCGA-JY-A93C TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OJ 
       25.41        23.18         8.94        24.00         3.68        21.01 
TCGA-L5-A4OP TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        7.17         0.36         3.95        13.48        16.47        13.55 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49Y 
        8.71        13.41         5.92        10.45        12.66        12.46 
TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-M9-A5M8 TCGA-Q9-A6FU 
       12.49        22.39        25.25        10.52        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A8WC TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW TCGA-V5-AASX 
        7.82         1.45         5.29         3.42         9.27         4.44 
TCGA-VR-A8EO TCGA-VR-AA7B TCGA-X8-AAAR TCGA-Z6-AAPN 
       18.81        11.24        10.16         2.66 

$`DEL PEAK 53(XQ11.2) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 
        8.94        16.24        32.45         7.69         6.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS 
       20.09         0.85        20.78         2.63        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FB 
       14.86         4.67        14.50        12.16       122.10        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E 
       68.02         3.68        41.52        21.70        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       24.03         6.28         3.16        30.25         0.30         4.31 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        4.70        32.61        19.99        47.93        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.43         6.94         8.71         2.60        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NL 
        3.02        55.50         2.66        35.97        12.92        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49        21.37        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       46.09        10.36        12.43        13.41         0.10        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A3 
       15.35         0.10        13.25         0.10        12.59        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59         0.10        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
        4.47        12.33        12.00        12.23        12.03        13.18 
TCGA-LN-A9FO TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        0.13         8.02         7.59         5.06        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       29.59         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASV 
       12.69         7.00        20.02        20.38         4.80        15.35 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       19.96        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        30.71        18.18        42.87        46.19        15.06 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
        9.17        15.91         3.42         2.10        19.73 

  DEL PEAK 53(XQ11.2) MUTATED DEL PEAK 53(XQ11.2) WILD-TYPE 
                         0.36                          0.10 
  DEL PEAK 53(XQ11.2) MUTATED DEL PEAK 53(XQ11.2) WILD-TYPE 
                        44.75                        122.10 
  DEL PEAK 53(XQ11.2) MUTATED DEL PEAK 53(XQ11.2) WILD-TYPE 
                        10.88                         12.76 
[1] "0.4 - 44.8 (10.9)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "1.2"
D84V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 53(XQ11.2) MUTATED         1        1        0        0        11
  DEL PEAK 53(XQ11.2) WILD-TYPE       7        4        7        1        28
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 53(XQ11.2) MUTATED           6         5          1          5
  DEL PEAK 53(XQ11.2) WILD-TYPE        23        20         11          5
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 53(XQ11.2) MUTATED            0        1         0
  DEL PEAK 53(XQ11.2) WILD-TYPE          7        4         4
D84V3, multiclass
            clus
vv           DEL PEAK 53(XQ11.2) MUTATED DEL PEAK 53(XQ11.2) WILD-TYPE
  STAGE I                              1                             7
  STAGE IA                             1                             4
  STAGE IB                             0                             7
  STAGE II                             0                             1
  STAGE IIA                           11                            28
  STAGE IIB                            6                            23
  STAGE III                            5                            20
  STAGE IIIA                           1                            11
  STAGE IIIB                           5                             5
  STAGE IIIC                           0                             7
  STAGE IV                             1                             4
  STAGE IVA                            0                             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 53(XQ11.2) MUTATED       6  8 22  0
  DEL PEAK 53(XQ11.2) WILD-TYPE    25 28 63  5
D84V4, multiclass
       clus
vv      DEL PEAK 53(XQ11.2) MUTATED DEL PEAK 53(XQ11.2) WILD-TYPE
  T0+T1                           6                            25
  T2                              8                            28
  T3                             22                            63
  T4                              0                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 53(XQ11.2) MUTATED   17 13  5  1
  DEL PEAK 53(XQ11.2) WILD-TYPE 54 51  7  7
D84V5, multiclass
    clus
vv   DEL PEAK 53(XQ11.2) MUTATED DEL PEAK 53(XQ11.2) WILD-TYPE
  N0                          17                            54
  N1                          13                            51
  N2                           5                             7
  N3                           1                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V6, binary
                               cls
clus                             0  1
  DEL PEAK 53(XQ11.2) MUTATED   28  1
  DEL PEAK 53(XQ11.2) WILD-TYPE 98  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 53(XQ11.2) MUTATED     28    1
  DEL PEAK 53(XQ11.2) WILD-TYPE   98    8
   clus
vv  DEL PEAK 53(XQ11.2) MUTATED DEL PEAK 53(XQ11.2) WILD-TYPE
  0                          28                            98
  1                           1                             8
[1] 2 2
[1] FALSE
D84V7, binary
                               cls
clus                              0   1
  DEL PEAK 53(XQ11.2) MUTATED     7  33
  DEL PEAK 53(XQ11.2) WILD-TYPE  17 116
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 53(XQ11.2) MUTATED      7   33
  DEL PEAK 53(XQ11.2) WILD-TYPE   17  116
        clus
vv       DEL PEAK 53(XQ11.2) MUTATED DEL PEAK 53(XQ11.2) WILD-TYPE
  FEMALE                           7                            17
  MALE                            33                           116
[1] 2 2
[1] FALSE
D84V8, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 53(XQ11.2) MUTATED      10                         1    23
  DEL PEAK 53(XQ11.2) WILD-TYPE    31                         1    88
D84V9, multiclass
                           clus
vv                          DEL PEAK 53(XQ11.2) MUTATED
  ASIAN                                              10
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              23
                           clus
vv                          DEL PEAK 53(XQ11.2) WILD-TYPE
  ASIAN                                                31
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V10, binary
                               cls
clus                             0  1
  DEL PEAK 53(XQ11.2) MUTATED    1 18
  DEL PEAK 53(XQ11.2) WILD-TYPE  2 63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 53(XQ11.2) MUTATED      1   18
  DEL PEAK 53(XQ11.2) WILD-TYPE    2   63
                        clus
vv                       DEL PEAK 53(XQ11.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          18
                        clus
vv                       DEL PEAK 53(XQ11.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            63
[1] 2 2
[1] FALSE

Clustering(85) Variable = DEL PEAK 54(XQ21.33) MUTATION ANALYSIS
D85V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 54(XQ21.33) MUTATED   27 12
  DEL PEAK 54(XQ21.33) WILD-TYPE 73 59
  DEL PEAK 54(XQ21.33) MUTATED DEL PEAK 54(XQ21.33) WILD-TYPE 
                            39                            132 
  DEL PEAK 54(XQ21.33) MUTATED DEL PEAK 54(XQ21.33) WILD-TYPE 
                            12                             59 
$`DEL PEAK 54(XQ21.33) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GQ TCGA-IC-A6RF TCGA-JY-A6FH TCGA-JY-A938 TCGA-L5-A43M 
       25.78         4.21         6.21        42.77        25.41         8.94 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A88Y TCGA-L5-A891 
       21.01        47.93         7.17         3.16         0.36         3.95 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-LN-A49M TCGA-LN-A49W 
       13.48        16.47        13.55        13.22        12.66        13.25 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A5U7 
       12.46        12.49        22.39         0.10        11.54        25.25 
TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-R6-A6KZ TCGA-R6-A8W8 
       10.52        12.03         0.13        33.11         5.06         2.89 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
        1.45         7.00         3.42         4.80         9.27         4.44 
TCGA-VR-A8EO TCGA-VR-AA7B TCGA-ZR-A9CJ 
       18.81        11.24        19.73 

$`DEL PEAK 54(XQ21.33) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24        32.45         7.69        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
       44.75        60.39        68.02         3.68        41.52        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
       30.25         0.30         4.31        24.00         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS 
       32.61        19.99        18.35         3.32         1.38        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        4.90        29.00         7.13         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60        25.12         7.40         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       35.97        12.92         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
       13.41        27.12        83.24        52.57        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
        5.92        10.45        12.43        13.41         0.10        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 
       15.35         0.10         0.10        12.59        12.76        12.59 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HW 
       15.52        12.33        13.22         4.47        12.33        12.00 
TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.23        13.18         5.16         7.82         8.02         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       14.70         7.04        29.59         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV 
       15.78        12.69        20.02        20.38         5.29        15.35 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       19.96        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        30.71        18.18        42.87        46.19        15.06 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
        9.17        15.91        10.16         3.42         2.10         2.66 

  DEL PEAK 54(XQ21.33) MUTATED DEL PEAK 54(XQ21.33) WILD-TYPE 
                           0.1                            0.1 
  DEL PEAK 54(XQ21.33) MUTATED DEL PEAK 54(XQ21.33) WILD-TYPE 
                         47.93                         122.10 
  DEL PEAK 54(XQ21.33) MUTATED DEL PEAK 54(XQ21.33) WILD-TYPE 
                         11.54                          12.79 
[1] "0.1 - 47.9 (11.5)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "1.1"
D85V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 54(XQ21.33) MUTATED         1        4        1        1        10
  DEL PEAK 54(XQ21.33) WILD-TYPE       7        1        6        0        29
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 54(XQ21.33) MUTATED           3         7          0          1
  DEL PEAK 54(XQ21.33) WILD-TYPE        26        18         12          9
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 54(XQ21.33) MUTATED            1        1         0
  DEL PEAK 54(XQ21.33) WILD-TYPE          6        4         4
D85V3, multiclass
            clus
vv           DEL PEAK 54(XQ21.33) MUTATED DEL PEAK 54(XQ21.33) WILD-TYPE
  STAGE I                               1                              7
  STAGE IA                              4                              1
  STAGE IB                              1                              6
  STAGE II                              1                              0
  STAGE IIA                            10                             29
  STAGE IIB                             3                             26
  STAGE III                             7                             18
  STAGE IIIA                            0                             12
  STAGE IIIB                            1                              9
  STAGE IIIC                            1                              6
  STAGE IV                              1                              4
  STAGE IVA                             0                              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 54(XQ21.33) MUTATED       8  8 17  0
  DEL PEAK 54(XQ21.33) WILD-TYPE    23 28 68  5
D85V4, multiclass
       clus
vv      DEL PEAK 54(XQ21.33) MUTATED DEL PEAK 54(XQ21.33) WILD-TYPE
  T0+T1                            8                             23
  T2                               8                             28
  T3                              17                             68
  T4                               0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 54(XQ21.33) MUTATED   20 10  1  2
  DEL PEAK 54(XQ21.33) WILD-TYPE 51 54 11  6
D85V5, multiclass
    clus
vv   DEL PEAK 54(XQ21.33) MUTATED DEL PEAK 54(XQ21.33) WILD-TYPE
  N0                           20                             51
  N1                           10                             54
  N2                            1                             11
  N3                            2                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V6, binary
                                cls
clus                               0   1
  DEL PEAK 54(XQ21.33) MUTATED    26   1
  DEL PEAK 54(XQ21.33) WILD-TYPE 100   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 54(XQ21.33) MUTATED     26    1
  DEL PEAK 54(XQ21.33) WILD-TYPE  100    8
   clus
vv  DEL PEAK 54(XQ21.33) MUTATED DEL PEAK 54(XQ21.33) WILD-TYPE
  0                           26                            100
  1                            1                              8
[1] 2 2
[1] FALSE
D85V7, binary
                                cls
clus                               0   1
  DEL PEAK 54(XQ21.33) MUTATED     8  31
  DEL PEAK 54(XQ21.33) WILD-TYPE  16 118
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 54(XQ21.33) MUTATED      8   31
  DEL PEAK 54(XQ21.33) WILD-TYPE   16  118
        clus
vv       DEL PEAK 54(XQ21.33) MUTATED DEL PEAK 54(XQ21.33) WILD-TYPE
  FEMALE                            8                             16
  MALE                             31                            118
[1] 2 2
[1] FALSE
D85V8, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 54(XQ21.33) MUTATED      11                         1    23
  DEL PEAK 54(XQ21.33) WILD-TYPE    30                         1    88
D85V9, multiclass
                           clus
vv                          DEL PEAK 54(XQ21.33) MUTATED
  ASIAN                                               11
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               23
                           clus
vv                          DEL PEAK 54(XQ21.33) WILD-TYPE
  ASIAN                                                 30
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V10, binary
                                cls
clus                              0  1
  DEL PEAK 54(XQ21.33) MUTATED    0 20
  DEL PEAK 54(XQ21.33) WILD-TYPE  3 61
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 54(XQ21.33) MUTATED      0   20
  DEL PEAK 54(XQ21.33) WILD-TYPE    3   61
                        clus
vv                       DEL PEAK 54(XQ21.33) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           20
                        clus
vv                       DEL PEAK 54(XQ21.33) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                             61
[1] 2 2
[1] FALSE
