[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTBLCA-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/BLCA-TP/10005789/BLCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BLCA-TP/10013674/transformed.cor.cli.txt"

nPatients in clinical file=218, in cluster file=264, common to both=214
[1]  70 214
[1] "AMP PEAK  1(1P34.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                           62                           152 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                           62                           152 
[1] "AMP PEAK  2(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          106                           108 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          106                           108 
[1] "AMP PEAK  3(1Q23.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE 
                          112                           102 
  AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE 
                          112                           102 
[1] "AMP PEAK  4(3P25.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(3P25.2) MUTATED AMP PEAK  4(3P25.2) WILD-TYPE 
                          104                           110 
  AMP PEAK  4(3P25.2) MUTATED AMP PEAK  4(3P25.2) WILD-TYPE 
                          104                           110 
[1] "AMP PEAK  5(3Q26.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(3Q26.32) MUTATED AMP PEAK  5(3Q26.32) WILD-TYPE 
                           115                             99 
  AMP PEAK  5(3Q26.32) MUTATED AMP PEAK  5(3Q26.32) WILD-TYPE 
                           115                             99 
[1] "AMP PEAK  6(4P16.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE 
                           46                           168 
  AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE 
                           46                           168 
[1] "AMP PEAK  7(4Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE 
                           37                           177 
  AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE 
                           37                           177 
[1] "AMP PEAK  8(4Q31.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(4Q31.21) MUTATED AMP PEAK  8(4Q31.21) WILD-TYPE 
                            21                            193 
  AMP PEAK  8(4Q31.21) MUTATED AMP PEAK  8(4Q31.21) WILD-TYPE 
                            21                            193 
[1] "AMP PEAK  9(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                           102                            112 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                           102                            112 
[1] "AMP PEAK 10(6P22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                           88                           126 
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                           88                           126 
[1] "AMP PEAK 11(6Q21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                         18                         196 
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                         18                         196 
[1] "AMP PEAK 12(7P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(7P21.1) MUTATED AMP PEAK 12(7P21.1) WILD-TYPE 
                          112                           102 
  AMP PEAK 12(7P21.1) MUTATED AMP PEAK 12(7P21.1) WILD-TYPE 
                          112                           102 
[1] "AMP PEAK 13(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE 
                          111                           103 
  AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE 
                          111                           103 
[1] "AMP PEAK 14(8P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(8P11.23) MUTATED AMP PEAK 14(8P11.23) WILD-TYPE 
                            69                            145 
  AMP PEAK 14(8P11.23) MUTATED AMP PEAK 14(8P11.23) WILD-TYPE 
                            69                            145 
[1] "AMP PEAK 15(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(8P11.21) MUTATED AMP PEAK 15(8P11.21) WILD-TYPE 
                            69                            145 
  AMP PEAK 15(8P11.21) MUTATED AMP PEAK 15(8P11.21) WILD-TYPE 
                            69                            145 
[1] "AMP PEAK 16(8Q22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(8Q22.3) MUTATED AMP PEAK 16(8Q22.3) WILD-TYPE 
                          138                            76 
  AMP PEAK 16(8Q22.3) MUTATED AMP PEAK 16(8Q22.3) WILD-TYPE 
                          138                            76 
[1] "AMP PEAK 17(9P24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(9P24.1) MUTATED AMP PEAK 17(9P24.1) WILD-TYPE 
                           43                           171 
  AMP PEAK 17(9P24.1) MUTATED AMP PEAK 17(9P24.1) WILD-TYPE 
                           43                           171 
[1] "AMP PEAK 18(10P14) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(10P14) MUTATED AMP PEAK 18(10P14) WILD-TYPE 
                          92                          122 
  AMP PEAK 18(10P14) MUTATED AMP PEAK 18(10P14) WILD-TYPE 
                          92                          122 
[1] "AMP PEAK 19(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(11Q13.3) MUTATED AMP PEAK 19(11Q13.3) WILD-TYPE 
                            83                            131 
  AMP PEAK 19(11Q13.3) MUTATED AMP PEAK 19(11Q13.3) WILD-TYPE 
                            83                            131 
[1] "AMP PEAK 20(11Q22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(11Q22.2) MUTATED AMP PEAK 20(11Q22.2) WILD-TYPE 
                            41                            173 
  AMP PEAK 20(11Q22.2) MUTATED AMP PEAK 20(11Q22.2) WILD-TYPE 
                            41                            173 
[1] "AMP PEAK 21(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(12Q15) MUTATED AMP PEAK 21(12Q15) WILD-TYPE 
                          63                          151 
  AMP PEAK 21(12Q15) MUTATED AMP PEAK 21(12Q15) WILD-TYPE 
                          63                          151 
[1] "AMP PEAK 22(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(13Q22.1) MUTATED AMP PEAK 22(13Q22.1) WILD-TYPE 
                            68                            146 
  AMP PEAK 22(13Q22.1) MUTATED AMP PEAK 22(13Q22.1) WILD-TYPE 
                            68                            146 
[1] "AMP PEAK 23(14Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(14Q11.2) MUTATED AMP PEAK 23(14Q11.2) WILD-TYPE 
                            52                            162 
  AMP PEAK 23(14Q11.2) MUTATED AMP PEAK 23(14Q11.2) WILD-TYPE 
                            52                            162 
[1] "AMP PEAK 24(16P13.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(16P13.13) MUTATED AMP PEAK 24(16P13.13) WILD-TYPE 
                             45                             169 
  AMP PEAK 24(16P13.13) MUTATED AMP PEAK 24(16P13.13) WILD-TYPE 
                             45                             169 
[1] "AMP PEAK 25(16P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(16P11.2) MUTATED AMP PEAK 25(16P11.2) WILD-TYPE 
                            57                            157 
  AMP PEAK 25(16P11.2) MUTATED AMP PEAK 25(16P11.2) WILD-TYPE 
                            57                            157 
[1] "AMP PEAK 26(16Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(16Q22.1) MUTATED AMP PEAK 26(16Q22.1) WILD-TYPE 
                            62                            152 
  AMP PEAK 26(16Q22.1) MUTATED AMP PEAK 26(16Q22.1) WILD-TYPE 
                            62                            152 
[1] "AMP PEAK 27(17Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(17Q11.2) MUTATED AMP PEAK 27(17Q11.2) WILD-TYPE 
                            96                            118 
  AMP PEAK 27(17Q11.2) MUTATED AMP PEAK 27(17Q11.2) WILD-TYPE 
                            96                            118 
[1] "AMP PEAK 28(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE 
                          88                          126 
  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE 
                          88                          126 
[1] "AMP PEAK 29(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(19Q12) MUTATED AMP PEAK 29(19Q12) WILD-TYPE 
                          86                          128 
  AMP PEAK 29(19Q12) MUTATED AMP PEAK 29(19Q12) WILD-TYPE 
                          86                          128 
[1] "AMP PEAK 30(19Q13.43) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 30(19Q13.43) MUTATED AMP PEAK 30(19Q13.43) WILD-TYPE 
                             82                             132 
  AMP PEAK 30(19Q13.43) MUTATED AMP PEAK 30(19Q13.43) WILD-TYPE 
                             82                             132 
[1] "AMP PEAK 31(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 31(20Q11.21) MUTATED AMP PEAK 31(20Q11.21) WILD-TYPE 
                            140                              74 
  AMP PEAK 31(20Q11.21) MUTATED AMP PEAK 31(20Q11.21) WILD-TYPE 
                            140                              74 
[1] "AMP PEAK 32(22Q11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 32(22Q11.23) MUTATED AMP PEAK 32(22Q11.23) WILD-TYPE 
                             43                             171 
  AMP PEAK 32(22Q11.23) MUTATED AMP PEAK 32(22Q11.23) WILD-TYPE 
                             43                             171 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            43                            171 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            43                            171 
[1] "DEL PEAK  2(1Q32.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE 
                           40                           174 
  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE 
                           40                           174 
[1] "DEL PEAK  3(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           65                           149 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           65                           149 
[1] "DEL PEAK  4(2Q37.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                          108                           106 
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                          108                           106 
[1] "DEL PEAK  5(3P21.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                            65                            149 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                            65                            149 
[1] "DEL PEAK  6(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           64                           150 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           64                           150 
[1] "DEL PEAK  7(3P13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE 
                         59                         155 
  DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE 
                         59                         155 
[1] "DEL PEAK  8(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                           89                           125 
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                           89                           125 
[1] "DEL PEAK  9(4Q34.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(4Q34.2) MUTATED DEL PEAK  9(4Q34.2) WILD-TYPE 
                           97                           117 
  DEL PEAK  9(4Q34.2) MUTATED DEL PEAK  9(4Q34.2) WILD-TYPE 
                           97                           117 
[1] "DEL PEAK 10(5Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE 
                          106                           108 
  DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE 
                          106                           108 
[1] "DEL PEAK 11(5Q35.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(5Q35.1) MUTATED DEL PEAK 11(5Q35.1) WILD-TYPE 
                          100                           114 
  DEL PEAK 11(5Q35.1) MUTATED DEL PEAK 11(5Q35.1) WILD-TYPE 
                          100                           114 
[1] "DEL PEAK 12(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE 
                           54                           160 
  DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE 
                           54                           160 
[1] "DEL PEAK 13(6Q21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(6Q21) MUTATED DEL PEAK 13(6Q21) WILD-TYPE 
                         99                         115 
  DEL PEAK 13(6Q21) MUTATED DEL PEAK 13(6Q21) WILD-TYPE 
                         99                         115 
[1] "DEL PEAK 14(6Q27) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(6Q27) MUTATED DEL PEAK 14(6Q27) WILD-TYPE 
                         99                         115 
  DEL PEAK 14(6Q27) MUTATED DEL PEAK 14(6Q27) WILD-TYPE 
                         99                         115 
[1] "DEL PEAK 15(7Q36.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(7Q36.3) MUTATED DEL PEAK 15(7Q36.3) WILD-TYPE 
                           30                           184 
  DEL PEAK 15(7Q36.3) MUTATED DEL PEAK 15(7Q36.3) WILD-TYPE 
                           30                           184 
[1] "DEL PEAK 16(8P23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE 
                          119                            95 
  DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE 
                          119                            95 
[1] "DEL PEAK 17(8P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(8P12) MUTATED DEL PEAK 17(8P12) WILD-TYPE 
                        103                         111 
  DEL PEAK 17(8P12) MUTATED DEL PEAK 17(8P12) WILD-TYPE 
                        103                         111 
[1] "DEL PEAK 18(8P11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(8P11.21) MUTATED DEL PEAK 18(8P11.21) WILD-TYPE 
                            52                            162 
  DEL PEAK 18(8P11.21) MUTATED DEL PEAK 18(8P11.21) WILD-TYPE 
                            52                            162 
[1] "DEL PEAK 19(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE 
                         92                         122 
  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE 
                         92                         122 
[1] "DEL PEAK 20(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE 
                          123                            91 
  DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE 
                          123                            91 
[1] "DEL PEAK 21(9Q33.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(9Q33.2) MUTATED DEL PEAK 21(9Q33.2) WILD-TYPE 
                           83                           131 
  DEL PEAK 21(9Q33.2) MUTATED DEL PEAK 21(9Q33.2) WILD-TYPE 
                           83                           131 
[1] "DEL PEAK 22(10P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(10P12.1) MUTATED DEL PEAK 22(10P12.1) WILD-TYPE 
                            37                            177 
  DEL PEAK 22(10P12.1) MUTATED DEL PEAK 22(10P12.1) WILD-TYPE 
                            37                            177 
[1] "DEL PEAK 23(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(10Q23.31) MUTATED DEL PEAK 23(10Q23.31) WILD-TYPE 
                             86                             128 
  DEL PEAK 23(10Q23.31) MUTATED DEL PEAK 23(10Q23.31) WILD-TYPE 
                             86                             128 
[1] "DEL PEAK 24(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(11P15.5) MUTATED DEL PEAK 24(11P15.5) WILD-TYPE 
                           102                            112 
  DEL PEAK 24(11P15.5) MUTATED DEL PEAK 24(11P15.5) WILD-TYPE 
                           102                            112 
[1] "DEL PEAK 25(11Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(11Q23.3) MUTATED DEL PEAK 25(11Q23.3) WILD-TYPE 
                            76                            138 
  DEL PEAK 25(11Q23.3) MUTATED DEL PEAK 25(11Q23.3) WILD-TYPE 
                            76                            138 
[1] "DEL PEAK 26(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                            87                            127 
  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                            87                            127 
[1] "DEL PEAK 27(14Q12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(14Q12) MUTATED DEL PEAK 27(14Q12) WILD-TYPE 
                          63                          151 
  DEL PEAK 27(14Q12) MUTATED DEL PEAK 27(14Q12) WILD-TYPE 
                          63                          151 
[1] "DEL PEAK 28(14Q24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(14Q24.1) MUTATED DEL PEAK 28(14Q24.1) WILD-TYPE 
                            65                            149 
  DEL PEAK 28(14Q24.1) MUTATED DEL PEAK 28(14Q24.1) WILD-TYPE 
                            65                            149 
[1] "DEL PEAK 29(15Q13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(15Q13.1) MUTATED DEL PEAK 29(15Q13.1) WILD-TYPE 
                            87                            127 
  DEL PEAK 29(15Q13.1) MUTATED DEL PEAK 29(15Q13.1) WILD-TYPE 
                            87                            127 
[1] "DEL PEAK 30(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(16P13.3) MUTATED DEL PEAK 30(16P13.3) WILD-TYPE 
                            85                            129 
  DEL PEAK 30(16P13.3) MUTATED DEL PEAK 30(16P13.3) WILD-TYPE 
                            85                            129 
[1] "DEL PEAK 31(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE 
                            61                            153 
  DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE 
                            61                            153 
[1] "DEL PEAK 32(17P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(17P12) MUTATED DEL PEAK 32(17P12) WILD-TYPE 
                         109                          105 
  DEL PEAK 32(17P12) MUTATED DEL PEAK 32(17P12) WILD-TYPE 
                         109                          105 
[1] "DEL PEAK 33(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(18Q21.2) MUTATED DEL PEAK 33(18Q21.2) WILD-TYPE 
                            96                            118 
  DEL PEAK 33(18Q21.2) MUTATED DEL PEAK 33(18Q21.2) WILD-TYPE 
                            96                            118 
[1] "DEL PEAK 34(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE 
                            80                            134 
  DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE 
                            80                            134 
[1] "DEL PEAK 35(22Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(22Q13.31) MUTATED DEL PEAK 35(22Q13.31) WILD-TYPE 
                             94                             120 
  DEL PEAK 35(22Q13.31) MUTATED DEL PEAK 35(22Q13.31) WILD-TYPE 
                             94                             120 
[1] "DEL PEAK 36(XP11.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE 
                           50                           164 
  DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE 
                           50                           164 
[1] "DEL PEAK 37(XQ21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE 
                            43                            171 
  DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE 
                            43                            171 
[1] "DEL PEAK 38(XQ23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(XQ23) MUTATED DEL PEAK 38(XQ23) WILD-TYPE 
                         40                         174 
  DEL PEAK 38(XQ23) MUTATED DEL PEAK 38(XQ23) WILD-TYPE 
                         40                         174 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "KARNOFSKYPERFORMANCESCORE"             
[16] "HISTOLOGICALTYPE"                      
[17] "RADIATIONS.RADIATION.REGIMENINDICATION"
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "NUMBER.OF.LYMPH.NODES"                 
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 214 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
        1219           NA           NA           NA          377           NA 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
         363           NA           NA           NA           NA           NA 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
          NA           NA           NA           NA           NA           NA 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
         522          170          111           NA          390           63 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
         469          873          304          864           NA           59 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
         700           14           13           21           NA           NA 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
          NA           NA            4            2            3            2 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
           3            3           NA           NA          219          166 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
         158          496           NA          284           77           NA 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
         955          560          578          271         3981         3420 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
         491          536          475           55          322           NA 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
        3767         2656           67          121          238           NA 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
         319         1529          648          609           NA          252 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
          NA         4283         1460           NA         1952         1476 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC 
        2330         2049          477          982          933         1326 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
          NA          796          750            3           15           16 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
          NA           18           17           20           42           25 
TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
          37          392          477           NA          209           NA 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
         378          363          483         1397           NA          683 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
         501          390           NA          401           NA           NA 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
          60          699          454          455          454          110 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
         369          407         1130           NA          209           NA 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
          NA          208           NA          209         1511           81 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD 
         147           NA          194         1541          283          204 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
         125           81           67          122          462          217 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
         106          124           NA          197         1884          931 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
         173           NA         1072          525          214           NA 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
          26           88           68          481          137          484 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP 
         428          540           34           81          235           64 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
          95          638           67          195          233          344 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QG 
         134          195          187          173          232           NA 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
         237          126          203          195          580          351 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
          46          205         1174          266          105          142 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
          76          197          320           53           55          130 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
         194          193          105          410          372          507 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
        2705         2964         1709           NA 
Variable 1:'AGE':	nDistinctValues=47,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=146,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=48,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=24,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                         "NEOPLASM.DISEASESTAGE"      
 [3] "PATHOLOGY.T.STAGE"           "PATHOLOGY.N.STAGE"          
 [5] "PATHOLOGY.M.STAGE"           "GENDER"                     
 [7] "KARNOFSKY.PERFORMANCE.SCORE" "NUMBERPACKYEARSSMOKED"      
 [9] "NUMBER.OF.LYMPH.NODES"       "RACE"                       
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 214 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=47, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=5, 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   1  60 101  32 
[1] "table(vv)"
vv
T0+T1+T2       T3       T4 
      62      101       32 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1   1  60 101  32 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T0+T1+T2       T3       T4 
      62      101       32 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
130  22  38   7 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
130  22  38   7 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
130  22  38   7 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
130  22  38   7 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=8, binary=FALSE, numeric=TRUE
NUMBERPACKYEARSSMOKED, nv=48, binary=FALSE, numeric=TRUE
NUMBER.OF.LYMPH.NODES, nv=15, binary=FALSE, numeric=TRUE
RACE, nv=3, 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    44  18
  AMP PEAK  1(1P34.2) WILD-TYPE 107  39
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                           62                           146 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                           18                            39 
$`AMP PEAK  1(1P34.2) MUTATED`
TCGA-BT-A20J TCGA-BT-A20R TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       19.04         5.06        17.16         3.65        12.82         2.07 
TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A3QU 
        9.99         8.98         1.94         0.43        12.92         5.19 
TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IL 
        2.53        18.41         8.91        10.59       123.85         3.98 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3X2 TCGA-DK-A6AV 
        7.82         8.22        21.30        20.02        17.98        64.18 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A541 TCGA-E7-A5KE TCGA-FD-A3B5 TCGA-FD-A3B7 
       15.35        26.17         0.59         0.56         8.94         4.01 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
       45.93        24.30        22.45        19.79         1.97        22.98 
TCGA-FD-A43Y TCGA-FD-A5BU TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TC TCGA-FD-A6TG 
       12.13         6.87         6.87        49.68         9.30         2.66 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A2EL TCGA-G2-A3IE TCGA-GC-A3BM 
        4.01        15.19         4.08        26.93        20.12         2.89 
TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GU-A42P 
       15.81        14.07         1.12         7.73        20.98         6.41 
TCGA-GV-A3JW TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A6MB 
        6.41        19.07        11.54        38.60         4.67         4.27 
TCGA-MV-A51V TCGA-XF-A8HD 
       13.48        88.93 

$`AMP PEAK  1(1P34.2) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T 
       11.93        32.84        12.16        17.88        19.50        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH 
       14.96         5.06         8.35         8.25         5.59         4.67 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C 
       15.42        28.70        28.41        23.01         0.46         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
        0.13         0.07         0.10         0.07         0.10         0.10 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        4.90         7.20         5.46        16.31         1.84         9.34 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
        2.14        31.40        19.00       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK 
       17.62        15.62         1.81         7.79        87.32         2.20 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       10.49        50.27         9.67         8.28        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       48.00        48.53        76.60        67.36        15.68        32.28 
TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       30.67        43.59        24.66         0.10         0.49         0.53 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 
        0.66         1.38         0.82         1.22        12.89        15.68 
TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SM TCGA-FD-A3SN 
        6.87        12.43        11.93        15.88        16.47        12.82 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
        5.52        13.18        46.78        14.93        14.96        14.93 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX 
        3.62        13.38        37.15        11.01         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
        6.84        27.45         2.66         4.83         6.28         6.38 
TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
       50.66         6.71         4.11         2.20         7.13         3.48 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO 
        3.25         6.48        61.94        30.61         5.69        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC 
       17.26         7.04         0.85         2.24         4.50        15.91 
TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q 
       17.75         2.66         2.10         3.12         2.20         7.66 
TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       11.31         4.41         6.15         5.69         7.63         7.79 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-K4-A3WS 
        4.14         6.67         6.41         1.51         6.74         8.75 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
        3.45         2.50         6.48        10.52         1.74         1.81 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HE 
        6.38         6.35         3.45        12.23        16.67        97.45 
TCGA-XF-A8HF TCGA-XF-A8HG 
       56.19        15.35 

  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                         0.43                          0.07 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                       123.85                        140.81 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                       10.290                         7.725 
[1] "0.4 - 123.8 (10.3)" "0.1 - 140.8 (7.7)" 
[1] "hr=" "1"  
D1V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  1(1P34.2) MUTATED          1       0       19        17       23
  AMP PEAK  1(1P34.2) WILD-TYPE        0       2       49        55       44
D1V3, multiclass
           clus
vv          AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             0                             2
  STAGE II                           19                            49
  STAGE III                          17                            55
  STAGE IV                           23                            44
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  AMP PEAK  1(1P34.2) MUTATED         21 27 10
  AMP PEAK  1(1P34.2) WILD-TYPE       41 74 22
D1V4, multiclass
          clus
vv         AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  T0+T1+T2                          21                            41
  T3                                27                            74
  T4                                10                            22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  1(1P34.2) MUTATED   34  9 13  2
  AMP PEAK  1(1P34.2) WILD-TYPE 96 13 25  5
D1V5, multiclass
    clus
vv   AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  N0                          34                            96
  N1                           9                            13
  N2                          13                            25
  N3                           2                             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                            M0 M1 MX
  AMP PEAK  1(1P34.2) MUTATED   30  2 30
  AMP PEAK  1(1P34.2) WILD-TYPE 76  3 72
D1V6, multiclass
    clus
vv   AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  M0                          30                            76
  M1                           2                             3
  MX                          30                            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"
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P34.2) MUTATED    17  45
  AMP PEAK  1(1P34.2) WILD-TYPE  33 119
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.2) MUTATED     17   45
  AMP PEAK  1(1P34.2) WILD-TYPE   33  119
        clus
vv       AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  FEMALE                          17                            33
  MALE                            45                           119
[1] 2 2
[1] FALSE
D1V8, continuous
D1V9, continuous
D1V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1P34.2) MUTATED       3                         3    50
  AMP PEAK  1(1P34.2) WILD-TYPE    19                         8   120
D1V11, multiclass
                           clus
vv                          AMP PEAK  1(1P34.2) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              50
                           clus
vv                          AMP PEAK  1(1P34.2) WILD-TYPE
  ASIAN                                                19
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                               120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = AMP PEAK  2(1Q21.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  2(1Q21.3) MUTATED   71 34
  AMP PEAK  2(1Q21.3) WILD-TYPE 80 23
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          105                           103 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           34                            23 
$`AMP PEAK  2(1Q21.3) MUTATED`
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20T 
        2.66         6.74        19.04        32.84         5.06        14.89 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A42C 
        5.06         8.35        17.16         5.59         3.65        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A47V TCGA-CU-A3KJ TCGA-CU-A3QU 
        8.98         1.94         0.43         0.10         5.46         5.19 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD 
        1.84         2.53         2.14        18.41       130.88       112.44 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
        1.81        10.59         7.79       123.85         2.20         3.98 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A3X2 
        7.82         8.22        21.30        20.02        48.00        17.98 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       67.36        15.68        43.59        15.35        26.17        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A7DV 
        0.10         0.49         0.59         0.56         0.66         1.22 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO 
        4.01        45.93        24.30        22.45        16.47         5.52 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BT 
       19.79         1.97        22.98        14.93        12.13        11.01 
TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TE 
        6.87        27.45         6.87         6.28         9.30         4.11 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
        2.20         4.01        15.19         3.48         4.08         3.25 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3OO 
        6.48        17.26        20.12         0.85         2.89        15.81 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS 
        4.50        17.75         1.12         7.73         2.10        20.98 
TCGA-GU-A42P TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        6.41         4.41         6.41         6.15         5.69         7.63 
TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE 
        4.14         6.41        19.07        11.54         1.51        38.60 
TCGA-K4-A3WS TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
        8.75         1.74         4.27         6.35         3.45        13.48 
TCGA-PQ-A6FI TCGA-XF-A8HD TCGA-XF-A8HG 
       12.23        88.93        15.35 

$`AMP PEAK  2(1Q21.3) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O 
       40.08         7.33        12.39         6.58        11.93        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A3PH TCGA-BT-A3PJ 
       17.88        19.50        14.96         8.25         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR 
        2.07        15.42         9.99        28.41        23.01         0.46 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
        0.69         0.13         0.07         0.07         0.10         0.10 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A6 
       12.92         4.90         7.20        16.31         9.34        31.40 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I6 
       19.00         8.91        16.14        17.62        15.62        87.32 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       10.49        50.27         9.67         8.28        10.55       140.81 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E7-A4XJ 
       64.18        48.53        76.60        32.28        30.67         0.53 
TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
        1.38         0.82        12.89        15.68         8.94         6.87 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ 
       12.43        11.93        15.88        12.82        13.18        46.78 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BV 
       14.96        14.93         3.62        13.38        37.15         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
        5.69         6.84        49.68         2.66         4.83         6.38 
TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FJ-A3Z9 TCGA-G2-A2EF TCGA-G2-A2EJ 
       50.66         6.71         2.66         7.13        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-GC-A3I6 TCGA-GC-A3RC 
        5.69        26.93        35.24         7.04         2.24        15.91 
TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
       14.07         2.66         3.12         2.20         7.66        11.31 
TCGA-GV-A3QH TCGA-GV-A3QK TCGA-H4-A2HQ TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        7.79         6.67         6.74         3.45         4.67         2.50 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A83P TCGA-PQ-A6FN TCGA-XF-A8HE 
        6.48        10.52         1.81         6.38        16.67        97.45 
TCGA-XF-A8HF 
       56.19 

  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                         0.10                          0.07 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                       130.88                        140.81 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                         6.87                         10.52 
[1] "0.1 - 130.9 (6.9)"  "0.1 - 140.8 (10.5)"
[1] "hr=" "1.7"
D2V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  2(1Q21.3) MUTATED          1       0       33        28       42
  AMP PEAK  2(1Q21.3) WILD-TYPE        0       2       35        44       25
D2V3, multiclass
           clus
vv          AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             0                             2
  STAGE II                           33                            35
  STAGE III                          28                            44
  STAGE IV                           42                            25
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  AMP PEAK  2(1Q21.3) MUTATED         30 49 18
  AMP PEAK  2(1Q21.3) WILD-TYPE       32 52 14
D2V4, multiclass
          clus
vv         AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  T0+T1+T2                          30                            32
  T3                                49                            52
  T4                                18                            14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  2(1Q21.3) MUTATED   55 14 24  5
  AMP PEAK  2(1Q21.3) WILD-TYPE 75  8 14  2
D2V5, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  N0                          55                            75
  N1                          14                             8
  N2                          24                            14
  N3                           5                             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                            M0 M1 MX
  AMP PEAK  2(1Q21.3) MUTATED   49  4 52
  AMP PEAK  2(1Q21.3) WILD-TYPE 57  1 50
D2V6, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  M0                          49                            57
  M1                           4                             1
  MX                          52                            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"
D2V7, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   22 84
  AMP PEAK  2(1Q21.3) WILD-TYPE 28 80
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     22   84
  AMP PEAK  2(1Q21.3) WILD-TYPE   28   80
        clus
vv       AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  FEMALE                          22                            28
  MALE                            84                            80
[1] 2 2
[1] FALSE
D2V8, continuous
D2V9, continuous
D2V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1Q21.3) MUTATED       7                         4    88
  AMP PEAK  2(1Q21.3) WILD-TYPE    15                         7    82
D2V11, multiclass
                           clus
vv                          AMP PEAK  2(1Q21.3) MUTATED
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              88
                           clus
vv                          AMP PEAK  2(1Q21.3) WILD-TYPE
  ASIAN                                                15
  BLACK OR AFRICAN AMERICAN                             7
  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"

Clustering(3) Variable = AMP PEAK  3(1Q23.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  3(1Q23.3) MUTATED   79 31
  AMP PEAK  3(1Q23.3) WILD-TYPE 72 26
  AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE 
                          110                            98 
  AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE 
                           31                            26 
$`AMP PEAK  3(1Q23.3) MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20T 
       40.08         2.66         6.74        19.04        32.84        14.89 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        5.06         8.35        17.16         5.59         3.65         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS 
       12.82         2.07        28.70         8.98         1.94         0.43 
TCGA-CF-A47V TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 
        0.10         7.20         5.46         1.84         2.53         2.14 
TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       18.41       130.88       112.44        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS 
       87.32         2.20         3.98         7.82         8.22        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B2 
       21.30        20.02        48.00        17.98        67.36        15.68 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A541 
       43.59        26.17        24.66         0.10         0.49         0.59 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A7DV TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3NA 
        0.56         0.66         1.22        15.68         4.01        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR 
       24.30        22.45        16.47         5.52        13.18        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BT 
        1.97        22.98        14.93         3.62        12.13        11.01 
TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG 
        6.87        27.45         6.28         9.30         4.11         2.66 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
        2.20         4.01        15.19         3.48         4.08         3.25 
TCGA-G2-A2EF TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3WC TCGA-GC-A3YS 
       61.94         0.85         2.89        15.81        17.75         1.12 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GU-A42P TCGA-GV-A3JV TCGA-GV-A3JW 
        7.73         2.10        20.98         6.41         4.41         6.41 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A40G TCGA-GV-A6ZA 
        6.15         5.69         7.63         4.14        19.07        11.54 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC 
        1.51         6.74        38.60         8.75         3.45         6.48 
TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
        1.74         4.27         6.35         3.45        13.48        12.23 
TCGA-XF-A8HD TCGA-XF-A8HG 
       88.93        15.35 

$`AMP PEAK  3(1Q23.3) WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P 
        7.33        12.39         6.58        11.93        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A42B TCGA-BT-A42E 
       19.50         5.06        14.96         8.25        15.42         9.99 
TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
       28.41        23.01         0.46         0.69         0.13         0.07 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3QU 
        0.07         0.10         0.10        12.92         4.90         5.19 
TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE 
       16.31         9.34        31.40        19.00         8.91        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A3IQ TCGA-DK-A3IV TCGA-DK-A3WW 
       17.62        15.62         1.81        10.49         9.67         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 
       10.55       140.81        64.18        48.53        76.60        32.28 
TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E7-A4XJ TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A3B3 
       30.67        15.35         0.53         1.38         0.82        12.89 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SN 
        8.94         6.87        12.43        11.93        15.88        12.82 
TCGA-FD-A3SQ TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BV 
       46.78        14.96        14.93        13.38        37.15         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        5.69         6.84         6.87        49.68         2.66         4.83 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FJ-A3Z9 TCGA-FT-A61P TCGA-G2-A2EJ 
        6.38        50.66         6.71         7.13         6.48        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
        5.69        26.93        35.24        17.26         7.04        20.12 
TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A3OQ 
        2.24         4.50        15.91        14.07         2.66         3.12 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E 
        2.20         7.66        11.31         7.79         6.67         6.41 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A83P TCGA-PQ-A6FN 
        4.67         2.50        10.52         1.81         6.38        16.67 
TCGA-XF-A8HE TCGA-XF-A8HF 
       97.45        56.19 

  AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE 
                         0.10                          0.07 
  AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE 
                       130.88                        140.81 
  AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE 
                         7.68                         10.24 
[1] "0.1 - 130.9 (7.7)"  "0.1 - 140.8 (10.2)"
[1] "hr=" "1.2"
D3V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  3(1Q23.3) MUTATED          1       1       35        31       42
  AMP PEAK  3(1Q23.3) WILD-TYPE        0       1       33        41       25
D3V3, multiclass
           clus
vv          AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             1                             1
  STAGE II                           35                            33
  STAGE III                          31                            41
  STAGE IV                           42                            25
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  AMP PEAK  3(1Q23.3) MUTATED         36 48 19
  AMP PEAK  3(1Q23.3) WILD-TYPE       26 53 13
D3V4, multiclass
          clus
vv         AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE
  T0+T1+T2                          36                            26
  T3                                48                            53
  T4                                19                            13
[1] 3 2
[1] 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(1Q23.3) MUTATED   61 13 23  7
  AMP PEAK  3(1Q23.3) WILD-TYPE 69  9 15  0
D3V5, multiclass
    clus
vv   AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE
  N0                          61                            69
  N1                          13                             9
  N2                          23                            15
  N3                           7                             0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 MX
  AMP PEAK  3(1Q23.3) MUTATED   50  5 56
  AMP PEAK  3(1Q23.3) WILD-TYPE 56  0 46
D3V6, multiclass
    clus
vv   AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE
  M0                          50                            56
  M1                           5                             0
  MX                          56                            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"
D3V7, binary
                               cls
clus                             0  1
  AMP PEAK  3(1Q23.3) MUTATED   22 90
  AMP PEAK  3(1Q23.3) WILD-TYPE 28 74
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q23.3) MUTATED     22   90
  AMP PEAK  3(1Q23.3) WILD-TYPE   28   74
        clus
vv       AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE
  FEMALE                          22                            28
  MALE                            90                            74
[1] 2 2
[1] FALSE
D3V8, continuous
D3V9, continuous
D3V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(1Q23.3) MUTATED       7                         6    91
  AMP PEAK  3(1Q23.3) WILD-TYPE    15                         5    79
D3V11, multiclass
                           clus
vv                          AMP PEAK  3(1Q23.3) MUTATED
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                              91
                           clus
vv                          AMP PEAK  3(1Q23.3) WILD-TYPE
  ASIAN                                                15
  BLACK OR AFRICAN AMERICAN                             5
  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"

Clustering(4) Variable = AMP PEAK  4(3P25.2) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  4(3P25.2) MUTATED   74 26
  AMP PEAK  4(3P25.2) WILD-TYPE 77 31
  AMP PEAK  4(3P25.2) MUTATED AMP PEAK  4(3P25.2) WILD-TYPE 
                          100                           108 
  AMP PEAK  4(3P25.2) MUTATED AMP PEAK  4(3P25.2) WILD-TYPE 
                           26                            31 
$`AMP PEAK  4(3P25.2) MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20W 
       40.08         7.33         2.66        12.39        32.84         8.35 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42C 
       17.16         5.59         3.65         4.67         2.07        28.70 
TCGA-CF-A1HR TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
        0.46         4.90         7.20         5.19        16.31         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD 
        2.53         2.14        31.40        18.41       130.88       112.44 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IN 
        1.81        10.59       123.85        87.32         7.82         8.22 
TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B2 
       50.27        20.02        48.00        17.98        64.18        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       32.28        30.67        15.35        26.17         0.10         0.49 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A7DV TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3SJ 
        0.59         0.56         1.22         8.94         6.87        24.30 
TCGA-FD-A3SL TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A5C0 
       22.45        22.98        14.93        14.93         5.36         6.87 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
        4.83         6.28         6.71         4.11         2.66         2.20 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P 
        4.01        15.19         3.48         4.08         3.25         6.48 
TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3OO 
       61.94        35.24        17.26        20.12         0.85        15.81 
TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P 
        4.50        14.07         2.10        20.98         2.20         6.41 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
        4.41         6.41         5.69         7.63         7.79         4.14 
TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WS 
        6.67        19.07        11.54         1.51        38.60         8.75 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A6MB TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
        3.45         4.67         4.27         6.35         3.45        13.48 
TCGA-PQ-A6FI TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
       12.23        88.93        56.19        15.35 

$`AMP PEAK  4(3P25.2) WILD-TYPE`
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        6.74         6.58        11.93        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       19.50         5.06        14.89        14.96         5.06         8.25 
TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
       12.82        15.42         9.99        28.41         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       23.01         0.43         0.69         0.13         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A72E 
        0.07         0.10         0.10        12.92         5.46         9.34 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 
       19.00         8.91        16.14        17.62        15.62         7.79 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW 
        2.20         3.98        10.49        21.30         9.67         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-E5-A2PC 
       10.55       140.81        48.53        76.60        67.36        43.59 
TCGA-E7-A3X6 TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A3B3 
       24.66         0.53         0.66         1.38         0.82        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       15.68         4.01        12.43        11.93        15.88        45.93 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       16.47        12.82         5.52        13.18        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
        1.97        14.96         3.62        12.13        13.38        37.15 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 
       11.01         6.87         5.69         6.84        27.45        49.68 
TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FJ-A3Z9 TCGA-G2-A2EJ 
        2.66         6.38        50.66         9.30         7.13        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RC 
        5.69        26.93         7.04         2.89         2.24        15.91 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GU-A42Q 
       17.75         1.12         2.66         7.73         3.12         7.66 
TCGA-GU-A42R TCGA-GV-A3JX TCGA-GV-A40E TCGA-H4-A2HQ TCGA-K4-A4AB TCGA-K4-A4AC 
       11.31         6.15         6.41         6.74         2.50         6.48 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-PQ-A6FN TCGA-XF-A8HE 
       10.52         1.74         1.81         6.38        16.67        97.45 

  AMP PEAK  4(3P25.2) MUTATED AMP PEAK  4(3P25.2) WILD-TYPE 
                         0.10                          0.07 
  AMP PEAK  4(3P25.2) MUTATED AMP PEAK  4(3P25.2) WILD-TYPE 
                       130.88                        140.81 
  AMP PEAK  4(3P25.2) MUTATED AMP PEAK  4(3P25.2) WILD-TYPE 
                        7.710                         9.505 
[1] "0.1 - 130.9 (7.7)" "0.1 - 140.8 (9.5)"
[1] "hr=" "1.1"
D4V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  4(3P25.2) MUTATED          1       1       31        31       38
  AMP PEAK  4(3P25.2) WILD-TYPE        0       1       37        41       29
D4V3, multiclass
           clus
vv          AMP PEAK  4(3P25.2) MUTATED AMP PEAK  4(3P25.2) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             1                             1
  STAGE II                           31                            37
  STAGE III                          31                            41
  STAGE IV                           38                            29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  AMP PEAK  4(3P25.2) MUTATED         30 44 19
  AMP PEAK  4(3P25.2) WILD-TYPE       32 57 13
D4V4, multiclass
          clus
vv         AMP PEAK  4(3P25.2) MUTATED AMP PEAK  4(3P25.2) WILD-TYPE
  T0+T1+T2                          30                            32
  T3                                44                            57
  T4                                19                            13
[1] 3 2
[1] 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(3P25.2) MUTATED   55 10 26  4
  AMP PEAK  4(3P25.2) WILD-TYPE 75 12 12  3
D4V5, multiclass
    clus
vv   AMP PEAK  4(3P25.2) MUTATED AMP PEAK  4(3P25.2) WILD-TYPE
  N0                          55                            75
  N1                          10                            12
  N2                          26                            12
  N3                           4                             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                            M0 M1 MX
  AMP PEAK  4(3P25.2) MUTATED   50  2 51
  AMP PEAK  4(3P25.2) WILD-TYPE 56  3 51
D4V6, multiclass
    clus
vv   AMP PEAK  4(3P25.2) MUTATED AMP PEAK  4(3P25.2) WILD-TYPE
  M0                          50                            56
  M1                           2                             3
  MX                          51                            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"
D4V7, binary
                               cls
clus                             0  1
  AMP PEAK  4(3P25.2) MUTATED   17 87
  AMP PEAK  4(3P25.2) WILD-TYPE 33 77
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(3P25.2) MUTATED     17   87
  AMP PEAK  4(3P25.2) WILD-TYPE   33   77
        clus
vv       AMP PEAK  4(3P25.2) MUTATED AMP PEAK  4(3P25.2) WILD-TYPE
  FEMALE                          17                            33
  MALE                            87                            77
[1] 2 2
[1] FALSE
D4V8, continuous
D4V9, continuous
D4V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(3P25.2) MUTATED       8                         2    88
  AMP PEAK  4(3P25.2) WILD-TYPE    14                         9    82
D4V11, multiclass
                           clus
vv                          AMP PEAK  4(3P25.2) MUTATED
  ASIAN                                               8
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              88
                           clus
vv                          AMP PEAK  4(3P25.2) WILD-TYPE
  ASIAN                                                14
  BLACK OR AFRICAN AMERICAN                             9
  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"

Clustering(5) Variable = AMP PEAK  5(3Q26.32) MUTATION ANALYSIS
D5V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  5(3Q26.32) MUTATED   84 28
  AMP PEAK  5(3Q26.32) WILD-TYPE 67 29
  AMP PEAK  5(3Q26.32) MUTATED AMP PEAK  5(3Q26.32) WILD-TYPE 
                           112                             96 
  AMP PEAK  5(3Q26.32) MUTATED AMP PEAK  5(3Q26.32) WILD-TYPE 
                            28                             29 
$`AMP PEAK  5(3Q26.32) MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74        12.39        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
       19.04        32.84         5.06         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       17.16         5.59         4.67        12.82         2.07        28.70 
TCGA-BT-A42E TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        9.99         0.46         0.43        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
        5.46        16.31         1.84         2.53        31.40        18.41 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A3IK 
      130.88       112.44        16.14         1.81        10.59         2.20 
TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A3X2 
        7.82        10.49        50.27        20.02        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ 
       64.18        15.68        32.28        30.67        43.59        15.35 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A7DV TCGA-FD-A3B3 
        0.10         0.49         0.59         0.56         1.22        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       15.68         6.87        11.93        45.93        24.30        22.45 
TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY 
       14.93        14.93        12.13         6.87         5.36         6.84 
TCGA-FD-A5C0 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG 
        6.87         4.83         6.28         9.30         4.11         2.66 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF 
        2.20         4.01         3.48         4.08         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-GC-A3I6 
       30.61        35.24        17.26         7.04         0.85         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75         1.12 
TCGA-GC-A6I1 TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A42Q TCGA-GV-A3JW TCGA-GV-A3JX 
        2.66        20.98         6.41         7.66         6.41         6.15 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA 
        7.63         7.79         4.14         6.67        19.07        11.54 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A6MB 
        6.74        38.60         8.75         3.45         4.67         4.27 
TCGA-PQ-A6FI TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
       12.23        88.93        56.19        15.35 

$`AMP PEAK  5(3Q26.32) WILD-TYPE`
TCGA-BT-A0S7 TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U 
        6.58        12.16        17.88        19.50        14.89        14.96 
TCGA-BT-A2LD TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
        3.65        15.42        28.41         8.98         1.94        23.01 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69         0.13         0.07         0.10         0.07         0.10 
TCGA-CF-A47Y TCGA-CU-A3QU TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
        0.10         5.19         9.34         2.14        19.00         8.91 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IL 
       17.62        15.62         7.79       123.85        87.32         3.98 
TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        8.22        21.30         9.67         8.28        10.55       140.81 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4XJ 
       48.53        76.60        67.36        26.17        24.66         0.53 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 
        0.66         1.38         0.82         8.94         4.01        12.43 
TCGA-FD-A3N6 TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       15.88        16.47        12.82         5.52        13.18        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A5BR 
       19.79         1.97        22.98        14.96         3.62        13.38 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62N 
       37.15        11.01         5.69        27.45        49.68         2.66 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FT-A3EE 
        6.38        50.66         6.71        15.19         7.13         3.25 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IE TCGA-GC-A3BM TCGA-GD-A2C5 TCGA-GD-A3OP 
        5.69        26.93        20.12         2.89         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A40E 
        3.12         2.20        11.31         4.41         5.69         6.41 
TCGA-H4-A2HO TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
        1.51         2.50         6.48        10.52         1.74         1.81 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-XF-A8HE 
        6.38         6.35         3.45        13.48        16.67        97.45 

  AMP PEAK  5(3Q26.32) MUTATED AMP PEAK  5(3Q26.32) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK  5(3Q26.32) MUTATED AMP PEAK  5(3Q26.32) WILD-TYPE 
                        130.88                         140.81 
  AMP PEAK  5(3Q26.32) MUTATED AMP PEAK  5(3Q26.32) WILD-TYPE 
                         8.300                          8.925 
[1] "0.1 - 130.9 (8.3)" "0.1 - 140.8 (8.9)"
[1] "hr=" "1.2"
D5V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  5(3Q26.32) MUTATED          1       1       34        40       36
  AMP PEAK  5(3Q26.32) WILD-TYPE        0       1       34        32       31
D5V3, multiclass
           clus
vv          AMP PEAK  5(3Q26.32) MUTATED AMP PEAK  5(3Q26.32) WILD-TYPE
  STAGE 0A                             1                              0
  STAGE I                              1                              1
  STAGE II                            34                             34
  STAGE III                           40                             32
  STAGE IV                            36                             31
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  AMP PEAK  5(3Q26.32) MUTATED         31 55 17
  AMP PEAK  5(3Q26.32) WILD-TYPE       31 46 15
D5V4, multiclass
          clus
vv         AMP PEAK  5(3Q26.32) MUTATED AMP PEAK  5(3Q26.32) WILD-TYPE
  T0+T1+T2                           31                             31
  T3                                 55                             46
  T4                                 17                             15
[1] 3 2
[1] 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(3Q26.32) MUTATED   68  8 26  4
  AMP PEAK  5(3Q26.32) WILD-TYPE 62 14 12  3
D5V5, multiclass
    clus
vv   AMP PEAK  5(3Q26.32) MUTATED AMP PEAK  5(3Q26.32) WILD-TYPE
  N0                           68                             62
  N1                            8                             14
  N2                           26                             12
  N3                            4                              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                             M0 M1 MX
  AMP PEAK  5(3Q26.32) MUTATED   58  3 53
  AMP PEAK  5(3Q26.32) WILD-TYPE 48  2 49
D5V6, multiclass
    clus
vv   AMP PEAK  5(3Q26.32) MUTATED AMP PEAK  5(3Q26.32) WILD-TYPE
  M0                           58                             48
  M1                            3                              2
  MX                           53                             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"
D5V7, binary
                                cls
clus                              0  1
  AMP PEAK  5(3Q26.32) MUTATED   28 87
  AMP PEAK  5(3Q26.32) WILD-TYPE 22 77
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(3Q26.32) MUTATED     28   87
  AMP PEAK  5(3Q26.32) WILD-TYPE   22   77
        clus
vv       AMP PEAK  5(3Q26.32) MUTATED AMP PEAK  5(3Q26.32) WILD-TYPE
  FEMALE                           28                             22
  MALE                             87                             77
[1] 2 2
[1] FALSE
D5V8, continuous
D5V9, continuous
D5V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(3Q26.32) MUTATED       8                         7    94
  AMP PEAK  5(3Q26.32) WILD-TYPE    14                         4    76
D5V11, multiclass
                           clus
vv                          AMP PEAK  5(3Q26.32) MUTATED
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               94
                           clus
vv                          AMP PEAK  5(3Q26.32) WILD-TYPE
  ASIAN                                                 14
  BLACK OR AFRICAN AMERICAN                              4
  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"

Clustering(6) Variable = AMP PEAK  6(4P16.3) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  6(4P16.3) MUTATED    35   8
  AMP PEAK  6(4P16.3) WILD-TYPE 116  49
  AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE 
                           43                           165 
  AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE 
                            8                            49 
$`AMP PEAK  6(4P16.3) MUTATED`
TCGA-BL-A0C8 TCGA-BT-A20P TCGA-BT-A20T TCGA-BT-A3PJ TCGA-C4-A0F0 TCGA-C4-A0F6 
       40.08        17.88        14.89        12.82         1.94        23.01 
TCGA-CF-A27C TCGA-CF-A47V TCGA-CF-A47X TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A1A5 
        0.69         0.10         0.10         5.46         1.84         2.14 
TCGA-DK-A1A6 TCGA-DK-A1AC TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IS 
       31.40       130.88         7.79        87.32         7.82        50.27 
TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-E5-A4U1 TCGA-E7-A541 TCGA-E7-A5KE TCGA-FD-A3NA 
       64.18        67.36        26.17         0.59         0.56        45.93 
TCGA-FD-A3SL TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A6TC TCGA-FD-A6TE 
       22.45         5.36        27.45        49.68         9.30         4.11 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RC TCGA-GU-A42R 
       35.24        17.26         0.85         2.89        15.91        11.31 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-K4-A3WS TCGA-K4-A4AC TCGA-K4-A6FZ TCGA-K4-A6MB 
       11.54         1.51         8.75         6.48         1.81         4.27 
TCGA-MV-A51V 
       13.48 

$`AMP PEAK  6(4P16.3) WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
        7.33         2.66         6.74        12.39         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       19.04        32.84        12.16        19.50         5.06        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16         5.59         3.65 
TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
        4.67         2.07        15.42        28.70         9.99        28.41 
TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W 
        8.98         0.46         0.43         0.13         0.07         0.07 
TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL 
        0.10        12.92         4.90         7.20         5.19        16.31 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD 
        9.34         2.53        18.41        19.00         8.91       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 
       16.14        17.62        15.62         1.81        10.59       123.85 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU 
        2.20         3.98         8.22        10.49        21.30        20.02 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
        9.67         8.28        10.55       140.81        48.00        17.98 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC 
       48.53        76.60        15.68        32.28        30.67        43.59 
TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KF 
       15.35        24.66         0.10         0.49         0.53         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
        1.38         0.82         1.22        12.89        15.68         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SJ 
        6.87         4.01        12.43        11.93        15.88        24.30 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       16.47        12.82         5.52        13.18        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
        1.97        22.98        14.93        14.96        14.93         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
       12.13        13.38        37.15        11.01         6.87         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
        6.84         6.87         2.66         4.83         6.28         6.38 
TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 
       50.66         6.71         2.66         2.20         4.01        15.19 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF 
        7.13         3.48         4.08         3.25         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3I6 
       30.61         5.69        26.93         7.04        20.12         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
       15.81         4.50        14.07        17.75         1.12         2.66 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P 
        7.73         2.10         3.12        20.98         2.20         6.41 
TCGA-GU-A42Q TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        7.66         4.41         6.41         6.15         5.69         7.63 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HQ 
        7.79         4.14         6.67         6.41        19.07         6.74 
TCGA-HQ-A2OE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ 
       38.60         3.45         4.67         2.50        10.52         1.74 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD 
        6.38         6.35         3.45        12.23        16.67        88.93 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       97.45        56.19        15.35 

  AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE 
                         0.10                          0.07 
  AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE 
                       130.88                        140.81 
  AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE 
                        11.31                          8.25 
[1] "0.1 - 130.9 (11.3)" "0.1 - 140.8 (8.2)" 
[1] "hr=" "1.9"
D6V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  6(4P16.3) MUTATED          1       1       19        16        8
  AMP PEAK  6(4P16.3) WILD-TYPE        0       1       49        56       59
D6V3, multiclass
           clus
vv          AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             1                             1
  STAGE II                           19                            49
  STAGE III                          16                            56
  STAGE IV                            8                            59
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  AMP PEAK  6(4P16.3) MUTATED         20 20  4
  AMP PEAK  6(4P16.3) WILD-TYPE       42 81 28
D6V4, multiclass
          clus
vv         AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE
  T0+T1+T2                          20                            42
  T3                                20                            81
  T4                                 4                            28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  6(4P16.3) MUTATED   34  5  2  2
  AMP PEAK  6(4P16.3) WILD-TYPE 96 17 36  5
D6V5, multiclass
    clus
vv   AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE
  N0                          34                            96
  N1                           5                            17
  N2                           2                            36
  N3                           2                             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                            M0 M1 MX
  AMP PEAK  6(4P16.3) MUTATED   30  1 14
  AMP PEAK  6(4P16.3) WILD-TYPE 76  4 88
D6V6, multiclass
    clus
vv   AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE
  M0                          30                            76
  M1                           1                             4
  MX                          14                            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"
D6V7, binary
                               cls
clus                              0   1
  AMP PEAK  6(4P16.3) MUTATED    10  36
  AMP PEAK  6(4P16.3) WILD-TYPE  40 128
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(4P16.3) MUTATED     10   36
  AMP PEAK  6(4P16.3) WILD-TYPE   40  128
        clus
vv       AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE
  FEMALE                          10                            40
  MALE                            36                           128
[1] 2 2
[1] FALSE
D6V8, continuous
D6V9, continuous
D6V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(4P16.3) MUTATED       9                         0    32
  AMP PEAK  6(4P16.3) WILD-TYPE    13                        11   138
D6V11, multiclass
                           clus
vv                          AMP PEAK  6(4P16.3) MUTATED
  ASIAN                                               9
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              32
                           clus
vv                          AMP PEAK  6(4P16.3) WILD-TYPE
  ASIAN                                                13
  BLACK OR AFRICAN AMERICAN                            11
  WHITE                                               138
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = AMP PEAK  7(4Q13.3) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  7(4Q13.3) MUTATED    27  10
  AMP PEAK  7(4Q13.3) WILD-TYPE 124  47
  AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE 
                           37                           171 
  AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE 
                           10                            47 
$`AMP PEAK  7(4Q13.3) MUTATED`
TCGA-BT-A20N TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0F6 
       32.84         3.65         2.07        28.70         9.99        23.01 
TCGA-CF-A47X TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A2I2 TCGA-DK-A2I6 
        0.10         5.46         2.14        18.41         7.79        87.32 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-E5-A4U1 TCGA-E7-A541 
       48.00        17.98        64.18        67.36        26.17         0.59 
TCGA-FD-A3NA TCGA-FD-A3SR TCGA-FD-A43Y TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A5C0 
       45.93        19.79        12.13         5.36        27.45         6.87 
TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TE TCGA-G2-A2EJ TCGA-G2-A3VY TCGA-GC-A3WC 
        6.38         9.30         4.11        30.61         0.85        17.75 
TCGA-GD-A2C5 TCGA-GU-A42P TCGA-GV-A3JW TCGA-GV-A6ZA TCGA-K4-A3WV TCGA-LT-A5Z6 
        7.73         6.41         6.41        11.54         4.67         3.45 
TCGA-MV-A51V 
       13.48 

$`AMP PEAK  7(4Q13.3) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       11.93        19.04        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
       14.89        14.96         5.06         8.35         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0EZ 
        5.59         4.67        12.82        15.42        28.41         8.98 
TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        1.94         0.46         0.43         0.69         0.13         0.07 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        0.10         0.07         0.10        12.92         4.90         7.20 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 
        5.19        16.31         1.84         9.34         2.53        31.40 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00         8.91       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       15.62         1.81        10.59       123.85         2.20         3.98 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        7.82         8.22        10.49        50.27        21.30        20.02 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 
        9.67         8.28        10.55       140.81        48.53        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 
       15.68        32.28        30.67        43.59        15.35        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        0.10         0.49         0.53         0.56         0.66         1.38 
TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
        0.82         1.22        12.89        15.68         8.94         6.87 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL 
        4.01        12.43        11.93        15.88        24.30        22.45 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS 
       16.47        12.82         5.52        13.18        46.78         1.97 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR 
       22.98        14.93        14.96        14.93         3.62        13.38 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C1 
       37.15        11.01         6.87         5.69         6.84        49.68 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TG 
        2.66         4.83         6.28        50.66         6.71         2.66 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        2.20         4.01        15.19         7.13         3.48         4.08 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        3.25         6.48        61.94         5.69        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
       17.26         7.04        20.12         2.89         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OP 
        4.50        15.91        14.07         1.12         2.66         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV 
        3.12        20.98         2.20         7.66        11.31         4.41 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
        6.15         5.69         7.63         7.79         4.14         6.67 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS 
        6.41        19.07         1.51         6.74        38.60         8.75 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
        3.45         2.50         6.48        10.52         1.74         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD 
        4.27         6.38         6.35        12.23        16.67        88.93 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       97.45        56.19        15.35 

  AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE 
                         0.10                          0.07 
  AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE 
                        87.32                        140.81 
  AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE 
                         9.99                          8.28 
[1] "0.1 - 87.3 (10.0)" "0.1 - 140.8 (8.3)"
[1] "hr=" "1.2"
D7V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  7(4Q13.3) MUTATED          1       0       14        11       11
  AMP PEAK  7(4Q13.3) WILD-TYPE        0       2       54        61       56
D7V3, multiclass
           clus
vv          AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             0                             2
  STAGE II                           14                            54
  STAGE III                          11                            61
  STAGE IV                           11                            56
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  AMP PEAK  7(4Q13.3) MUTATED         12 18  3
  AMP PEAK  7(4Q13.3) WILD-TYPE       50 83 29
D7V4, multiclass
          clus
vv         AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE
  T0+T1+T2                          12                            50
  T3                                18                            83
  T4                                 3                            29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK  7(4Q13.3) MUTATED    23   4   6   1
  AMP PEAK  7(4Q13.3) WILD-TYPE 107  18  32   6
D7V5, multiclass
    clus
vv   AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE
  N0                          23                           107
  N1                           4                            18
  N2                           6                            32
  N3                           1                             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"
                               vv
clus                            M0 M1 MX
  AMP PEAK  7(4Q13.3) MUTATED   18  0 18
  AMP PEAK  7(4Q13.3) WILD-TYPE 88  5 84
D7V6, multiclass
    clus
vv   AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE
  M0                          18                            88
  M1                           0                             5
  MX                          18                            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"
D7V7, binary
                               cls
clus                              0   1
  AMP PEAK  7(4Q13.3) MUTATED    14  23
  AMP PEAK  7(4Q13.3) WILD-TYPE  36 141
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4Q13.3) MUTATED     14   23
  AMP PEAK  7(4Q13.3) WILD-TYPE   36  141
        clus
vv       AMP PEAK  7(4Q13.3) MUTATED AMP PEAK  7(4Q13.3) WILD-TYPE
  FEMALE                          14                            36
  MALE                            23                           141
[1] 2 2
[1] FALSE
D7V8, continuous
D7V9, continuous
D7V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(4Q13.3) MUTATED       3                         1    28
  AMP PEAK  7(4Q13.3) WILD-TYPE    19                        10   142
D7V11, multiclass
                           clus
vv                          AMP PEAK  7(4Q13.3) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              28
                           clus
vv                          AMP PEAK  7(4Q13.3) WILD-TYPE
  ASIAN                                                19
  BLACK OR AFRICAN AMERICAN                            10
  WHITE                                               142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = AMP PEAK  8(4Q31.21) MUTATION ANALYSIS
D8V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  8(4Q31.21) MUTATED    14   7
  AMP PEAK  8(4Q31.21) WILD-TYPE 137  50
  AMP PEAK  8(4Q31.21) MUTATED AMP PEAK  8(4Q31.21) WILD-TYPE 
                            21                            187 
  AMP PEAK  8(4Q31.21) MUTATED AMP PEAK  8(4Q31.21) WILD-TYPE 
                             7                             50 
$`AMP PEAK  8(4Q31.21) MUTATED`
TCGA-BL-A13J TCGA-C4-A0F6 TCGA-CF-A47V TCGA-CF-A47X TCGA-CU-A3KJ TCGA-DK-A1AE 
        2.66        23.01         0.10         0.10         5.46        16.14 
TCGA-DK-A2I2 TCGA-DK-A3IQ TCGA-DK-A3X1 TCGA-DK-A6B1 TCGA-E5-A4U1 TCGA-FD-A3B7 
        7.79        10.49        48.00        67.36        26.17         4.01 
TCGA-FD-A3NA TCGA-FD-A43N TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A6TD TCGA-GC-A3YS 
       45.93        22.98        27.45         6.87         6.71         1.12 
TCGA-GU-A42P TCGA-GV-A3QH TCGA-PQ-A6FI 
        6.41         7.79        12.23 

$`AMP PEAK  8(4Q31.21) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         6.74        12.39         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
       14.89        14.96         5.06         8.35         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
        5.59         3.65         4.67        12.82         2.07        15.42 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HR 
       28.70         9.99        28.41         8.98         1.94         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47Y 
        0.43         0.69         0.13         0.07         0.07         0.10 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       12.92         4.90         7.20         5.19        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
        9.34         2.53         2.14        31.40        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
        8.91       130.88       112.44        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       10.59       123.85        87.32         2.20         3.98         7.82 
TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
        8.22        50.27        21.30        20.02         9.67         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       10.55       140.81        17.98        64.18        48.53        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 
       15.68        32.28        30.67        43.59        15.35        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.10         0.49         0.53         0.59         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
        1.38         0.82         1.22        12.89        15.68         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL 
        6.87        12.43        11.93        15.88        24.30        22.45 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       16.47        12.82         5.52        13.18        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
        1.97        14.93        14.96        14.93         3.62        12.13 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       13.38        37.15        11.01         6.87         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
        6.84        49.68         2.66         4.83         6.28         6.38 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       50.66         9.30         4.11         2.66         2.20         4.01 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P 
       15.19         7.13         3.48         4.08         3.25         6.48 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       61.94        30.61         5.69        26.93        35.24        17.26 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        7.04        20.12         0.85         2.89         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A2C5 
        4.50        15.91        14.07        17.75         2.66         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12        20.98         2.20         7.66        11.31 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI 
        4.41         6.41         6.15         5.69         7.63         4.14 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
        6.67         6.41        19.07        11.54         1.51         6.74 
TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
       38.60         8.75         3.45         4.67         2.50         6.48 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R 
       10.52         1.74         1.81         4.27         6.38         6.35 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        3.45        13.48        16.67        88.93        97.45        56.19 
TCGA-XF-A8HG 
       15.35 

  AMP PEAK  8(4Q31.21) MUTATED AMP PEAK  8(4Q31.21) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK  8(4Q31.21) MUTATED AMP PEAK  8(4Q31.21) WILD-TYPE 
                         67.36                         140.81 
  AMP PEAK  8(4Q31.21) MUTATED AMP PEAK  8(4Q31.21) WILD-TYPE 
                          7.79                           8.75 
[1] "0.1 - 67.4 (7.8)"  "0.1 - 140.8 (8.8)"
[1] "hr=" "1.1"
D8V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  8(4Q31.21) MUTATED          0       0        7         8        6
  AMP PEAK  8(4Q31.21) WILD-TYPE        1       2       61        64       61
D8V3, multiclass
           clus
vv          AMP PEAK  8(4Q31.21) MUTATED AMP PEAK  8(4Q31.21) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              0                              2
  STAGE II                             7                             61
  STAGE III                            8                             64
  STAGE IV                             6                             61
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  AMP PEAK  8(4Q31.21) MUTATED          6 13  1
  AMP PEAK  8(4Q31.21) WILD-TYPE       56 88 31
D8V4, multiclass
          clus
vv         AMP PEAK  8(4Q31.21) MUTATED AMP PEAK  8(4Q31.21) WILD-TYPE
  T0+T1+T2                            6                             56
  T3                                 13                             88
  T4                                  1                             31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK  8(4Q31.21) MUTATED    14   3   2   1
  AMP PEAK  8(4Q31.21) WILD-TYPE 116  19  36   6
D8V5, multiclass
    clus
vv   AMP PEAK  8(4Q31.21) MUTATED AMP PEAK  8(4Q31.21) WILD-TYPE
  N0                           14                            116
  N1                            3                             19
  N2                            2                             36
  N3                            1                              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"
                                vv
clus                             M0 M1 MX
  AMP PEAK  8(4Q31.21) MUTATED   12  0  9
  AMP PEAK  8(4Q31.21) WILD-TYPE 94  5 93
D8V6, multiclass
    clus
vv   AMP PEAK  8(4Q31.21) MUTATED AMP PEAK  8(4Q31.21) WILD-TYPE
  M0                           12                             94
  M1                            0                              5
  MX                            9                             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"
D8V7, binary
                                cls
clus                               0   1
  AMP PEAK  8(4Q31.21) MUTATED     4  17
  AMP PEAK  8(4Q31.21) WILD-TYPE  46 147
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(4Q31.21) MUTATED      4   17
  AMP PEAK  8(4Q31.21) WILD-TYPE   46  147
        clus
vv       AMP PEAK  8(4Q31.21) MUTATED AMP PEAK  8(4Q31.21) WILD-TYPE
  FEMALE                            4                             46
  MALE                             17                            147
[1] 2 2
[1] FALSE
D8V8, continuous
D8V9, continuous
D8V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(4Q31.21) MUTATED       2                         1    16
  AMP PEAK  8(4Q31.21) WILD-TYPE    20                        10   154
D8V11, multiclass
                           clus
vv                          AMP PEAK  8(4Q31.21) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               16
                           clus
vv                          AMP PEAK  8(4Q31.21) WILD-TYPE
  ASIAN                                                 20
  BLACK OR AFRICAN AMERICAN                             10
  WHITE                                                154
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = AMP PEAK  9(5P15.33) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  9(5P15.33) MUTATED   72 27
  AMP PEAK  9(5P15.33) WILD-TYPE 79 30
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                            99                            109 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                            27                             30 
$`AMP PEAK  9(5P15.33) MUTATED`
TCGA-BL-A0C8 TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A20P TCGA-BT-A20T TCGA-BT-A20V 
       40.08         6.74        12.39        17.88        14.89         5.06 
TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E 
        8.35        17.16        12.82         2.07        28.70         9.99 
TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A47S TCGA-CU-A0YN TCGA-CU-A0YR 
        8.98        23.01         0.43         0.13        12.92         7.20 
TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1AD TCGA-DK-A2I4 TCGA-DK-A2I6 
        5.19         1.84         2.53       112.44       123.85        87.32 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WX TCGA-DK-A6AV 
        7.82         8.22        20.02         9.67        10.55        64.18 
TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       67.36        32.28        30.67        15.35        26.17        24.66 
TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
        0.49         0.59         1.22        12.89        15.68         8.94 
TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       11.93        45.93        24.30        12.82         5.52        13.18 
TCGA-FD-A3SR TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY 
       19.79        12.13        13.38         6.87         5.36         6.84 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TC 
       49.68         2.66         4.83         6.28         6.38         9.30 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-FT-A3EE 
        6.71         4.11         2.66         2.20         4.08         3.25 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
        6.48        61.94        35.24         7.04        20.12         0.85 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS 
        2.24        15.81         4.50        15.91        14.07         1.12 
TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GU-A42P TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ 
        2.10        20.98         6.41         4.41         6.15         5.69 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HQ 
        7.63         7.79         4.14         6.41        19.07         6.74 
TCGA-HQ-A2OE TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-LC-A66R 
       38.60         2.50         6.48         1.81         4.27         6.35 
TCGA-MV-A51V TCGA-PQ-A6FN TCGA-XF-A8HF 
       13.48        16.67        56.19 

$`AMP PEAK  9(5P15.33) WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        7.33         2.66         6.58        11.93        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LB 
       12.16        19.50         5.06        14.96         8.25         5.59 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR 
        3.65         4.67        15.42        28.41         1.94         0.46 
TCGA-CF-A27C TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
        0.69         0.07         0.10         0.07         0.10         0.10 
TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 
        4.90         5.46        16.31         9.34         2.14        31.40 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF 
       18.41        19.00         8.91       130.88        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL 
       15.62         1.81        10.59         7.79         2.20         3.98 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 
       10.49        50.27        21.30         8.28       140.81        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-E5-A2PC TCGA-E7-A3Y1 
       17.98        48.53        76.60        15.68        43.59         0.10 
TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A3B6 
        0.53         0.56         0.66         1.38         0.82         6.87 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SQ 
        4.01        12.43        15.88        22.45        16.47        46.78 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
        1.97        22.98        14.93        14.96        14.93         3.62 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A6TA 
       37.15        11.01         5.69        27.45         6.87        50.66 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-G2-A2EJ TCGA-G2-A2EK 
        4.01        15.19         7.13         3.48        30.61         5.69 
TCGA-G2-A2EL TCGA-G2-A2ES TCGA-GC-A3BM TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A2C5 
       26.93        17.26         2.89        17.75         2.66         7.73 
TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3QK 
        3.12         2.20         7.66        11.31         6.41         6.67 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A54R 
       11.54         1.51         8.75         3.45         4.67        10.52 
TCGA-K4-A5RJ TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-XF-A8HD TCGA-XF-A8HE 
        1.74         6.38         3.45        12.23        88.93        97.45 
TCGA-XF-A8HG 
       15.35 

  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                          0.13                           0.07 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                        123.85                         140.81 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                          8.35                           8.75 
[1] "0.1 - 123.8 (8.3)" "0.1 - 140.8 (8.8)"
[1] "hr=" "1"  
D9V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  9(5P15.33) MUTATED          0       1       31        39       29
  AMP PEAK  9(5P15.33) WILD-TYPE        1       1       37        33       38
D9V3, multiclass
           clus
vv          AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              1                              1
  STAGE II                            31                             37
  STAGE III                           39                             33
  STAGE IV                            29                             38
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  AMP PEAK  9(5P15.33) MUTATED         28 46 16
  AMP PEAK  9(5P15.33) WILD-TYPE       34 55 16
D9V4, multiclass
          clus
vv         AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  T0+T1+T2                           28                             34
  T3                                 46                             55
  T4                                 16                             16
[1] 3 2
[1] 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(5P15.33) MUTATED   60 10 17  3
  AMP PEAK  9(5P15.33) WILD-TYPE 70 12 21  4
D9V5, multiclass
    clus
vv   AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  N0                           60                             70
  N1                           10                             12
  N2                           17                             21
  N3                            3                              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                             M0 M1 MX
  AMP PEAK  9(5P15.33) MUTATED   46  2 53
  AMP PEAK  9(5P15.33) WILD-TYPE 60  3 49
D9V6, multiclass
    clus
vv   AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  M0                           46                             60
  M1                            2                              3
  MX                           53                             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"
D9V7, binary
                                cls
clus                              0  1
  AMP PEAK  9(5P15.33) MUTATED   23 79
  AMP PEAK  9(5P15.33) WILD-TYPE 27 85
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED     23   79
  AMP PEAK  9(5P15.33) WILD-TYPE   27   85
        clus
vv       AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  FEMALE                           23                             27
  MALE                             79                             85
[1] 2 2
[1] FALSE
D9V8, continuous
D9V9, continuous
D9V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(5P15.33) MUTATED       9                         8    80
  AMP PEAK  9(5P15.33) WILD-TYPE    13                         3    90
D9V11, multiclass
                           clus
vv                          AMP PEAK  9(5P15.33) MUTATED
  ASIAN                                                9
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                               80
                           clus
vv                          AMP PEAK  9(5P15.33) WILD-TYPE
  ASIAN                                                 13
  BLACK OR AFRICAN AMERICAN                              3
  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"

Clustering(10) Variable = AMP PEAK 10(6P22.3) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 10(6P22.3) MUTATED   67 21
  AMP PEAK 10(6P22.3) WILD-TYPE 84 36
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                           88                           120 
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                           21                            36 
$`AMP PEAK 10(6P22.3) MUTATED`
TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20R TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LD 
        2.66         6.58         5.06         8.35        17.16         3.65 
TCGA-BT-A3PJ TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A1HS TCGA-CF-A47V TCGA-CF-A47X 
       12.82        28.70         8.98         0.43         0.10         0.10 
TCGA-CU-A0YN TCGA-CU-A3QU TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC 
       12.92         5.19         2.14        31.40        18.41       130.88 
TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IL 
      112.44        10.59         7.79       123.85        87.32         3.98 
TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3WX TCGA-DK-A6AV TCGA-DK-A6B1 
        7.82        50.27        20.02        10.55        64.18        67.36 
TCGA-DK-A6B2 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE 
       15.68        43.59        15.35         0.49         0.59         0.56 
TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SJ 
        1.22        12.89         6.87         4.01        11.93        24.30 
TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A5BU TCGA-FD-A5C1 
       13.18        19.79        22.98        14.93         6.87        49.68 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FJ-A3Z7 
        6.28        50.66         9.30         4.11         2.66        15.19 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A3VY 
        3.48         4.08         3.25         6.48        61.94         0.85 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
        2.89         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GU-A42P TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3JZ 
        1.12         7.73         6.41        11.31         6.41         5.69 
TCGA-GV-A3QH TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-K4-A3WV 
        7.79         6.41        19.07        11.54        38.60         4.67 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 
        6.48        10.52         4.27         6.38         6.35         3.45 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HF 
       12.23        16.67        88.93        56.19 

$`AMP PEAK 10(6P22.3) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J 
       40.08         7.33         6.74        12.39        11.93        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U 
       32.84        12.16        17.88        19.50        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B 
        5.06         8.25         5.59         4.67         2.07        15.42 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C 
        9.99        28.41         1.94        23.01         0.46         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A0YR 
        0.13         0.07         0.07         0.10         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1AA 
        5.46        16.31         1.84         9.34         2.53        19.00 
TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A3IK 
        8.91        16.14        17.62        15.62         1.81         2.20 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY 
        8.22        10.49        21.30         9.67         8.28       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-A6B6 
       48.00        17.98        48.53        76.60        32.28        30.67 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A677 
       26.17        24.66         0.10         0.53         0.66         1.38 
TCGA-E7-A678 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA 
        0.82        15.68         8.94        12.43        15.88        45.93 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SS 
       22.45        16.47        12.82         5.52        46.78         1.97 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       14.96        14.93         3.62        12.13        13.38        37.15 
TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       11.01         5.36         5.69         6.84        27.45         6.87 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TD TCGA-FD-A6TH TCGA-FD-A6TI 
        2.66         4.83         6.38         6.71         2.20         4.01 
TCGA-FJ-A3Z9 TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
        7.13        30.61         5.69        26.93        35.24        17.26 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ 
        7.04        20.12        17.75         2.66         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QF 
       20.98         2.20         7.66         4.41         6.15         7.63 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A3WU 
        4.14         6.67         1.51         6.74         8.75         3.45 
TCGA-K4-A4AB TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-MV-A51V TCGA-XF-A8HE TCGA-XF-A8HG 
        2.50         1.74         1.81        13.48        97.45        15.35 

  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                         0.10                          0.07 
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                       130.88                        140.81 
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                        8.665                         8.515 
[1] "0.1 - 130.9 (8.7)" "0.1 - 140.8 (8.5)"
[1] "hr=" "1.3"
D10V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 10(6P22.3) MUTATED          1       0       33        22       30
  AMP PEAK 10(6P22.3) WILD-TYPE        0       2       35        50       37
D10V3, multiclass
           clus
vv          AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             0                             2
  STAGE II                           33                            35
  STAGE III                          22                            50
  STAGE IV                           30                            37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  AMP PEAK 10(6P22.3) MUTATED         33 35 11
  AMP PEAK 10(6P22.3) WILD-TYPE       29 66 21
D10V4, multiclass
          clus
vv         AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE
  T0+T1+T2                          33                            29
  T3                                35                            66
  T4                                11                            21
[1] 3 2
[1] 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(6P22.3) MUTATED   49 12 15  5
  AMP PEAK 10(6P22.3) WILD-TYPE 81 10 23  2
D10V5, multiclass
    clus
vv   AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE
  N0                          49                            81
  N1                          12                            10
  N2                          15                            23
  N3                           5                             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                            M0 M1 MX
  AMP PEAK 10(6P22.3) MUTATED   41  2 44
  AMP PEAK 10(6P22.3) WILD-TYPE 65  3 58
D10V6, multiclass
    clus
vv   AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE
  M0                          41                            65
  M1                           2                             3
  MX                          44                            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"
D10V7, binary
                               cls
clus                             0  1
  AMP PEAK 10(6P22.3) MUTATED   21 67
  AMP PEAK 10(6P22.3) WILD-TYPE 29 97
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P22.3) MUTATED     21   67
  AMP PEAK 10(6P22.3) WILD-TYPE   29   97
        clus
vv       AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE
  FEMALE                          21                            29
  MALE                            67                            97
[1] 2 2
[1] FALSE
D10V8, continuous
D10V9, continuous
D10V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(6P22.3) MUTATED       7                         4    72
  AMP PEAK 10(6P22.3) WILD-TYPE    15                         7    98
D10V11, multiclass
                           clus
vv                          AMP PEAK 10(6P22.3) MUTATED
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              72
                           clus
vv                          AMP PEAK 10(6P22.3) WILD-TYPE
  ASIAN                                                15
  BLACK OR AFRICAN AMERICAN                             7
  WHITE                                                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = AMP PEAK 11(6Q21) MUTATION ANALYSIS
D11V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 11(6Q21) MUTATED    15   3
  AMP PEAK 11(6Q21) WILD-TYPE 136  54
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                         18                         190 
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                          3                          54 
$`AMP PEAK 11(6Q21) MUTATED`
TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A2LA TCGA-CF-A47V TCGA-CU-A0YR TCGA-DK-A1A3 
        6.58        19.04        17.16         0.10         7.20         2.53 
TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A3WX TCGA-DK-A6B5 TCGA-FD-A43P TCGA-FJ-A3Z7 
       18.41       130.88        10.55        32.28        14.93        15.19 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3YS TCGA-GD-A2C5 
        3.48         4.08         2.89        15.81         1.12         7.73 

$`AMP PEAK 11(6Q21) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74        12.39        11.93 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD 
       14.96         5.06         8.35         8.25         5.59         3.65 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         2.07        15.42        28.70         9.99 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       28.41         8.98         1.94        23.01         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
        0.69         0.13         0.07         0.07         0.10         0.10 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       12.92         4.90         5.46         5.19        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD 
        9.34         2.14        31.40        19.00         8.91       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20         3.98         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       10.49        50.27        21.30        20.02         9.67         8.28 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
      140.81        48.00        17.98        64.18        48.53        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       67.36        15.68        30.67        43.59        15.35        26.17 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE 
       24.66         0.10         0.49         0.53         0.59         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 
        0.66         1.38         0.82         1.22        12.89        15.68 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94         6.87         4.01        12.43        11.93        15.88 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       45.93        24.30        22.45        16.47        12.82         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S 
       13.18        46.78        19.79         1.97        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.93         3.62        12.13        13.38        37.15        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
        6.87         5.36         5.69         6.84        27.45         6.87 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       49.68         2.66         4.83         6.28         6.38        50.66 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
        9.30         6.71         4.11         2.66         2.20         4.01 
TCGA-FJ-A3Z9 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        7.13         3.25         6.48        61.94        30.61         5.69 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       26.93        35.24        17.26         7.04        20.12         0.85 
TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 
        2.24         4.50        15.91        14.07        17.75         2.66 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q 
        2.10         3.12        20.98         2.20         6.41         7.66 
TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       11.31         4.41         6.41         6.15         5.69         7.63 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        7.79         4.14         6.67         6.41        19.07        11.54 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        1.51         6.74        38.60         8.75         3.45         4.67 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
        2.50         6.48        10.52         1.74         1.81         4.27 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        6.38         6.35         3.45        13.48        12.23        16.67 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       88.93        97.45        56.19        15.35 

  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                       0.10                        0.07 
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                     130.88                      140.81 
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                       9.14                        8.55 
[1] "0.1 - 130.9 (9.1)" "0.1 - 140.8 (8.6)"
[1] "hr=" "1.6"
D11V2, continuous
                             vv
clus                          STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 11(6Q21) MUTATED          0       0        5         5        8
  AMP PEAK 11(6Q21) WILD-TYPE        1       2       63        67       59
D11V3, multiclass
           clus
vv          AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  STAGE 0A                          0                           1
  STAGE I                           0                           2
  STAGE II                          5                          63
  STAGE III                         5                          67
  STAGE IV                          8                          59
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1+T2 T3 T4
  AMP PEAK 11(6Q21) MUTATED          6  7  3
  AMP PEAK 11(6Q21) WILD-TYPE       56 94 29
D11V4, multiclass
          clus
vv         AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  T0+T1+T2                         6                          56
  T3                               7                          94
  T4                               3                          29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2  N3
  AMP PEAK 11(6Q21) MUTATED    10   1   6   1
  AMP PEAK 11(6Q21) WILD-TYPE 120  21  32   6
D11V5, multiclass
    clus
vv   AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  N0                        10                         120
  N1                         1                          21
  N2                         6                          32
  N3                         1                           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"
                             vv
clus                          M0 M1 MX
  AMP PEAK 11(6Q21) MUTATED   11  1  6
  AMP PEAK 11(6Q21) WILD-TYPE 95  4 96
D11V6, multiclass
    clus
vv   AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  M0                        11                          95
  M1                         1                           4
  MX                         6                          96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                             cls
clus                            0   1
  AMP PEAK 11(6Q21) MUTATED     3  15
  AMP PEAK 11(6Q21) WILD-TYPE  47 149
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(6Q21) MUTATED      3   15
  AMP PEAK 11(6Q21) WILD-TYPE   47  149
        clus
vv       AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  FEMALE                         3                          47
  MALE                          15                         149
[1] 2 2
[1] FALSE
D11V8, continuous
D11V9, continuous
D11V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(6Q21) MUTATED       1                         1    16
  AMP PEAK 11(6Q21) WILD-TYPE    21                        10   154
D11V11, multiclass
                           clus
vv                          AMP PEAK 11(6Q21) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                         1
  WHITE                                            16
                           clus
vv                          AMP PEAK 11(6Q21) WILD-TYPE
  ASIAN                                              21
  BLACK OR AFRICAN AMERICAN                          10
  WHITE                                             154
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = AMP PEAK 12(7P21.1) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 12(7P21.1) MUTATED   76 34
  AMP PEAK 12(7P21.1) WILD-TYPE 75 23
  AMP PEAK 12(7P21.1) MUTATED AMP PEAK 12(7P21.1) WILD-TYPE 
                          110                            98 
  AMP PEAK 12(7P21.1) MUTATED AMP PEAK 12(7P21.1) WILD-TYPE 
                           34                            23 
$`AMP PEAK 12(7P21.1) MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20O 
       40.08         2.66        12.39         6.58        32.84        12.16 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16         5.59         3.65 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 
       12.82         2.07        28.70         9.99        28.41        23.01 
TCGA-CF-A1HR TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A72E 
        0.46        12.92         4.90         5.46         5.19         9.34 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A2I1 TCGA-DK-A2I2 
        2.53         2.14        18.41       130.88        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20         3.98         7.82         8.22 
TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       50.27        20.02         9.67        48.00        17.98        64.18 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ 
       67.36        15.68        30.67        43.59        15.35         0.49 
TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
        0.59         1.22        12.89        15.68         8.94         6.87 
TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
        4.01        11.93        24.30        46.78        19.79         1.97 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BT 
       22.98        14.93        14.93         3.62        13.38        11.01 
TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P 
        5.36        27.45         6.87        49.68         4.83         6.28 
TCGA-FD-A62S TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 
        6.38         6.71         4.11         2.66         4.01        15.19 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A3VY 
        3.48         4.08         3.25         6.48        35.24         0.85 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS 
        2.89         2.24         4.50        15.91        14.07         1.12 
TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GV-A3JW 
        7.73        20.98         2.20         6.41         7.66         6.41 
TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HQ 
        5.69         4.14         6.67         6.41        11.54         6.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-MV-A51V TCGA-XF-A8HD 
        1.81         4.27         6.38         6.35        13.48        88.93 
TCGA-XF-A8HF TCGA-XF-A8HG 
       56.19        15.35 

$`AMP PEAK 12(7P21.1) WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20P TCGA-BT-A20Q 
        7.33         6.74        11.93        19.04        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A3PH TCGA-BT-A42B TCGA-C4-A0EZ 
        5.06        14.89        14.96         4.67        15.42         8.98 
TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        1.94         0.43         0.69         0.13         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A5W6 
        0.07         0.10         0.10         7.20        16.31         1.84 
TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       31.40        19.00         8.91       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3WW TCGA-DK-A3WX 
       15.62         1.81        10.49        21.30         8.28        10.55 
TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-E5-A4U1 TCGA-E7-A3X6 
      140.81        48.53        76.60        32.28        26.17        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        0.10         0.53         0.56         0.66         1.38         0.82 
TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       12.43        15.88        45.93        22.45        16.47        12.82 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BU 
        5.52        13.18        14.96        12.13        37.15         6.87 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TH 
        5.69         6.84         2.66        50.66         9.30         2.20 
TCGA-FJ-A3Z9 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES 
        7.13        61.94        30.61         5.69        26.93        17.26 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3OO TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OP 
        7.04        20.12        15.81        17.75         2.66         2.10 
TCGA-GD-A3OQ TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH 
        3.12        11.31         4.41         6.15         7.63         7.79 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       19.07         1.51        38.60         8.75         3.45         4.67 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-LT-A5Z6 TCGA-PQ-A6FI 
        2.50         6.48        10.52         1.74         3.45        12.23 
TCGA-PQ-A6FN TCGA-XF-A8HE 
       16.67        97.45 

  AMP PEAK 12(7P21.1) MUTATED AMP PEAK 12(7P21.1) WILD-TYPE 
                         0.46                          0.07 
  AMP PEAK 12(7P21.1) MUTATED AMP PEAK 12(7P21.1) WILD-TYPE 
                       130.88                        140.81 
  AMP PEAK 12(7P21.1) MUTATED AMP PEAK 12(7P21.1) WILD-TYPE 
                         8.02                          9.14 
[1] "0.5 - 130.9 (8.0)" "0.1 - 140.8 (9.1)"
[1] "hr=" "1.3"
D12V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 12(7P21.1) MUTATED          1       1       27        40       42
  AMP PEAK 12(7P21.1) WILD-TYPE        0       1       41        32       25
D12V3, multiclass
           clus
vv          AMP PEAK 12(7P21.1) MUTATED AMP PEAK 12(7P21.1) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             1                             1
  STAGE II                           27                            41
  STAGE III                          40                            32
  STAGE IV                           42                            25
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  AMP PEAK 12(7P21.1) MUTATED         28 55 20
  AMP PEAK 12(7P21.1) WILD-TYPE       34 46 12
D12V4, multiclass
          clus
vv         AMP PEAK 12(7P21.1) MUTATED AMP PEAK 12(7P21.1) WILD-TYPE
  T0+T1+T2                          28                            34
  T3                                55                            46
  T4                                20                            12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK 12(7P21.1) MUTATED   60 13 24  6
  AMP PEAK 12(7P21.1) WILD-TYPE 70  9 14  1
D12V5, multiclass
    clus
vv   AMP PEAK 12(7P21.1) MUTATED AMP PEAK 12(7P21.1) WILD-TYPE
  N0                          60                            70
  N1                          13                             9
  N2                          24                            14
  N3                           6                             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                            M0 M1 MX
  AMP PEAK 12(7P21.1) MUTATED   52  2 57
  AMP PEAK 12(7P21.1) WILD-TYPE 54  3 45
D12V6, multiclass
    clus
vv   AMP PEAK 12(7P21.1) MUTATED AMP PEAK 12(7P21.1) WILD-TYPE
  M0                          52                            54
  M1                           2                             3
  MX                          57                            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"
D12V7, binary
                               cls
clus                             0  1
  AMP PEAK 12(7P21.1) MUTATED   25 87
  AMP PEAK 12(7P21.1) WILD-TYPE 25 77
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7P21.1) MUTATED     25   87
  AMP PEAK 12(7P21.1) WILD-TYPE   25   77
        clus
vv       AMP PEAK 12(7P21.1) MUTATED AMP PEAK 12(7P21.1) WILD-TYPE
  FEMALE                          25                            25
  MALE                            87                            77
[1] 2 2
[1] FALSE
D12V8, continuous
D12V9, continuous
D12V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(7P21.1) MUTATED       6                         8    96
  AMP PEAK 12(7P21.1) WILD-TYPE    16                         3    74
D12V11, multiclass
                           clus
vv                          AMP PEAK 12(7P21.1) MUTATED
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                           8
  WHITE                                              96
                           clus
vv                          AMP PEAK 12(7P21.1) WILD-TYPE
  ASIAN                                                16
  BLACK OR AFRICAN AMERICAN                             3
  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"

Clustering(13) Variable = AMP PEAK 13(7P11.2) MUTATION ANALYSIS
D13V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 13(7P11.2) MUTATED   74 35
  AMP PEAK 13(7P11.2) WILD-TYPE 77 22
  AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE 
                          109                            99 
  AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE 
                           35                            22 
$`AMP PEAK 13(7P11.2) MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N 
       40.08         2.66        12.39         6.58        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       12.16         5.06         8.35         8.25        17.16         5.59 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 
        3.65        12.82        28.70         9.99        28.41        23.01 
TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A3 
        0.43        12.92         4.90         5.46         9.34         2.53 
TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 
        2.14        18.41       130.88       112.44         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        7.79       123.85        87.32         2.20         3.98         7.82 
TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 
        8.22        50.27        20.02         9.67        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ 
       64.18        67.36        30.67        43.59        15.35         0.49 
TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        0.59         1.22        12.89         8.94         6.87         4.01 
TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
       11.93        24.30        46.78        19.79         1.97        22.98 
TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BZ 
       14.93        14.93         3.62        13.38         5.36        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TD 
        6.87        49.68         4.83         6.28         6.38         6.71 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
        4.11         2.66         4.01         3.48         4.08         3.25 
TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB 
        6.48        35.24         0.85         2.89         2.24         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P 
       15.91        14.07         7.73        20.98         2.20         6.41 
TCGA-GU-A42Q TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK 
        7.66         6.41         5.69         7.63         7.79         6.67 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WV 
        6.41        19.07        11.54         6.74        38.60         4.67 
TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-MV-A51V TCGA-XF-A8HD TCGA-XF-A8HF 
        1.81         6.38         6.35        13.48        88.93        56.19 
TCGA-XF-A8HG 
       15.35 

$`AMP PEAK 13(7P11.2) WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
        7.33         6.74        11.93        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-C4-A0EZ 
       14.89        14.96         4.67         2.07        15.42         8.98 
TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        1.94         0.46         0.69         0.13         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL 
        0.07         0.10         0.10         7.20         5.19        16.31 
TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF 
        1.84        31.40        19.00         8.91        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       15.62        10.49        21.30         8.28        10.55       140.81 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A4U1 TCGA-E7-A3X6 
       48.53        76.60        15.68        32.28        26.17        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        0.10         0.53         0.56         0.66         1.38         0.82 
TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM 
       15.68        12.43        15.88        45.93        22.45        16.47 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BS 
       12.82         5.52        13.18        14.96        12.13        37.15 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A6TA 
       11.01         6.87         5.69         6.84         2.66        50.66 
TCGA-FD-A6TC TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-G2-A2EF TCGA-G2-A2EJ 
        9.30         2.20        15.19         7.13        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3OO 
        5.69        26.93        17.26         7.04        20.12        15.81 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GU-A42R 
       17.75         1.12         2.66         2.10         3.12        11.31 
TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QI TCGA-H4-A2HO TCGA-K4-A3WS TCGA-K4-A3WU 
        4.41         6.15         4.14         1.51         8.75         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-LT-A5Z6 
        2.50         6.48        10.52         1.74         4.27         3.45 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HE 
       12.23        16.67        97.45 

  AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE 
                         0.43                          0.07 
  AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE 
                       130.88                        140.81 
  AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE 
                         8.22                          8.98 
[1] "0.4 - 130.9 (8.2)" "0.1 - 140.8 (9.0)"
[1] "hr=" "1.3"
D13V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 13(7P11.2) MUTATED          1       1       30        37       40
  AMP PEAK 13(7P11.2) WILD-TYPE        0       1       38        35       27
D13V3, multiclass
           clus
vv          AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             1                             1
  STAGE II                           30                            38
  STAGE III                          37                            35
  STAGE IV                           40                            27
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  AMP PEAK 13(7P11.2) MUTATED         30 53 18
  AMP PEAK 13(7P11.2) WILD-TYPE       32 48 14
D13V4, multiclass
          clus
vv         AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE
  T0+T1+T2                          30                            32
  T3                                53                            48
  T4                                18                            14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK 13(7P11.2) MUTATED   59  9 27  6
  AMP PEAK 13(7P11.2) WILD-TYPE 71 13 11  1
D13V5, multiclass
    clus
vv   AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE
  N0                          59                            71
  N1                           9                            13
  N2                          27                            11
  N3                           6                             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                            M0 M1 MX
  AMP PEAK 13(7P11.2) MUTATED   52  2 56
  AMP PEAK 13(7P11.2) WILD-TYPE 54  3 46
D13V6, multiclass
    clus
vv   AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE
  M0                          52                            54
  M1                           2                             3
  MX                          56                            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"
D13V7, binary
                               cls
clus                             0  1
  AMP PEAK 13(7P11.2) MUTATED   27 84
  AMP PEAK 13(7P11.2) WILD-TYPE 23 80
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7P11.2) MUTATED     27   84
  AMP PEAK 13(7P11.2) WILD-TYPE   23   80
        clus
vv       AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE
  FEMALE                          27                            23
  MALE                            84                            80
[1] 2 2
[1] FALSE
D13V8, continuous
D13V9, continuous
D13V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(7P11.2) MUTATED       6                         7    94
  AMP PEAK 13(7P11.2) WILD-TYPE    16                         4    76
D13V11, multiclass
                           clus
vv                          AMP PEAK 13(7P11.2) MUTATED
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              94
                           clus
vv                          AMP PEAK 13(7P11.2) WILD-TYPE
  ASIAN                                                16
  BLACK OR AFRICAN AMERICAN                             4
  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"

Clustering(14) Variable = AMP PEAK 14(8P11.23) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 14(8P11.23) MUTATED    48  20
  AMP PEAK 14(8P11.23) WILD-TYPE 103  37
  AMP PEAK 14(8P11.23) MUTATED AMP PEAK 14(8P11.23) WILD-TYPE 
                            68                            140 
  AMP PEAK 14(8P11.23) MUTATED AMP PEAK 14(8P11.23) WILD-TYPE 
                            20                             37 
$`AMP PEAK 14(8P11.23) MUTATED`
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20V TCGA-BT-A2LA 
        2.66         6.74        12.39        32.84         5.06        17.16 
TCGA-BT-A2LD TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CU-A3QU TCGA-CU-A72E 
        3.65         9.99        23.01         0.69         5.19         9.34 
TCGA-DK-A1A5 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IQ 
        2.14       112.44        10.59        87.32         2.20        10.49 
TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-DK-A6B6 TCGA-E5-A2PC 
       50.27        20.02        10.55        17.98        30.67        43.59 
TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A677 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ 
       24.66         0.49         1.38         4.01        45.93        24.30 
TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43U 
       16.47        46.78        19.79         1.97        14.93        14.93 
TCGA-FD-A5BS TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A6TD TCGA-FD-A6TI TCGA-FJ-A3ZE 
       37.15        49.68         4.83         6.71         4.01         3.48 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM 
        3.25         6.48        17.26        20.12         0.85         2.89 
TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GD-A2C5 TCGA-GD-A6C6 TCGA-GV-A3JV TCGA-GV-A3JW 
        2.24        14.07         7.73         2.20         4.41         6.41 
TCGA-GV-A3JX TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-K4-A3WU 
        6.15         4.14         6.41        11.54        38.60         3.45 
TCGA-K4-A3WV TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-PQ-A6FI TCGA-XF-A8HD 
        4.67        10.52         1.81         4.27        12.23        88.93 
TCGA-XF-A8HF TCGA-XF-A8HG 
       56.19        15.35 

$`AMP PEAK 14(8P11.23) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
       40.08         7.33         6.58        11.93        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W 
       17.88        19.50         5.06        14.89        14.96         8.35 
TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
        8.25         5.59         4.67        12.82         2.07        15.42 
TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS 
       28.70        28.41         8.98         1.94         0.46         0.43 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
        0.13         0.07         0.10         0.07         0.10         0.10 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 
       12.92         4.90         7.20         5.46        16.31         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.53        31.40        18.41        19.00         8.91       130.88 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 
       16.14        17.62        15.62         1.81         7.79       123.85 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW 
        3.98         7.82         8.22        21.30         9.67         8.28 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
      140.81        48.00        64.18        48.53        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       15.68        32.28        15.35        26.17         0.10         0.53 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 
        0.59         0.56         0.66         0.82         1.22        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       15.68         8.94         6.87        12.43        11.93        15.88 
TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S 
       22.45        12.82         5.52        13.18        22.98        14.96 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
        3.62        12.13        13.38        11.01         6.87         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P 
        5.69         6.84        27.45         6.87         2.66         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
        6.38        50.66         9.30         4.11         2.66         2.20 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       15.19         7.13         4.08        61.94        30.61         5.69 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       26.93        35.24         7.04        15.81         4.50        15.91 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
       17.75         1.12         2.66         2.10         3.12        20.98 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        6.41         7.66        11.31         5.69         7.63         7.79 
TCGA-GV-A3QK TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A4AB 
        6.67        19.07         1.51         6.74         8.75         2.50 
TCGA-K4-A4AC TCGA-K4-A5RJ TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
        6.48         1.74         6.38         6.35         3.45        13.48 
TCGA-PQ-A6FN TCGA-XF-A8HE 
       16.67        97.45 

  AMP PEAK 14(8P11.23) MUTATED AMP PEAK 14(8P11.23) WILD-TYPE 
                          0.49                           0.07 
  AMP PEAK 14(8P11.23) MUTATED AMP PEAK 14(8P11.23) WILD-TYPE 
                        112.44                         140.81 
  AMP PEAK 14(8P11.23) MUTATED AMP PEAK 14(8P11.23) WILD-TYPE 
                        10.240                          8.265 
[1] "0.5 - 112.4 (10.2)" "0.1 - 140.8 (8.3)" 
[1] "hr=" "1"  
D14V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 14(8P11.23) MUTATED          1       0       20        24       22
  AMP PEAK 14(8P11.23) WILD-TYPE        0       2       48        48       45
D14V3, multiclass
           clus
vv          AMP PEAK 14(8P11.23) MUTATED AMP PEAK 14(8P11.23) WILD-TYPE
  STAGE 0A                             1                              0
  STAGE I                              0                              2
  STAGE II                            20                             48
  STAGE III                           24                             48
  STAGE IV                            22                             45
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  AMP PEAK 14(8P11.23) MUTATED         21 34  9
  AMP PEAK 14(8P11.23) WILD-TYPE       41 67 23
D14V4, multiclass
          clus
vv         AMP PEAK 14(8P11.23) MUTATED AMP PEAK 14(8P11.23) WILD-TYPE
  T0+T1+T2                           21                             41
  T3                                 34                             67
  T4                                  9                             23
[1] 3 2
[1] 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(8P11.23) MUTATED   38  7 15  2
  AMP PEAK 14(8P11.23) WILD-TYPE 92 15 23  5
D14V5, multiclass
    clus
vv   AMP PEAK 14(8P11.23) MUTATED AMP PEAK 14(8P11.23) WILD-TYPE
  N0                           38                             92
  N1                            7                             15
  N2                           15                             23
  N3                            2                              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                             M0 M1 MX
  AMP PEAK 14(8P11.23) MUTATED   29  2 37
  AMP PEAK 14(8P11.23) WILD-TYPE 77  3 65
D14V6, multiclass
    clus
vv   AMP PEAK 14(8P11.23) MUTATED AMP PEAK 14(8P11.23) WILD-TYPE
  M0                           29                             77
  M1                            2                              3
  MX                           37                             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"
D14V7, binary
                                cls
clus                               0   1
  AMP PEAK 14(8P11.23) MUTATED    13  56
  AMP PEAK 14(8P11.23) WILD-TYPE  37 108
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(8P11.23) MUTATED     13   56
  AMP PEAK 14(8P11.23) WILD-TYPE   37  108
        clus
vv       AMP PEAK 14(8P11.23) MUTATED AMP PEAK 14(8P11.23) WILD-TYPE
  FEMALE                           13                             37
  MALE                             56                            108
[1] 2 2
[1] FALSE
D14V8, continuous
D14V9, continuous
D14V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(8P11.23) MUTATED       5                         3    56
  AMP PEAK 14(8P11.23) WILD-TYPE    17                         8   114
D14V11, multiclass
                           clus
vv                          AMP PEAK 14(8P11.23) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               56
                           clus
vv                          AMP PEAK 14(8P11.23) WILD-TYPE
  ASIAN                                                 17
  BLACK OR AFRICAN AMERICAN                              8
  WHITE                                                114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = AMP PEAK 15(8P11.21) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(8P11.21) MUTATED    50  18
  AMP PEAK 15(8P11.21) WILD-TYPE 101  39
  AMP PEAK 15(8P11.21) MUTATED AMP PEAK 15(8P11.21) WILD-TYPE 
                            68                            140 
  AMP PEAK 15(8P11.21) MUTATED AMP PEAK 15(8P11.21) WILD-TYPE 
                            18                             39 
$`AMP PEAK 15(8P11.21) MUTATED`
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LD 
        6.74        12.39        32.84         8.35        17.16         3.65 
TCGA-BT-A3PJ TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47X TCGA-CU-A0YN 
       12.82         9.99        23.01         0.69         0.10        12.92 
TCGA-CU-A3QU TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I1 
        5.19         9.34        31.40        18.41       112.44        10.59 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU 
      123.85        87.32         2.20        10.49        50.27        20.02 
TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A677 
       10.55        17.98        30.67        43.59         0.49         1.38 
TCGA-E7-A7DV TCGA-FD-A3NA TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        1.22        45.93        46.78        19.79         1.97        22.98 
TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A5BS TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
       14.93        14.93        37.15        49.68         2.66         4.83 
TCGA-FD-A6TI TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2ES TCGA-GC-A3BM TCGA-GC-A3I6 
        4.01         3.25         6.48        17.26         2.89         2.24 
TCGA-GC-A3RB TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ 
        4.50        20.98         2.20         4.41         6.15         5.69 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A2OE 
        7.63         7.79         4.14         6.41        11.54        38.60 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-PQ-A6FI TCGA-XF-A8HD 
        8.75         3.45         1.81         4.27        12.23        88.93 
TCGA-XF-A8HF TCGA-XF-A8HG 
       56.19        15.35 

$`AMP PEAK 15(8P11.21) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
       40.08         7.33         2.66         6.58        11.93        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B 
        5.06         8.25         5.59         4.67         2.07        15.42 
TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS 
       28.70        28.41         8.98         1.94         0.46         0.43 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YO 
        0.13         0.07         0.10         0.07         0.10         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 
        7.20         5.46        16.31         1.84         2.53         2.14 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00         8.91       130.88        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT 
        1.81         7.79         3.98         7.82         8.22        21.30 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW 
        9.67         8.28       140.81        48.00        64.18        48.53 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A4TZ TCGA-E5-A4U1 
       76.60        67.36        15.68        32.28        15.35        26.17 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
       24.66         0.10         0.53         0.59         0.56         0.66 
TCGA-E7-A678 TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        0.82        12.89        15.68         8.94         6.87         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       12.43        11.93        15.88        24.30        22.45        16.47 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y 
       12.82         5.52        13.18        14.96         3.62        12.13 
TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       13.38        11.01         6.87         5.36         5.69         6.84 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC 
       27.45         6.87         6.28         6.38        50.66         9.30 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        6.71         4.11         2.66         2.20        15.19         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.48         4.08        61.94        30.61         5.69        26.93 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3OO TCGA-GC-A3RC 
       35.24         7.04        20.12         0.85        15.81        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP 
       14.07        17.75         1.12         2.66         7.73         2.10 
TCGA-GD-A3OQ TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3QK 
        3.12         6.41         7.66        11.31         6.41         6.67 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
       19.07         1.51         6.74         4.67         2.50         6.48 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
       10.52         1.74         6.38         6.35         3.45        13.48 
TCGA-PQ-A6FN TCGA-XF-A8HE 
       16.67        97.45 

  AMP PEAK 15(8P11.21) MUTATED AMP PEAK 15(8P11.21) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK 15(8P11.21) MUTATED AMP PEAK 15(8P11.21) WILD-TYPE 
                        123.85                         140.81 
  AMP PEAK 15(8P11.21) MUTATED AMP PEAK 15(8P11.21) WILD-TYPE 
                        10.520                          7.805 
[1] "0.1 - 123.8 (10.5)" "0.1 - 140.8 (7.8)" 
[1] "hr=" "1.3"
D15V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 15(8P11.21) MUTATED          1       0       17        28       21
  AMP PEAK 15(8P11.21) WILD-TYPE        0       2       51        44       46
D15V3, multiclass
           clus
vv          AMP PEAK 15(8P11.21) MUTATED AMP PEAK 15(8P11.21) WILD-TYPE
  STAGE 0A                             1                              0
  STAGE I                              0                              2
  STAGE II                            17                             51
  STAGE III                           28                             44
  STAGE IV                            21                             46
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  AMP PEAK 15(8P11.21) MUTATED         18 38  9
  AMP PEAK 15(8P11.21) WILD-TYPE       44 63 23
D15V4, multiclass
          clus
vv         AMP PEAK 15(8P11.21) MUTATED AMP PEAK 15(8P11.21) WILD-TYPE
  T0+T1+T2                           18                             44
  T3                                 38                             63
  T4                                  9                             23
[1] 3 2
[1] 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(8P11.21) MUTATED   40  8 12  4
  AMP PEAK 15(8P11.21) WILD-TYPE 90 14 26  3
D15V5, multiclass
    clus
vv   AMP PEAK 15(8P11.21) MUTATED AMP PEAK 15(8P11.21) WILD-TYPE
  N0                           40                             90
  N1                            8                             14
  N2                           12                             26
  N3                            4                              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                             M0 M1 MX
  AMP PEAK 15(8P11.21) MUTATED   32  0 37
  AMP PEAK 15(8P11.21) WILD-TYPE 74  5 65
D15V6, multiclass
    clus
vv   AMP PEAK 15(8P11.21) MUTATED AMP PEAK 15(8P11.21) WILD-TYPE
  M0                           32                             74
  M1                            0                              5
  MX                           37                             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"
D15V7, binary
                                cls
clus                               0   1
  AMP PEAK 15(8P11.21) MUTATED    11  58
  AMP PEAK 15(8P11.21) WILD-TYPE  39 106
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8P11.21) MUTATED     11   58
  AMP PEAK 15(8P11.21) WILD-TYPE   39  106
        clus
vv       AMP PEAK 15(8P11.21) MUTATED AMP PEAK 15(8P11.21) WILD-TYPE
  FEMALE                           11                             39
  MALE                             58                            106
[1] 2 2
[1] FALSE
D15V8, continuous
D15V9, continuous
D15V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(8P11.21) MUTATED       6                         1    57
  AMP PEAK 15(8P11.21) WILD-TYPE    16                        10   113
D15V11, multiclass
                           clus
vv                          AMP PEAK 15(8P11.21) MUTATED
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               57
                           clus
vv                          AMP PEAK 15(8P11.21) WILD-TYPE
  ASIAN                                                 16
  BLACK OR AFRICAN AMERICAN                             10
  WHITE                                                113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = AMP PEAK 16(8Q22.3) MUTATION ANALYSIS
D16V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 16(8Q22.3) MUTATED   98 38
  AMP PEAK 16(8Q22.3) WILD-TYPE 53 19
  AMP PEAK 16(8Q22.3) MUTATED AMP PEAK 16(8Q22.3) WILD-TYPE 
                          136                            72 
  AMP PEAK 16(8Q22.3) MUTATED AMP PEAK 16(8Q22.3) WILD-TYPE 
                           38                            19 
$`AMP PEAK 16(8Q22.3) MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A20J TCGA-BT-A20N 
       40.08         2.66         6.74        12.39        19.04        32.84 
TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.89         5.06         8.35         8.25        17.16         5.59 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
        3.65        12.82        15.42        28.70         9.99        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
        8.98         1.94        23.01         0.43         0.69         0.13 
TCGA-CF-A47X TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 
        0.10        12.92         7.20         5.46         5.19         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC 
        9.34         2.53         2.14        31.40        18.41       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
      112.44        16.14        10.59       123.85        87.32         2.20 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3WX 
        7.82         8.22        10.49        50.27        20.02        10.55 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A2PC 
       48.00        17.98        64.18        15.68        30.67        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE 
       15.35        26.17         0.49         0.53         0.59         0.56 
TCGA-E7-A677 TCGA-E7-A7DV TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N6 
        1.38         1.22         8.94         6.87         4.01        15.88 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43U 
       45.93        24.30        13.18        46.78        22.98        14.93 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ 
       13.38        37.15        11.01         5.36         5.69        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TD 
        6.87        49.68         4.83         6.28         6.38         6.71 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        4.11         2.66         2.20         4.01        15.19         7.13 
TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE 
        3.48         3.25         5.69        35.24        17.26        20.12 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC 
        0.85         2.89         2.24         4.50        14.07        17.75 
TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P 
        2.66         2.10         3.12        20.98         2.20         6.41 
TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       11.31         4.41         6.41         6.15         5.69         7.63 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
        7.79         4.14         6.41        11.54         1.51         6.74 
TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A6FZ 
       38.60         8.75         3.45         2.50         6.48         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
        4.27         6.38         6.35         3.45        13.48        12.23 
TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
       16.67        88.93        56.19        15.35 

$`AMP PEAK 16(8Q22.3) WILD-TYPE`
TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        7.33         6.58        11.93        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A3PH TCGA-BT-A3PK TCGA-CF-A1HR TCGA-CF-A47T 
        5.06        14.96         4.67         2.07         0.46         0.07 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A3YL TCGA-DK-A1AA 
        0.10         0.07         0.10         4.90        16.31        19.00 
TCGA-DK-A1AB TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A3IL 
        8.91        17.62        15.62         1.81         7.79         3.98 
TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 
       21.30         9.67         8.28       140.81        48.53        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A5KF TCGA-E7-A678 
       67.36        32.28        24.66         0.10         0.66         0.82 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3SL TCGA-FD-A3SM 
       12.89        15.68        12.43        11.93        22.45        16.47 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S 
       12.82         5.52        19.79         1.97        14.93        14.96 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BU TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A6TA 
        3.62        12.13         6.87         6.84         2.66        50.66 
TCGA-FD-A6TC TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL 
        9.30         4.08         6.48        61.94        30.61        26.93 
TCGA-G2-A3IB TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GU-A42Q 
        7.04        15.81        15.91         1.12         7.73         7.66 
TCGA-GV-A3QK TCGA-GV-A40G TCGA-K4-A3WV TCGA-K4-A54R TCGA-K4-A5RJ TCGA-XF-A8HE 
        6.67        19.07         4.67        10.52         1.74        97.45 

  AMP PEAK 16(8Q22.3) MUTATED AMP PEAK 16(8Q22.3) WILD-TYPE 
                         0.10                          0.07 
  AMP PEAK 16(8Q22.3) MUTATED AMP PEAK 16(8Q22.3) WILD-TYPE 
                       130.88                        140.81 
  AMP PEAK 16(8Q22.3) MUTATED AMP PEAK 16(8Q22.3) WILD-TYPE 
                        8.020                        10.095 
[1] "0.1 - 130.9 (8.0)"  "0.1 - 140.8 (10.1)"
[1] "hr=" "1.1"
D16V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 16(8Q22.3) MUTATED          1       2       39        48       45
  AMP PEAK 16(8Q22.3) WILD-TYPE        0       0       29        24       22
D16V3, multiclass
           clus
vv          AMP PEAK 16(8Q22.3) MUTATED AMP PEAK 16(8Q22.3) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             2                             0
  STAGE II                           39                            29
  STAGE III                          48                            24
  STAGE IV                           45                            22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  AMP PEAK 16(8Q22.3) MUTATED         39 66 21
  AMP PEAK 16(8Q22.3) WILD-TYPE       23 35 11
D16V4, multiclass
          clus
vv         AMP PEAK 16(8Q22.3) MUTATED AMP PEAK 16(8Q22.3) WILD-TYPE
  T0+T1+T2                          39                            23
  T3                                66                            35
  T4                                21                            11
[1] 3 2
[1] 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(8Q22.3) MUTATED   79 19 24  4
  AMP PEAK 16(8Q22.3) WILD-TYPE 51  3 14  3
D16V5, multiclass
    clus
vv   AMP PEAK 16(8Q22.3) MUTATED AMP PEAK 16(8Q22.3) WILD-TYPE
  N0                          79                            51
  N1                          19                             3
  N2                          24                            14
  N3                           4                             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                            M0 M1 MX
  AMP PEAK 16(8Q22.3) MUTATED   64  3 70
  AMP PEAK 16(8Q22.3) WILD-TYPE 42  2 32
D16V6, multiclass
    clus
vv   AMP PEAK 16(8Q22.3) MUTATED AMP PEAK 16(8Q22.3) WILD-TYPE
  M0                          64                            42
  M1                           3                             2
  MX                          70                            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"
D16V7, binary
                               cls
clus                              0   1
  AMP PEAK 16(8Q22.3) MUTATED    28 110
  AMP PEAK 16(8Q22.3) WILD-TYPE  22  54
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(8Q22.3) MUTATED     28  110
  AMP PEAK 16(8Q22.3) WILD-TYPE   22   54
        clus
vv       AMP PEAK 16(8Q22.3) MUTATED AMP PEAK 16(8Q22.3) WILD-TYPE
  FEMALE                          28                            22
  MALE                           110                            54
[1] 2 2
[1] FALSE
D16V8, continuous
D16V9, continuous
D16V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(8Q22.3) MUTATED      12                         6   112
  AMP PEAK 16(8Q22.3) WILD-TYPE    10                         5    58
D16V11, multiclass
                           clus
vv                          AMP PEAK 16(8Q22.3) MUTATED
  ASIAN                                              12
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                             112
                           clus
vv                          AMP PEAK 16(8Q22.3) WILD-TYPE
  ASIAN                                                10
  BLACK OR AFRICAN AMERICAN                             5
  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"

Clustering(17) Variable = AMP PEAK 17(9P24.1) MUTATION ANALYSIS
D17V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 17(9P24.1) MUTATED    31  12
  AMP PEAK 17(9P24.1) WILD-TYPE 120  45
  AMP PEAK 17(9P24.1) MUTATED AMP PEAK 17(9P24.1) WILD-TYPE 
                           43                           165 
  AMP PEAK 17(9P24.1) MUTATED AMP PEAK 17(9P24.1) WILD-TYPE 
                           12                            45 
$`AMP PEAK 17(9P24.1) MUTATED`
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20V TCGA-BT-A3PJ TCGA-CU-A0YR TCGA-CU-A3QU 
        6.74         6.58         5.06        12.82         7.20         5.19 
TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IM 
        2.14       130.88       112.44       123.85        87.32         7.82 
TCGA-DK-A6B6 TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SL 
       30.67        12.89         6.87         4.01        11.93        22.45 
TCGA-FD-A43P TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A62N TCGA-FD-A6TD 
       14.93        11.01         6.87         5.69         2.66         6.71 
TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A3IE TCGA-GC-A3BM 
        2.20        15.19        61.94        30.61        20.12         2.89 
TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GV-A3JZ TCGA-GV-A3QF 
        2.24        15.91         7.73         2.10         5.69         7.63 
TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-K4-A6FZ TCGA-LC-A66R TCGA-XF-A8HF 
        4.14         6.41        19.07         1.81         6.35        56.19 
TCGA-XF-A8HG 
       15.35 

$`AMP PEAK 17(9P24.1) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J 
       40.08         7.33         2.66        12.39        11.93        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
       14.96         8.35         8.25        17.16         5.59         3.65 
TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
        4.67         2.07        15.42        28.70         9.99        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        8.98         1.94        23.01         0.46         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
        0.13         0.07         0.10         0.07         0.10         0.10 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
       12.92         4.90         5.46        16.31         1.84         9.34 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE 
        2.53        31.40        18.41        19.00         8.91        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK 
       17.62        15.62         1.81        10.59         7.79         2.20 
TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        3.98         8.22        10.49        50.27        21.30        20.02 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
        9.67         8.28        10.55       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       64.18        48.53        76.60        67.36        15.68        32.28 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       43.59        15.35        26.17        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        0.53         0.59         0.56         0.66         1.38         0.82 
TCGA-E7-A7DV TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA 
        1.22        15.68         8.94        12.43        15.88        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       24.30        16.47        12.82         5.52        13.18        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       19.79         1.97        22.98        14.96        14.93         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ 
       12.13        13.38        37.15         5.36         6.84        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
        6.87        49.68         4.83         6.28         6.38        50.66 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        9.30         4.11         2.66         4.01         7.13         3.48 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        4.08         3.25         6.48         5.69        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD 
       17.26         7.04         0.85        15.81         4.50        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       17.75         1.12         2.66         3.12        20.98         2.20 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
        6.41         7.66        11.31         4.41         6.41         6.15 
TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        7.79         6.67        11.54         1.51         6.74        38.60 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        8.75         3.45         4.67         2.50         6.48        10.52 
TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
        1.74         4.27         6.38         3.45        13.48        12.23 
TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE 
       16.67        88.93        97.45 

  AMP PEAK 17(9P24.1) MUTATED AMP PEAK 17(9P24.1) WILD-TYPE 
                         1.81                          0.07 
  AMP PEAK 17(9P24.1) MUTATED AMP PEAK 17(9P24.1) WILD-TYPE 
                       130.88                        140.81 
  AMP PEAK 17(9P24.1) MUTATED AMP PEAK 17(9P24.1) WILD-TYPE 
                         7.63                          8.94 
[1] "1.8 - 130.9 (7.6)" "0.1 - 140.8 (8.9)"
[1] "hr=" "1"  
D17V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 17(9P24.1) MUTATED          0       0       13        16       14
  AMP PEAK 17(9P24.1) WILD-TYPE        1       2       55        56       53
D17V3, multiclass
           clus
vv          AMP PEAK 17(9P24.1) MUTATED AMP PEAK 17(9P24.1) WILD-TYPE
  STAGE 0A                            0                             1
  STAGE I                             0                             2
  STAGE II                           13                            55
  STAGE III                          16                            56
  STAGE IV                           14                            53
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  AMP PEAK 17(9P24.1) MUTATED         11 20  7
  AMP PEAK 17(9P24.1) WILD-TYPE       51 81 25
D17V4, multiclass
          clus
vv         AMP PEAK 17(9P24.1) MUTATED AMP PEAK 17(9P24.1) WILD-TYPE
  T0+T1+T2                          11                            51
  T3                                20                            81
  T4                                 7                            25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK 17(9P24.1) MUTATED    25   3  10   2
  AMP PEAK 17(9P24.1) WILD-TYPE 105  19  28   5
D17V5, multiclass
    clus
vv   AMP PEAK 17(9P24.1) MUTATED AMP PEAK 17(9P24.1) WILD-TYPE
  N0                          25                           105
  N1                           3                            19
  N2                          10                            28
  N3                           2                             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                            M0 M1 MX
  AMP PEAK 17(9P24.1) MUTATED   17  1 25
  AMP PEAK 17(9P24.1) WILD-TYPE 89  4 77
D17V6, multiclass
    clus
vv   AMP PEAK 17(9P24.1) MUTATED AMP PEAK 17(9P24.1) WILD-TYPE
  M0                          17                            89
  M1                           1                             4
  MX                          25                            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"
D17V7, binary
                               cls
clus                              0   1
  AMP PEAK 17(9P24.1) MUTATED     7  36
  AMP PEAK 17(9P24.1) WILD-TYPE  43 128
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9P24.1) MUTATED      7   36
  AMP PEAK 17(9P24.1) WILD-TYPE   43  128
        clus
vv       AMP PEAK 17(9P24.1) MUTATED AMP PEAK 17(9P24.1) WILD-TYPE
  FEMALE                           7                            43
  MALE                            36                           128
[1] 2 2
[1] FALSE
D17V8, continuous
D17V9, continuous
D17V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(9P24.1) MUTATED       1                         5    37
  AMP PEAK 17(9P24.1) WILD-TYPE    21                         6   133
D17V11, multiclass
                           clus
vv                          AMP PEAK 17(9P24.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              37
                           clus
vv                          AMP PEAK 17(9P24.1) WILD-TYPE
  ASIAN                                                21
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                               133
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = AMP PEAK 18(10P14) MUTATION ANALYSIS
D18V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 18(10P14) MUTATED   59 30
  AMP PEAK 18(10P14) WILD-TYPE 92 27
  AMP PEAK 18(10P14) MUTATED AMP PEAK 18(10P14) WILD-TYPE 
                          89                          119 
  AMP PEAK 18(10P14) MUTATED AMP PEAK 18(10P14) WILD-TYPE 
                          30                           27 
$`AMP PEAK 18(10P14) MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20Q TCGA-BT-A20R 
       40.08         2.66         6.58        32.84        19.50         5.06 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42E 
        5.06         8.35         5.59         3.65        12.82         9.99 
TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU 
        8.98        23.01         0.43        12.92         5.46         5.19 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AC TCGA-DK-A1AD 
        1.84         2.53         2.14        31.40       130.88       112.44 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IV 
        1.81        10.59        87.32         3.98         8.22         9.67 
TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A4U1 
       48.00        64.18        67.36        15.68        30.67        26.17 
TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3NA 
        1.22        12.89         8.94         6.87        11.93        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43Y 
       24.30        19.79         1.97        22.98        14.93        12.13 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TE 
       13.38        37.15        27.45         6.87        49.68         4.11 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2ES 
        2.66         4.01        15.19         3.25         6.48        17.26 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A2C5 
       20.12         0.85         4.50        14.07         2.66         7.73 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF 
       20.98         2.20         6.41         6.41         5.69         7.63 
TCGA-GV-A3QH TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS 
        7.79         6.41        11.54         6.74        38.60         8.75 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R 
        6.48        10.52         1.74         1.81         6.38         6.35 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
        3.45        13.48        88.93        56.19        15.35 

$`AMP PEAK 18(10P14) WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        7.33         6.74        12.39        11.93        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH 
       17.88        14.89        14.96         8.25        17.16         4.67 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR 
        2.07        15.42        28.70        28.41         1.94         0.46 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        0.69         0.13         0.07         0.10         0.07         0.10 
TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A7 
        0.10         4.90         7.20        16.31         9.34        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 
       19.00         8.91        16.14        17.62        15.62         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
      123.85         2.20         7.82        10.49        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW 
       20.02         8.28        10.55       140.81        17.98        48.53 
TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 
       76.60        32.28        43.59        15.35        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        0.49         0.53         0.59         0.56         0.66         1.38 
TCGA-E7-A678 TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SL 
        0.82        15.68         4.01        12.43        15.88        22.45 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43S 
       16.47        12.82         5.52        13.18        46.78        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       14.93         3.62        11.01         6.87         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
        6.84         2.66         4.83         6.28         6.38        50.66 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TH TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        9.30         6.71         2.20         7.13         3.48         4.08 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB 
       61.94        30.61         5.69        26.93        35.24         7.04 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS 
        2.89         2.24        15.81        15.91        17.75         1.12 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JX 
        2.10         3.12         7.66        11.31         4.41         6.15 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G TCGA-H4-A2HO TCGA-K4-A3WU TCGA-K4-A3WV 
        4.14         6.67        19.07         1.51         3.45         4.67 
TCGA-K4-A4AB TCGA-K4-A6MB TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HE 
        2.50         4.27        12.23        16.67        97.45 

  AMP PEAK 18(10P14) MUTATED AMP PEAK 18(10P14) WILD-TYPE 
                        0.43                         0.07 
  AMP PEAK 18(10P14) MUTATED AMP PEAK 18(10P14) WILD-TYPE 
                      130.88                       140.81 
  AMP PEAK 18(10P14) MUTATED AMP PEAK 18(10P14) WILD-TYPE 
                        8.94                         8.25 
[1] "0.4 - 130.9 (8.9)" "0.1 - 140.8 (8.2)"
[1] "hr=" "1.3"
D18V2, continuous
                              vv
clus                           STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 18(10P14) MUTATED          1       1       27        28       33
  AMP PEAK 18(10P14) WILD-TYPE        0       1       41        44       34
D18V3, multiclass
           clus
vv          AMP PEAK 18(10P14) MUTATED AMP PEAK 18(10P14) WILD-TYPE
  STAGE 0A                           1                            0
  STAGE I                            1                            1
  STAGE II                          27                           41
  STAGE III                         28                           44
  STAGE IV                          33                           34
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1+T2 T3 T4
  AMP PEAK 18(10P14) MUTATED         26 42 15
  AMP PEAK 18(10P14) WILD-TYPE       36 59 17
D18V4, multiclass
          clus
vv         AMP PEAK 18(10P14) MUTATED AMP PEAK 18(10P14) WILD-TYPE
  T0+T1+T2                         26                           36
  T3                               42                           59
  T4                               15                           17
[1] 3 2
[1] 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(10P14) MUTATED   47 12 18  4
  AMP PEAK 18(10P14) WILD-TYPE 83 10 20  3
D18V5, multiclass
    clus
vv   AMP PEAK 18(10P14) MUTATED AMP PEAK 18(10P14) WILD-TYPE
  N0                         47                           83
  N1                         12                           10
  N2                         18                           20
  N3                          4                            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                           M0 M1 MX
  AMP PEAK 18(10P14) MUTATED   41  2 48
  AMP PEAK 18(10P14) WILD-TYPE 65  3 54
D18V6, multiclass
    clus
vv   AMP PEAK 18(10P14) MUTATED AMP PEAK 18(10P14) WILD-TYPE
  M0                         41                           65
  M1                          2                            3
  MX                         48                           54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                              cls
clus                            0  1
  AMP PEAK 18(10P14) MUTATED   22 70
  AMP PEAK 18(10P14) WILD-TYPE 28 94
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(10P14) MUTATED     22   70
  AMP PEAK 18(10P14) WILD-TYPE   28   94
        clus
vv       AMP PEAK 18(10P14) MUTATED AMP PEAK 18(10P14) WILD-TYPE
  FEMALE                         22                           28
  MALE                           70                           94
[1] 2 2
[1] FALSE
D18V8, continuous
D18V9, continuous
D18V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(10P14) MUTATED       6                         5    75
  AMP PEAK 18(10P14) WILD-TYPE    16                         6    95
D18V11, multiclass
                           clus
vv                          AMP PEAK 18(10P14) MUTATED
  ASIAN                                              6
  BLACK OR AFRICAN AMERICAN                          5
  WHITE                                             75
                           clus
vv                          AMP PEAK 18(10P14) WILD-TYPE
  ASIAN                                               16
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = AMP PEAK 19(11Q13.3) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 19(11Q13.3) MUTATED   59 23
  AMP PEAK 19(11Q13.3) WILD-TYPE 92 34
  AMP PEAK 19(11Q13.3) MUTATED AMP PEAK 19(11Q13.3) WILD-TYPE 
                            82                            126 
  AMP PEAK 19(11Q13.3) MUTATED AMP PEAK 19(11Q13.3) WILD-TYPE 
                            23                             34 
$`AMP PEAK 19(11Q13.3) MUTATED`
TCGA-BL-A13J TCGA-BT-A20N TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B 
        2.66        32.84        17.16         4.67        12.82        15.42 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A47V 
       28.70         9.99        28.41        23.01         0.43         0.10 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A1A3 
       12.92         4.90         7.20         5.46         1.84         2.53 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AF TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 
        2.14        31.40        17.62        10.59         7.79        87.32 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A3X2 
        3.98         7.82        10.49        10.55        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A5KE TCGA-E7-A5KF 
       64.18        30.67        43.59        26.17         0.56         0.66 
TCGA-E7-A7DV TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ 
        1.22         8.94         6.87         4.01        45.93        24.30 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BT 
       22.98        14.93        14.93        12.13        13.38        11.01 
TCGA-FD-A5BV TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 
        5.36         2.66         6.38         2.66         4.01        15.19 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RC 
       17.26         7.04        20.12         2.89         2.24        15.91 
TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GV-A3JV 
       14.07         2.66         7.73        20.98         2.20         4.41 
TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
        6.41         5.69         7.63         7.79         4.14         6.67 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A4AB 
        6.41        19.07         6.74        38.60         4.67         2.50 
TCGA-K4-A4AC TCGA-LC-A66R TCGA-PQ-A6FI TCGA-XF-A8HF 
        6.48         6.35        12.23        56.19 

$`AMP PEAK 19(11Q13.3) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         6.74        12.39         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       19.04        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD 
       14.96         5.06         8.35         8.25         5.59         3.65 
TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S 
        2.07         8.98         1.94         0.46         0.69         0.13 
TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A3QU TCGA-CU-A3YL 
        0.07         0.07         0.10         0.10         5.19        16.31 
TCGA-CU-A72E TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
        9.34        18.41        19.00         8.91       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IN 
       16.14        15.62         1.81       123.85         2.20         8.22 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY 
       50.27        21.30        20.02         9.67         8.28       140.81 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A4TZ 
       48.53        76.60        67.36        15.68        32.28        15.35 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A677 
       24.66         0.10         0.49         0.53         0.59         1.38 
TCGA-E7-A678 TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        0.82        12.89        15.68        12.43        11.93        15.88 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       22.45        16.47        12.82         5.52        13.18        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BU 
       19.79         1.97        14.96         3.62        37.15         6.87 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O 
        5.69         6.84        27.45         6.87        49.68         4.83 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH 
        6.28        50.66         9.30         6.71         4.11         2.20 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF 
        7.13         3.48         4.08         3.25         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3VY TCGA-GC-A3OO 
       30.61         5.69        26.93        35.24         0.85        15.81 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GU-A42P 
        4.50        17.75         1.12         2.10         3.12         6.41 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JX TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-K4-A3WS 
        7.66        11.31         6.15        11.54         1.51         8.75 
TCGA-K4-A3WU TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        3.45        10.52         1.74         1.81         4.27         6.38 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG 
        3.45        13.48        16.67        88.93        97.45        15.35 

  AMP PEAK 19(11Q13.3) MUTATED AMP PEAK 19(11Q13.3) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK 19(11Q13.3) MUTATED AMP PEAK 19(11Q13.3) WILD-TYPE 
                         87.32                         140.81 
  AMP PEAK 19(11Q13.3) MUTATED AMP PEAK 19(11Q13.3) WILD-TYPE 
                         7.805                          8.830 
[1] "0.1 - 87.3 (7.8)"  "0.1 - 140.8 (8.8)"
[1] "hr=" "1.1"
D19V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 19(11Q13.3) MUTATED          0       0       28        25       28
  AMP PEAK 19(11Q13.3) WILD-TYPE        1       2       40        47       39
D19V3, multiclass
           clus
vv          AMP PEAK 19(11Q13.3) MUTATED AMP PEAK 19(11Q13.3) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              0                              2
  STAGE II                            28                             40
  STAGE III                           25                             47
  STAGE IV                            28                             39
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  AMP PEAK 19(11Q13.3) MUTATED         27 36 12
  AMP PEAK 19(11Q13.3) WILD-TYPE       35 65 20
D19V4, multiclass
          clus
vv         AMP PEAK 19(11Q13.3) MUTATED AMP PEAK 19(11Q13.3) WILD-TYPE
  T0+T1+T2                           27                             35
  T3                                 36                             65
  T4                                 12                             20
[1] 3 2
[1] 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(11Q13.3) MUTATED   46  8 17  4
  AMP PEAK 19(11Q13.3) WILD-TYPE 84 14 21  3
D19V5, multiclass
    clus
vv   AMP PEAK 19(11Q13.3) MUTATED AMP PEAK 19(11Q13.3) WILD-TYPE
  N0                           46                             84
  N1                            8                             14
  N2                           17                             21
  N3                            4                              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                             M0 M1 MX
  AMP PEAK 19(11Q13.3) MUTATED   37  1 45
  AMP PEAK 19(11Q13.3) WILD-TYPE 69  4 57
D19V6, multiclass
    clus
vv   AMP PEAK 19(11Q13.3) MUTATED AMP PEAK 19(11Q13.3) WILD-TYPE
  M0                           37                             69
  M1                            1                              4
  MX                           45                             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"
D19V7, binary
                                cls
clus                               0   1
  AMP PEAK 19(11Q13.3) MUTATED    20  63
  AMP PEAK 19(11Q13.3) WILD-TYPE  30 101
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(11Q13.3) MUTATED     20   63
  AMP PEAK 19(11Q13.3) WILD-TYPE   30  101
        clus
vv       AMP PEAK 19(11Q13.3) MUTATED AMP PEAK 19(11Q13.3) WILD-TYPE
  FEMALE                           20                             30
  MALE                             63                            101
[1] 2 2
[1] FALSE
D19V8, continuous
D19V9, continuous
D19V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(11Q13.3) MUTATED       7                         6    65
  AMP PEAK 19(11Q13.3) WILD-TYPE    15                         5   105
D19V11, multiclass
                           clus
vv                          AMP PEAK 19(11Q13.3) MUTATED
  ASIAN                                                7
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               65
                           clus
vv                          AMP PEAK 19(11Q13.3) WILD-TYPE
  ASIAN                                                 15
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = AMP PEAK 20(11Q22.2) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 20(11Q22.2) MUTATED    32   9
  AMP PEAK 20(11Q22.2) WILD-TYPE 119  48
  AMP PEAK 20(11Q22.2) MUTATED AMP PEAK 20(11Q22.2) WILD-TYPE 
                            41                            167 
  AMP PEAK 20(11Q22.2) MUTATED AMP PEAK 20(11Q22.2) WILD-TYPE 
                             9                             48 
$`AMP PEAK 20(11Q22.2) MUTATED`
TCGA-BT-A20W TCGA-BT-A3PJ TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CU-A0YR 
        8.35        12.82         9.99         1.94        23.01         7.20 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3WX 
        1.84         2.53        10.59        87.32         3.98        10.55 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-E5-A2PC TCGA-E7-A5KF TCGA-E7-A7DV TCGA-FD-A3B6 
       48.00        17.98        43.59         0.66         1.22         6.87 
TCGA-FD-A3NA TCGA-FD-A43P TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BZ TCGA-FD-A5C1 
       45.93        14.93        13.38        11.01        27.45        49.68 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3YS 
        2.66         4.01        15.19         2.24        15.91         1.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A40E TCGA-K4-A4AB 
       20.98         2.20         7.63         4.14         6.41         2.50 
TCGA-K4-A4AC TCGA-K4-A6MB TCGA-LC-A66R TCGA-PQ-A6FI TCGA-XF-A8HF 
        6.48         4.27         6.35        12.23        56.19 

$`AMP PEAK 20(11Q22.2) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       11.93        19.04        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
        5.06        14.89        14.96         5.06         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
        5.59         3.65         4.67         2.07        15.42        28.70 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
       28.41         8.98         0.46         0.43         0.69         0.13 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN 
        0.07         0.10         0.07         0.10         0.10        12.92 
TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A5 
        4.90         5.46         5.19        16.31         9.34         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       31.40        18.41        19.00         8.91       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 
       16.14        17.62        15.62         1.81         7.79       123.85 
TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
        2.20         7.82         8.22        10.49        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A6AV TCGA-DK-A6AW 
       20.02         9.67         8.28       140.81        64.18        48.53 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4TZ 
       76.60        67.36        15.68        32.28        30.67        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 
       26.17        24.66         0.10         0.49         0.53         0.59 
TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
        0.56         1.38         0.82        12.89        15.68         8.94 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL 
        4.01        12.43        11.93        15.88        24.30        22.45 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       16.47        12.82         5.52        13.18        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
        1.97        22.98        14.96        14.93         3.62        12.13 
TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       37.15         6.87         5.36         5.69         6.84         6.87 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC 
        2.66         4.83         6.28         6.38        50.66         9.30 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        6.71         4.11         2.20         7.13         3.48         4.08 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25         6.48        61.94        30.61         5.69        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM 
       35.24        17.26         7.04        20.12         0.85         2.89 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A2C5 
       15.81         4.50        14.07        17.75         2.66         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV 
        2.10         3.12         6.41         7.66        11.31         4.41 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40G 
        6.41         6.15         5.69         7.79         6.67        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU 
       11.54         1.51         6.74        38.60         8.75         3.45 
TCGA-K4-A3WV TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LT-A5Z6 
        4.67        10.52         1.74         1.81         6.38         3.45 
TCGA-MV-A51V TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG 
       13.48        16.67        88.93        97.45        15.35 

  AMP PEAK 20(11Q22.2) MUTATED AMP PEAK 20(11Q22.2) WILD-TYPE 
                          0.66                           0.07 
  AMP PEAK 20(11Q22.2) MUTATED AMP PEAK 20(11Q22.2) WILD-TYPE 
                         87.32                         140.81 
  AMP PEAK 20(11Q22.2) MUTATED AMP PEAK 20(11Q22.2) WILD-TYPE 
                          8.35                           8.75 
[1] "0.7 - 87.3 (8.3)"  "0.1 - 140.8 (8.8)"
[1] "hr=" "1.3"
D20V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 20(11Q22.2) MUTATED          0       0       13        13       15
  AMP PEAK 20(11Q22.2) WILD-TYPE        1       2       55        59       52
D20V3, multiclass
           clus
vv          AMP PEAK 20(11Q22.2) MUTATED AMP PEAK 20(11Q22.2) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              0                              2
  STAGE II                            13                             55
  STAGE III                           13                             59
  STAGE IV                            15                             52
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  AMP PEAK 20(11Q22.2) MUTATED         14 19  6
  AMP PEAK 20(11Q22.2) WILD-TYPE       48 82 26
D20V4, multiclass
          clus
vv         AMP PEAK 20(11Q22.2) MUTATED AMP PEAK 20(11Q22.2) WILD-TYPE
  T0+T1+T2                           14                             48
  T3                                 19                             82
  T4                                  6                             26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 20(11Q22.2) MUTATED    23   6   8   2
  AMP PEAK 20(11Q22.2) WILD-TYPE 107  16  30   5
D20V5, multiclass
    clus
vv   AMP PEAK 20(11Q22.2) MUTATED AMP PEAK 20(11Q22.2) WILD-TYPE
  N0                           23                            107
  N1                            6                             16
  N2                            8                             30
  N3                            2                              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                             M0 M1 MX
  AMP PEAK 20(11Q22.2) MUTATED   18  0 23
  AMP PEAK 20(11Q22.2) WILD-TYPE 88  5 79
D20V6, multiclass
    clus
vv   AMP PEAK 20(11Q22.2) MUTATED AMP PEAK 20(11Q22.2) WILD-TYPE
  M0                           18                             88
  M1                            0                              5
  MX                           23                             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"
D20V7, binary
                                cls
clus                               0   1
  AMP PEAK 20(11Q22.2) MUTATED     9  32
  AMP PEAK 20(11Q22.2) WILD-TYPE  41 132
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(11Q22.2) MUTATED      9   32
  AMP PEAK 20(11Q22.2) WILD-TYPE   41  132
        clus
vv       AMP PEAK 20(11Q22.2) MUTATED AMP PEAK 20(11Q22.2) WILD-TYPE
  FEMALE                            9                             41
  MALE                             32                            132
[1] 2 2
[1] FALSE
D20V8, continuous
D20V9, continuous
D20V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(11Q22.2) MUTATED       1                         1    37
  AMP PEAK 20(11Q22.2) WILD-TYPE    21                        10   133
D20V11, multiclass
                           clus
vv                          AMP PEAK 20(11Q22.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               37
                           clus
vv                          AMP PEAK 20(11Q22.2) WILD-TYPE
  ASIAN                                                 21
  BLACK OR AFRICAN AMERICAN                             10
  WHITE                                                133
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = AMP PEAK 21(12Q15) MUTATION ANALYSIS
D21V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 21(12Q15) MUTATED    40  19
  AMP PEAK 21(12Q15) WILD-TYPE 111  38
  AMP PEAK 21(12Q15) MUTATED AMP PEAK 21(12Q15) WILD-TYPE 
                          59                          149 
  AMP PEAK 21(12Q15) MUTATED AMP PEAK 21(12Q15) WILD-TYPE 
                          19                           38 
$`AMP PEAK 21(12Q15) MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20P 
       40.08         2.66         6.74         6.58        19.04        17.88 
TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PK TCGA-BT-A42C 
        5.06         5.06         8.25         5.59         2.07        28.70 
TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A5W6 TCGA-DK-A1A3 
        9.99        23.01         4.90         7.20         1.84         2.53 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A2I4 TCGA-DK-A3WX 
        2.14        31.40        18.41       130.88       123.85        10.55 
TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-E7-A541 TCGA-E7-A5KE TCGA-FD-A43Y 
       64.18        67.36        15.68         0.59         0.56        12.13 
TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TC 
        5.69        27.45        49.68         6.28         6.38         9.30 
TCGA-FD-A6TG TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EO 
        2.66        15.19         6.48        61.94         5.69        35.24 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GU-A42R TCGA-GV-A3JW 
        0.85         2.89         2.24        14.07        11.31         6.41 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HO TCGA-H4-A2HQ 
        7.79         4.14         6.67         6.41         1.51         6.74 
TCGA-HQ-A2OE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A83P TCGA-MV-A51V 
       38.60         3.45         4.67         6.38        13.48 

$`AMP PEAK 21(12Q15) WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20Q 
        7.33        12.39        11.93        32.84        12.16        19.50 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH 
       14.89        14.96         8.35        17.16         3.65         4.67 
TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HR 
       12.82        15.42        28.41         8.98         1.94         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69         0.13         0.07         0.10         0.07 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
        0.10         0.10        12.92         5.46         5.19        16.31 
TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
        9.34        19.00         8.91       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK 
       15.62         1.81        10.59         7.79        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
        3.98         7.82         8.22        10.49        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
       20.02         9.67         8.28       140.81        48.00        17.98 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ 
       48.53        76.60        32.28        30.67        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KF 
       26.17        24.66         0.10         0.49         0.53         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
        1.38         0.82         1.22        12.89        15.68         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
        6.87         4.01        12.43        11.93        15.88        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        22.45        16.47        12.82         5.52        13.18 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79         1.97        22.98        14.93        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       14.93         3.62        13.38        37.15        11.01         6.87 
TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TA 
        5.36         6.84         6.87         2.66         4.83        50.66 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        6.71         4.11         2.20         4.01         7.13         3.48 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB 
        4.08         3.25        30.61        26.93        17.26         7.04 
TCGA-G2-A3IE TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS 
       20.12        15.81         4.50        15.91        17.75         1.12 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
        2.66         7.73         2.10         3.12        20.98         2.20 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        6.41         7.66         4.41         6.15         5.69         7.63 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       19.07        11.54         8.75         2.50         6.48        10.52 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI 
        1.74         1.81         4.27         6.35         3.45        12.23 
TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       16.67        88.93        97.45        56.19        15.35 

  AMP PEAK 21(12Q15) MUTATED AMP PEAK 21(12Q15) WILD-TYPE 
                        0.56                         0.07 
  AMP PEAK 21(12Q15) MUTATED AMP PEAK 21(12Q15) WILD-TYPE 
                      130.88                       140.81 
  AMP PEAK 21(12Q15) MUTATED AMP PEAK 21(12Q15) WILD-TYPE 
                        6.74                         9.34 
[1] "0.6 - 130.9 (6.7)" "0.1 - 140.8 (9.3)"
[1] "hr=" "1.3"
D21V2, continuous
                              vv
clus                           STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 21(12Q15) MUTATED          0       1       21        22       18
  AMP PEAK 21(12Q15) WILD-TYPE        1       1       47        50       49
D21V3, multiclass
           clus
vv          AMP PEAK 21(12Q15) MUTATED AMP PEAK 21(12Q15) WILD-TYPE
  STAGE 0A                           0                            1
  STAGE I                            1                            1
  STAGE II                          21                           47
  STAGE III                         22                           50
  STAGE IV                          18                           49
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1+T2 T3 T4
  AMP PEAK 21(12Q15) MUTATED         18 25 12
  AMP PEAK 21(12Q15) WILD-TYPE       44 76 20
D21V4, multiclass
          clus
vv         AMP PEAK 21(12Q15) MUTATED AMP PEAK 21(12Q15) WILD-TYPE
  T0+T1+T2                         18                           44
  T3                               25                           76
  T4                               12                           20
[1] 3 2
[1] 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(12Q15) MUTATED   38  6 12  0
  AMP PEAK 21(12Q15) WILD-TYPE 92 16 26  7
D21V5, multiclass
    clus
vv   AMP PEAK 21(12Q15) MUTATED AMP PEAK 21(12Q15) WILD-TYPE
  N0                         38                           92
  N1                          6                           16
  N2                         12                           26
  N3                          0                            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"
                              vv
clus                           M0 M1 MX
  AMP PEAK 21(12Q15) MUTATED   36  1 25
  AMP PEAK 21(12Q15) WILD-TYPE 70  4 77
D21V6, multiclass
    clus
vv   AMP PEAK 21(12Q15) MUTATED AMP PEAK 21(12Q15) WILD-TYPE
  M0                         36                           70
  M1                          1                            4
  MX                         25                           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"
D21V7, binary
                              cls
clus                             0   1
  AMP PEAK 21(12Q15) MUTATED    17  46
  AMP PEAK 21(12Q15) WILD-TYPE  33 118
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(12Q15) MUTATED     17   46
  AMP PEAK 21(12Q15) WILD-TYPE   33  118
        clus
vv       AMP PEAK 21(12Q15) MUTATED AMP PEAK 21(12Q15) WILD-TYPE
  FEMALE                         17                           33
  MALE                           46                          118
[1] 2 2
[1] FALSE
D21V8, continuous
D21V9, continuous
D21V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(12Q15) MUTATED       7                         3    48
  AMP PEAK 21(12Q15) WILD-TYPE    15                         8   122
D21V11, multiclass
                           clus
vv                          AMP PEAK 21(12Q15) MUTATED
  ASIAN                                              7
  BLACK OR AFRICAN AMERICAN                          3
  WHITE                                             48
                           clus
vv                          AMP PEAK 21(12Q15) WILD-TYPE
  ASIAN                                               15
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                              122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = AMP PEAK 22(13Q22.1) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 22(13Q22.1) MUTATED    49  17
  AMP PEAK 22(13Q22.1) WILD-TYPE 102  40
  AMP PEAK 22(13Q22.1) MUTATED AMP PEAK 22(13Q22.1) WILD-TYPE 
                            66                            142 
  AMP PEAK 22(13Q22.1) MUTATED AMP PEAK 22(13Q22.1) WILD-TYPE 
                            17                             40 
$`AMP PEAK 22(13Q22.1) MUTATED`
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20Q TCGA-BT-A20U 
        6.74         6.58        19.04        32.84        19.50        14.96 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CU-A0YN 
        3.65        12.82         1.94         0.46         0.43        12.92 
TCGA-CU-A0YR TCGA-CU-A3YL TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
        7.20        16.31         1.81        87.32         2.20         3.98 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A6B1 
       10.49        50.27        21.30        20.02        48.00        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E7-A541 TCGA-FD-A3B5 TCGA-FD-A3B6 
       15.68        32.28        43.59         0.59         8.94         6.87 
TCGA-FD-A3N5 TCGA-FD-A3SM TCGA-FD-A43X TCGA-FD-A5BT TCGA-FD-A62O TCGA-FD-A6TC 
       11.93        16.47         3.62        11.01         4.83         9.30 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3ZE TCGA-FT-A61P TCGA-G2-A2EF 
        4.11         2.66         2.20         3.48         6.48        61.94 
TCGA-G2-A2EK TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GD-A3OP 
        5.69        15.81         4.50        15.91        17.75         2.10 
TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A42R TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       20.98         6.41        11.31         6.15         5.69         7.63 
TCGA-GV-A3QH TCGA-GV-A3QK TCGA-H4-A2HQ TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC 
        7.79         6.67         6.74         3.45         4.67         6.48 
TCGA-K4-A6MB TCGA-LC-A66R TCGA-MV-A51V TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
        4.27         6.35        13.48        88.93        56.19        15.35 

$`AMP PEAK 22(13Q22.1) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20O 
       40.08         7.33         2.66        12.39        11.93        12.16 
TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
       17.88         5.06        14.89         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       17.16         5.59         4.67         2.07        15.42        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47S 
        9.99        28.41         8.98        23.01         0.69         0.13 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YO 
        0.07         0.10         0.07         0.10         0.10         4.90 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.46         5.19         1.84         9.34         2.53         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       31.40        18.41        19.00         8.91       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       16.14        17.62        15.62        10.59         7.79       123.85 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        7.82         8.22         9.67         8.28        10.55       140.81 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B6 TCGA-E5-A4TZ 
       17.98        64.18        48.53        76.60        30.67        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KE 
       26.17        24.66         0.10         0.49         0.53         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 
        0.66         1.38         0.82         1.22        12.89        15.68 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        4.01        12.43        15.88        45.93        24.30        22.45 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       12.82         5.52        13.18        46.78        19.79         1.97 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BR 
       22.98        14.93        14.96        14.93        12.13        13.38 
TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       37.15         6.87         5.36         5.69         6.84        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
        6.87        49.68         2.66         6.28         6.38        50.66 
TCGA-FD-A6TD TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A3EE 
        6.71         4.01        15.19         7.13         4.08         3.25 
TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       30.61        26.93        35.24        17.26         7.04        20.12 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 
        0.85         2.89         2.24        14.07         1.12         2.66 
TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GV-A3JV TCGA-GV-A3JW 
        7.73         3.12         2.20         7.66         4.41         6.41 
TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE 
        4.14         6.41        19.07        11.54         1.51        38.60 
TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P 
        8.75         2.50        10.52         1.74         1.81         6.38 
TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HE 
        3.45        12.23        16.67        97.45 

  AMP PEAK 22(13Q22.1) MUTATED AMP PEAK 22(13Q22.1) WILD-TYPE 
                          0.43                           0.07 
  AMP PEAK 22(13Q22.1) MUTATED AMP PEAK 22(13Q22.1) WILD-TYPE 
                         88.93                         140.81 
  AMP PEAK 22(13Q22.1) MUTATED AMP PEAK 22(13Q22.1) WILD-TYPE 
                          7.71                           8.83 
[1] "0.4 - 88.9 (7.7)"  "0.1 - 140.8 (8.8)"
[1] "hr=" "1.1"
D22V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 22(13Q22.1) MUTATED          0       0       20        21       25
  AMP PEAK 22(13Q22.1) WILD-TYPE        1       2       48        51       42
D22V3, multiclass
           clus
vv          AMP PEAK 22(13Q22.1) MUTATED AMP PEAK 22(13Q22.1) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              0                              2
  STAGE II                            20                             48
  STAGE III                           21                             51
  STAGE IV                            25                             42
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  AMP PEAK 22(13Q22.1) MUTATED         19 33  9
  AMP PEAK 22(13Q22.1) WILD-TYPE       43 68 23
D22V4, multiclass
          clus
vv         AMP PEAK 22(13Q22.1) MUTATED AMP PEAK 22(13Q22.1) WILD-TYPE
  T0+T1+T2                           19                             43
  T3                                 33                             68
  T4                                  9                             23
[1] 3 2
[1] 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(13Q22.1) MUTATED   38  7 16  3
  AMP PEAK 22(13Q22.1) WILD-TYPE 92 15 22  4
D22V5, multiclass
    clus
vv   AMP PEAK 22(13Q22.1) MUTATED AMP PEAK 22(13Q22.1) WILD-TYPE
  N0                           38                             92
  N1                            7                             15
  N2                           16                             22
  N3                            3                              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                             M0 M1 MX
  AMP PEAK 22(13Q22.1) MUTATED   34  3 31
  AMP PEAK 22(13Q22.1) WILD-TYPE 72  2 71
D22V6, multiclass
    clus
vv   AMP PEAK 22(13Q22.1) MUTATED AMP PEAK 22(13Q22.1) WILD-TYPE
  M0                           34                             72
  M1                            3                              2
  MX                           31                             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"
D22V7, binary
                                cls
clus                               0   1
  AMP PEAK 22(13Q22.1) MUTATED    14  54
  AMP PEAK 22(13Q22.1) WILD-TYPE  36 110
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(13Q22.1) MUTATED     14   54
  AMP PEAK 22(13Q22.1) WILD-TYPE   36  110
        clus
vv       AMP PEAK 22(13Q22.1) MUTATED AMP PEAK 22(13Q22.1) WILD-TYPE
  FEMALE                           14                             36
  MALE                             54                            110
[1] 2 2
[1] FALSE
D22V8, continuous
D22V9, continuous
D22V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(13Q22.1) MUTATED       4                         3    56
  AMP PEAK 22(13Q22.1) WILD-TYPE    18                         8   114
D22V11, multiclass
                           clus
vv                          AMP PEAK 22(13Q22.1) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               56
                           clus
vv                          AMP PEAK 22(13Q22.1) WILD-TYPE
  ASIAN                                                 18
  BLACK OR AFRICAN AMERICAN                              8
  WHITE                                                114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = AMP PEAK 23(14Q11.2) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 23(14Q11.2) MUTATED    33  19
  AMP PEAK 23(14Q11.2) WILD-TYPE 118  38
  AMP PEAK 23(14Q11.2) MUTATED AMP PEAK 23(14Q11.2) WILD-TYPE 
                            52                            156 
  AMP PEAK 23(14Q11.2) MUTATED AMP PEAK 23(14Q11.2) WILD-TYPE 
                            19                             38 
$`AMP PEAK 23(14Q11.2) MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A3PH 
       40.08         2.66        12.39         6.58        32.84         4.67 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CU-A0YN 
       28.70         8.98         1.94        23.01         0.43        12.92 
TCGA-CU-A0YR TCGA-DK-A1A7 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN 
        7.20        18.41        87.32         2.20         7.82         8.22 
TCGA-DK-A3IT TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-FD-A3B3 
       21.30        10.55        17.98        30.67        43.59        12.89 
TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C1 
        4.01        11.93        11.01         5.69        27.45        49.68 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3ZE 
        4.83         6.38         6.71         4.11         2.20         3.48 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3YS 
       26.93        35.24         2.89         2.24         4.50         1.12 
TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-K4-A4AC 
        2.20         6.41         7.79         4.14         6.41         6.48 
TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-PQ-A6FN TCGA-XF-A8HG 
        1.81         3.45        16.67        15.35 

$`AMP PEAK 23(14Q11.2) WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        7.33         6.74        11.93        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       19.50         5.06        14.89        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
        8.25        17.16         5.59         3.65        12.82         2.07 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S 
       15.42         9.99        28.41         0.46         0.69         0.13 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YO 
        0.07         0.10         0.07         0.10         0.10         4.90 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        5.46         5.19        16.31         1.84         9.34         2.53 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
        2.14        31.40        19.00         8.91       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV 
      123.85         3.98        10.49        50.27        20.02         9.67 
TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
        8.28       140.81        48.00        64.18        48.53        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       67.36        15.68        32.28        15.35        26.17        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.10         0.49         0.53         0.59         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
        1.38         0.82         1.22        15.68         8.94         6.87 
TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       12.43        15.88        45.93        24.30        22.45        16.47 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       12.82         5.52        13.18        46.78        19.79         1.97 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
       22.98        14.93        14.96        14.93         3.62        12.13 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5C0 
       13.38        37.15         6.87         5.36         6.84         6.87 
TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TI 
        2.66         6.28        50.66         9.30         2.66         4.01 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF 
       15.19         7.13         4.08         3.25         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       30.61         5.69        17.26         7.04        20.12         0.85 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A2C5 
       15.81        15.91        14.07        17.75         2.66         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV 
        2.10         3.12        20.98         7.66        11.31         4.41 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40G 
        6.41         6.15         5.69         7.63         6.67        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU 
       11.54         1.51         6.74        38.60         8.75         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P 
        4.67         2.50        10.52         1.74         4.27         6.38 
TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        6.35        13.48        12.23        88.93        97.45        56.19 

  AMP PEAK 23(14Q11.2) MUTATED AMP PEAK 23(14Q11.2) WILD-TYPE 
                          0.43                           0.07 
  AMP PEAK 23(14Q11.2) MUTATED AMP PEAK 23(14Q11.2) WILD-TYPE 
                         87.32                         140.81 
  AMP PEAK 23(14Q11.2) MUTATED AMP PEAK 23(14Q11.2) WILD-TYPE 
                         7.495                          9.120 
[1] "0.4 - 87.3 (7.5)"  "0.1 - 140.8 (9.1)"
[1] "hr=" "1.6"
D23V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 23(14Q11.2) MUTATED          0       1       10        24       16
  AMP PEAK 23(14Q11.2) WILD-TYPE        1       1       58        48       51
D23V3, multiclass
           clus
vv          AMP PEAK 23(14Q11.2) MUTATED AMP PEAK 23(14Q11.2) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              1                              1
  STAGE II                            10                             58
  STAGE III                           24                             48
  STAGE IV                            16                             51
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  AMP PEAK 23(14Q11.2) MUTATED          8 33  4
  AMP PEAK 23(14Q11.2) WILD-TYPE       54 68 28
D23V4, multiclass
          clus
vv         AMP PEAK 23(14Q11.2) MUTATED AMP PEAK 23(14Q11.2) WILD-TYPE
  T0+T1+T2                            8                             54
  T3                                 33                             68
  T4                                  4                             28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 23(14Q11.2) MUTATED    30   7   9   1
  AMP PEAK 23(14Q11.2) WILD-TYPE 100  15  29   6
D23V5, multiclass
    clus
vv   AMP PEAK 23(14Q11.2) MUTATED AMP PEAK 23(14Q11.2) WILD-TYPE
  N0                           30                            100
  N1                            7                             15
  N2                            9                             29
  N3                            1                              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"
                                vv
clus                             M0 M1 MX
  AMP PEAK 23(14Q11.2) MUTATED   22  2 28
  AMP PEAK 23(14Q11.2) WILD-TYPE 84  3 74
D23V6, multiclass
    clus
vv   AMP PEAK 23(14Q11.2) MUTATED AMP PEAK 23(14Q11.2) WILD-TYPE
  M0                           22                             84
  M1                            2                              3
  MX                           28                             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"
D23V7, binary
                                cls
clus                               0   1
  AMP PEAK 23(14Q11.2) MUTATED    13  39
  AMP PEAK 23(14Q11.2) WILD-TYPE  37 125
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(14Q11.2) MUTATED     13   39
  AMP PEAK 23(14Q11.2) WILD-TYPE   37  125
        clus
vv       AMP PEAK 23(14Q11.2) MUTATED AMP PEAK 23(14Q11.2) WILD-TYPE
  FEMALE                           13                             37
  MALE                             39                            125
[1] 2 2
[1] FALSE
D23V8, continuous
D23V9, continuous
D23V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(14Q11.2) MUTATED       1                         3    44
  AMP PEAK 23(14Q11.2) WILD-TYPE    21                         8   126
D23V11, multiclass
                           clus
vv                          AMP PEAK 23(14Q11.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               44
                           clus
vv                          AMP PEAK 23(14Q11.2) WILD-TYPE
  ASIAN                                                 21
  BLACK OR AFRICAN AMERICAN                              8
  WHITE                                                126
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = AMP PEAK 24(16P13.13) MUTATION ANALYSIS
D24V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 24(16P13.13) MUTATED    31  14
  AMP PEAK 24(16P13.13) WILD-TYPE 120  43
  AMP PEAK 24(16P13.13) MUTATED AMP PEAK 24(16P13.13) WILD-TYPE 
                             45                             163 
  AMP PEAK 24(16P13.13) MUTATED AMP PEAK 24(16P13.13) WILD-TYPE 
                             14                              43 
$`AMP PEAK 24(16P13.13) MUTATED`
TCGA-BT-A0S7 TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-C4-A0EZ TCGA-CF-A47X 
        6.58         5.06         8.25        17.16         8.98         0.10 
TCGA-CU-A0YR TCGA-CU-A3QU TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
        7.20         5.19         7.79         3.98         7.82         8.22 
TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-E5-A2PC 
       50.27         9.67        48.00        67.36        15.68        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A5BY 
       15.35        26.17         0.49        45.93        24.30         6.84 
TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EO 
        6.71         2.66         4.01         3.48         3.25        35.24 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GD-A2C5 TCGA-GU-A42P 
       20.12         0.85         2.89         2.24         7.73         6.41 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WU 
        4.41         6.41         5.69         6.74        38.60         3.45 
TCGA-K4-A4AB TCGA-K4-A83P TCGA-LC-A66R 
        2.50         6.38         6.35 

$`AMP PEAK 24(16P13.13) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74        12.39        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
       14.89        14.96         8.35         5.59         3.65         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
       12.82         2.07        15.42        28.70         9.99        28.41 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
        1.94        23.01         0.46         0.43         0.69         0.13 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO 
        0.07         0.10         0.07         0.10        12.92         4.90 
TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.46        16.31         1.84         9.34         2.53         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       31.40        18.41        19.00         8.91       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 
       16.14        17.62        15.62         1.81        10.59       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW 
       87.32         2.20        10.49        21.30        20.02         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       10.55       140.81        17.98        64.18        48.53        76.60 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A541 
       32.28        30.67        24.66         0.10         0.53         0.59 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 
        0.56         0.66         1.38         0.82         1.22        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       15.68         8.94         6.87         4.01        12.43        11.93 
TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       15.88        22.45        16.47        12.82         5.52        13.18 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79         1.97        22.98        14.93        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.93         3.62        12.13        13.38        37.15        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        6.87         5.36         5.69        27.45         6.87        49.68 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC 
        2.66         4.83         6.28         6.38        50.66         9.30 
TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A61P 
        4.11         2.20        15.19         7.13         4.08         6.48 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB 
       61.94        30.61         5.69        26.93        17.26         7.04 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75         1.12 
TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q 
        2.66         2.10         3.12        20.98         2.20         7.66 
TCGA-GU-A42R TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       11.31         6.15         7.63         7.79         4.14         6.67 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-K4-A3WS TCGA-K4-A3WV 
        6.41        19.07        11.54         1.51         8.75         4.67 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-LT-A5Z6 
        6.48        10.52         1.74         1.81         4.27         3.45 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       13.48        12.23        16.67        88.93        97.45        56.19 
TCGA-XF-A8HG 
       15.35 

  AMP PEAK 24(16P13.13) MUTATED AMP PEAK 24(16P13.13) WILD-TYPE 
                           0.10                            0.07 
  AMP PEAK 24(16P13.13) MUTATED AMP PEAK 24(16P13.13) WILD-TYPE 
                          67.36                          140.81 
  AMP PEAK 24(16P13.13) MUTATED AMP PEAK 24(16P13.13) WILD-TYPE 
                           6.74                           10.52 
[1] "0.1 - 67.4 (6.7)"   "0.1 - 140.8 (10.5)"
[1] "hr=" "1.3"
D24V2, continuous
                                 vv
clus                              STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 24(16P13.13) MUTATED          0       0       11        12       21
  AMP PEAK 24(16P13.13) WILD-TYPE        1       2       57        60       46
D24V3, multiclass
           clus
vv          AMP PEAK 24(16P13.13) MUTATED AMP PEAK 24(16P13.13) WILD-TYPE
  STAGE 0A                              0                               1
  STAGE I                               0                               2
  STAGE II                             11                              57
  STAGE III                            12                              60
  STAGE IV                             21                              46
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1+T2 T3 T4
  AMP PEAK 24(16P13.13) MUTATED         13 15 12
  AMP PEAK 24(16P13.13) WILD-TYPE       49 86 20
D24V4, multiclass
          clus
vv         AMP PEAK 24(16P13.13) MUTATED AMP PEAK 24(16P13.13) WILD-TYPE
  T0+T1+T2                            13                              49
  T3                                  15                              86
  T4                                  12                              20
[1] 3 2
[1] 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(16P13.13) MUTATED    18   8  10   3
  AMP PEAK 24(16P13.13) WILD-TYPE 112  14  28   4
D24V5, multiclass
    clus
vv   AMP PEAK 24(16P13.13) MUTATED AMP PEAK 24(16P13.13) WILD-TYPE
  N0                            18                             112
  N1                             8                              14
  N2                            10                              28
  N3                             3                               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                              M0 M1 MX
  AMP PEAK 24(16P13.13) MUTATED   21  3 20
  AMP PEAK 24(16P13.13) WILD-TYPE 85  2 82
D24V6, multiclass
    clus
vv   AMP PEAK 24(16P13.13) MUTATED AMP PEAK 24(16P13.13) WILD-TYPE
  M0                            21                              85
  M1                             3                               2
  MX                            20                              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"
D24V7, binary
                                 cls
clus                                0   1
  AMP PEAK 24(16P13.13) MUTATED    10  35
  AMP PEAK 24(16P13.13) WILD-TYPE  40 129
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(16P13.13) MUTATED     10   35
  AMP PEAK 24(16P13.13) WILD-TYPE   40  129
        clus
vv       AMP PEAK 24(16P13.13) MUTATED AMP PEAK 24(16P13.13) WILD-TYPE
  FEMALE                            10                              40
  MALE                              35                             129
[1] 2 2
[1] FALSE
D24V8, continuous
D24V9, continuous
D24V10, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(16P13.13) MUTATED       3                         2    36
  AMP PEAK 24(16P13.13) WILD-TYPE    19                         9   134
D24V11, multiclass
                           clus
vv                          AMP PEAK 24(16P13.13) MUTATED
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                36
                           clus
vv                          AMP PEAK 24(16P13.13) WILD-TYPE
  ASIAN                                                  19
  BLACK OR AFRICAN AMERICAN                               9
  WHITE                                                 134
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = AMP PEAK 25(16P11.2) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 25(16P11.2) MUTATED    40  17
  AMP PEAK 25(16P11.2) WILD-TYPE 111  40
  AMP PEAK 25(16P11.2) MUTATED AMP PEAK 25(16P11.2) WILD-TYPE 
                            57                            151 
  AMP PEAK 25(16P11.2) MUTATED AMP PEAK 25(16P11.2) WILD-TYPE 
                            17                             40 
$`AMP PEAK 25(16P11.2) MUTATED`
TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
        2.66         6.58         5.06         5.06         8.25        17.16 
TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ TCGA-CF-A47X TCGA-CU-A0YN TCGA-CU-A3KJ 
       28.70         9.99         8.98         0.10        12.92         5.46 
TCGA-CU-A3QU TCGA-DK-A1A7 TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK 
        5.19        18.41        10.59         7.79        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6B2 TCGA-E5-A2PC 
        3.98        50.27         9.67        48.00        15.68        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-FD-A3B3 TCGA-FD-A3B6 
       15.35        26.17         0.49         0.56        12.89         6.87 
TCGA-FD-A3SJ TCGA-FD-A3SR TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BV TCGA-FD-A5BY 
       24.30        19.79        14.93        12.13         5.36         6.84 
TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P 
        6.71         2.66         4.01         3.48         3.25         6.48 
TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-A3IE TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3YS 
       61.94        35.24        20.12         2.89         2.24         1.12 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A3WU 
        4.41         6.41         5.69         6.74         8.75         3.45 
TCGA-K4-A4AB TCGA-K4-A6MB TCGA-K4-A83P 
        2.50         4.27         6.38 

$`AMP PEAK 25(16P11.2) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J 
       40.08         7.33         6.74        12.39        11.93        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U 
       32.84        12.16        17.88        19.50        14.89        14.96 
TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
        8.35         5.59         3.65         4.67        12.82         2.07 
TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       15.42        28.41         1.94        23.01         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
        0.69         0.13         0.07         0.10         0.07         0.10 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        4.90         7.20        16.31         1.84         9.34         2.53 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
        2.14        31.40        19.00         8.91       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A3IM 
       16.14        17.62        15.62         1.81       123.85         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX 
        8.22        10.49        21.30        20.02         8.28        10.55 
TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
      140.81        17.98        64.18        48.53        76.60        67.36 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A541 
       32.28        30.67        24.66         0.10         0.53         0.59 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B4 TCGA-FD-A3B5 
        0.66         1.38         0.82         1.22        15.68         8.94 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL 
        4.01        12.43        11.93        15.88        45.93        22.45 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS 
       16.47        12.82         5.52        13.18        46.78         1.97 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       22.98        14.93        14.96         3.62        13.38        37.15 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
       11.01         6.87         5.69        27.45         6.87        49.68 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC 
        2.66         4.83         6.28         6.38        50.66         9.30 
TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-G2-A2EJ 
        4.11         2.20        15.19         7.13         4.08        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-GC-A3OO 
        5.69        26.93        17.26         7.04         0.85        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A2C5 
        4.50        15.91        14.07        17.75         2.66         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q 
        2.10         3.12        20.98         2.20         6.41         7.66 
TCGA-GU-A42R TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       11.31         6.15         7.63         7.79         4.14         6.67 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WV 
        6.41        19.07        11.54         1.51        38.60         4.67 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-LC-A66R TCGA-LT-A5Z6 
        6.48        10.52         1.74         1.81         6.35         3.45 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       13.48        12.23        16.67        88.93        97.45        56.19 
TCGA-XF-A8HG 
       15.35 

  AMP PEAK 25(16P11.2) MUTATED AMP PEAK 25(16P11.2) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK 25(16P11.2) MUTATED AMP PEAK 25(16P11.2) WILD-TYPE 
                         87.32                         140.81 
  AMP PEAK 25(16P11.2) MUTATED AMP PEAK 25(16P11.2) WILD-TYPE 
                          6.74                          10.49 
[1] "0.1 - 87.3 (6.7)"   "0.1 - 140.8 (10.5)"
[1] "hr=" "1.3"
D25V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 25(16P11.2) MUTATED          0       0       13        17       27
  AMP PEAK 25(16P11.2) WILD-TYPE        1       2       55        55       40
D25V3, multiclass
           clus
vv          AMP PEAK 25(16P11.2) MUTATED AMP PEAK 25(16P11.2) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              0                              2
  STAGE II                            13                             55
  STAGE III                           17                             55
  STAGE IV                            27                             40
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  AMP PEAK 25(16P11.2) MUTATED         13 24 14
  AMP PEAK 25(16P11.2) WILD-TYPE       49 77 18
D25V4, multiclass
          clus
vv         AMP PEAK 25(16P11.2) MUTATED AMP PEAK 25(16P11.2) WILD-TYPE
  T0+T1+T2                           13                             49
  T3                                 24                             77
  T4                                 14                             18
[1] 3 2
[1] 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(16P11.2) MUTATED    26  11  12   3
  AMP PEAK 25(16P11.2) WILD-TYPE 104  11  26   4
D25V5, multiclass
    clus
vv   AMP PEAK 25(16P11.2) MUTATED AMP PEAK 25(16P11.2) WILD-TYPE
  N0                           26                            104
  N1                           11                             11
  N2                           12                             26
  N3                            3                              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                             M0 M1 MX
  AMP PEAK 25(16P11.2) MUTATED   28  3 26
  AMP PEAK 25(16P11.2) WILD-TYPE 78  2 76
D25V6, multiclass
    clus
vv   AMP PEAK 25(16P11.2) MUTATED AMP PEAK 25(16P11.2) WILD-TYPE
  M0                           28                             78
  M1                            3                              2
  MX                           26                             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"
D25V7, binary
                                cls
clus                               0   1
  AMP PEAK 25(16P11.2) MUTATED    15  42
  AMP PEAK 25(16P11.2) WILD-TYPE  35 122
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(16P11.2) MUTATED     15   42
  AMP PEAK 25(16P11.2) WILD-TYPE   35  122
        clus
vv       AMP PEAK 25(16P11.2) MUTATED AMP PEAK 25(16P11.2) WILD-TYPE
  FEMALE                           15                             35
  MALE                             42                            122
[1] 2 2
[1] FALSE
D25V8, continuous
D25V9, continuous
D25V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(16P11.2) MUTATED       3                         2    48
  AMP PEAK 25(16P11.2) WILD-TYPE    19                         9   122
D25V11, multiclass
                           clus
vv                          AMP PEAK 25(16P11.2) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               48
                           clus
vv                          AMP PEAK 25(16P11.2) WILD-TYPE
  ASIAN                                                 19
  BLACK OR AFRICAN AMERICAN                              9
  WHITE                                                122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = AMP PEAK 26(16Q22.1) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 26(16Q22.1) MUTATED    45  17
  AMP PEAK 26(16Q22.1) WILD-TYPE 106  40
  AMP PEAK 26(16Q22.1) MUTATED AMP PEAK 26(16Q22.1) WILD-TYPE 
                            62                            146 
  AMP PEAK 26(16Q22.1) MUTATED AMP PEAK 26(16Q22.1) WILD-TYPE 
                            17                             40 
$`AMP PEAK 26(16Q22.1) MUTATED`
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20V 
        2.66         6.74         6.58        32.84         5.06         5.06 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ 
        8.25        17.16        12.82        28.70         9.99         8.98 
TCGA-CF-A1HS TCGA-CF-A47X TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A2I1 TCGA-DK-A2I2 
        0.43         0.10         5.46         2.14        10.59         7.79 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X1 
        3.98         7.82        50.27        21.30         9.67        48.00 
TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A7DV TCGA-FD-A3B3 
       64.18        15.68        43.59        26.17         1.22        12.89 
TCGA-FD-A3SL TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BY 
       22.45        14.93        12.13        11.01         5.36         6.84 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TG 
       27.45         6.87         6.28         6.38         9.30         2.66 
TCGA-FD-A6TI TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EO TCGA-G2-A3VY TCGA-GC-A3BM 
        4.01         3.48         3.25        35.24         0.85         2.89 
TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OS 
        2.24         4.50         1.12         2.66         7.73        20.98 
TCGA-GV-A3JW TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
        6.41         1.51         6.74         8.75         3.45         2.50 
TCGA-K4-A6MB TCGA-LC-A66R 
        4.27         6.35 

$`AMP PEAK 26(16Q22.1) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
       40.08         7.33        12.39        11.93        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB 
       17.88        19.50        14.89        14.96         8.35         5.59 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F0 
        3.65         4.67         2.07        15.42        28.41         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       23.01         0.46         0.69         0.13         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU 
        0.07         0.10        12.92         4.90         7.20         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
       16.31         1.84         9.34         2.53        31.40        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00         8.91       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IN 
       15.62         1.81       123.85        87.32         2.20         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 
       10.49        20.02         8.28        10.55       140.81        17.98 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4TZ 
       48.53        76.60        67.36        32.28        30.67        15.35 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE 
       24.66         0.10         0.49         0.53         0.59         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
        0.66         1.38         0.82        15.68         8.94         6.87 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.43        11.93        15.88        45.93        24.30 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       16.47        12.82         5.52        13.18        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR 
        1.97        22.98        14.96        14.93         3.62        13.38 
TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
       37.15         6.87         5.69        49.68         2.66         4.83 
TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
       50.66         6.71         4.11         2.20        15.19         7.13 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        4.08         6.48        61.94        30.61         5.69        26.93 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
       17.26         7.04        20.12        15.81        15.91        14.07 
TCGA-GC-A3WC TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q 
       17.75         2.10         3.12         2.20         6.41         7.66 
TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       11.31         4.41         6.15         5.69         7.63         7.79 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A2OE 
        4.14         6.67         6.41        19.07        11.54        38.60 
TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P 
        4.67         6.48        10.52         1.74         1.81         6.38 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE 
        3.45        13.48        12.23        16.67        88.93        97.45 
TCGA-XF-A8HF TCGA-XF-A8HG 
       56.19        15.35 

  AMP PEAK 26(16Q22.1) MUTATED AMP PEAK 26(16Q22.1) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK 26(16Q22.1) MUTATED AMP PEAK 26(16Q22.1) WILD-TYPE 
                         64.18                         140.81 
  AMP PEAK 26(16Q22.1) MUTATED AMP PEAK 26(16Q22.1) WILD-TYPE 
                          6.79                          10.93 
[1] "0.1 - 64.2 (6.8)"   "0.1 - 140.8 (10.9)"
[1] "hr=" "1.3"
D26V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 26(16Q22.1) MUTATED          0       0       15        25       21
  AMP PEAK 26(16Q22.1) WILD-TYPE        1       2       53        47       46
D26V3, multiclass
           clus
vv          AMP PEAK 26(16Q22.1) MUTATED AMP PEAK 26(16Q22.1) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              0                              2
  STAGE II                            15                             53
  STAGE III                           25                             47
  STAGE IV                            21                             46
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  AMP PEAK 26(16Q22.1) MUTATED         12 30 14
  AMP PEAK 26(16Q22.1) WILD-TYPE       50 71 18
D26V4, multiclass
          clus
vv         AMP PEAK 26(16Q22.1) MUTATED AMP PEAK 26(16Q22.1) WILD-TYPE
  T0+T1+T2                           12                             50
  T3                                 30                             71
  T4                                 14                             18
[1] 3 2
[1] 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(16Q22.1) MUTATED   36  8  9  4
  AMP PEAK 26(16Q22.1) WILD-TYPE 94 14 29  3
D26V5, multiclass
    clus
vv   AMP PEAK 26(16Q22.1) MUTATED AMP PEAK 26(16Q22.1) WILD-TYPE
  N0                           36                             94
  N1                            8                             14
  N2                            9                             29
  N3                            4                              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                             M0 M1 MX
  AMP PEAK 26(16Q22.1) MUTATED   28  4 29
  AMP PEAK 26(16Q22.1) WILD-TYPE 78  1 73
D26V6, multiclass
    clus
vv   AMP PEAK 26(16Q22.1) MUTATED AMP PEAK 26(16Q22.1) WILD-TYPE
  M0                           28                             78
  M1                            4                              1
  MX                           29                             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"
D26V7, binary
                                cls
clus                               0   1
  AMP PEAK 26(16Q22.1) MUTATED    21  41
  AMP PEAK 26(16Q22.1) WILD-TYPE  29 123
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(16Q22.1) MUTATED     21   41
  AMP PEAK 26(16Q22.1) WILD-TYPE   29  123
        clus
vv       AMP PEAK 26(16Q22.1) MUTATED AMP PEAK 26(16Q22.1) WILD-TYPE
  FEMALE                           21                             29
  MALE                             41                            123
[1] 2 2
[1] FALSE
D26V8, continuous
D26V9, continuous
D26V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 26(16Q22.1) MUTATED       4                         4    48
  AMP PEAK 26(16Q22.1) WILD-TYPE    18                         7   122
D26V11, multiclass
                           clus
vv                          AMP PEAK 26(16Q22.1) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               48
                           clus
vv                          AMP PEAK 26(16Q22.1) WILD-TYPE
  ASIAN                                                 18
  BLACK OR AFRICAN AMERICAN                              7
  WHITE                                                122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = AMP PEAK 27(17Q11.2) MUTATION ANALYSIS
D27V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 27(17Q11.2) MUTATED   62 31
  AMP PEAK 27(17Q11.2) WILD-TYPE 89 26
  AMP PEAK 27(17Q11.2) MUTATED AMP PEAK 27(17Q11.2) WILD-TYPE 
                            93                            115 
  AMP PEAK 27(17Q11.2) MUTATED AMP PEAK 27(17Q11.2) WILD-TYPE 
                            31                             26 
$`AMP PEAK 27(17Q11.2) MUTATED`
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20P TCGA-BT-A20Q 
        2.66         6.74        12.39         6.58        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PH 
        5.06        14.89        14.96         8.35         3.65         4.67 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A47X TCGA-CU-A0YR TCGA-CU-A3YL 
       28.70         8.98         0.46         0.10         7.20        16.31 
TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD 
        1.84         2.14        31.40        18.41       130.88       112.44 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3X1 
       10.59         7.79         2.20         7.82        50.27        48.00 
TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ 
       17.98        67.36        32.28        30.67        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-FD-A3B5 
       26.17         0.49         0.59         0.56         1.38         8.94 
TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SP TCGA-FD-A3SQ 
        6.87        11.93        45.93        24.30        13.18        46.78 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BT 
       22.98        14.93        14.93         3.62        13.38        11.01 
TCGA-FD-A5BV TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TE TCGA-FD-A6TG 
        5.36        49.68         4.83        50.66         4.11         2.66 
TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FT-A3EE TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-A3VY 
        2.20        15.19         3.25        35.24        20.12         0.85 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 
        2.89         4.50         1.12         7.73         2.10         2.20 
TCGA-GU-A42P TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF 
        6.41        11.31         4.41         6.41         5.69         7.63 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HQ 
        7.79         4.14         6.67         6.41        19.07         6.74 
TCGA-HQ-A2OE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-PQ-A6FI 
       38.60         3.45         4.67         1.81         4.27        12.23 
TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
       88.93        56.19        15.35 

$`AMP PEAK 27(17Q11.2) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
       40.08         7.33        11.93        19.04        32.84        12.16 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PJ TCGA-BT-A3PK 
        5.06         8.25        17.16         5.59        12.82         2.07 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HS 
       15.42         9.99        28.41         1.94        23.01         0.43 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
        0.69         0.13         0.07         0.10         0.07         0.10 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A72E TCGA-DK-A1A3 
       12.92         4.90         5.46         5.19         9.34         2.53 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
       19.00         8.91        16.14        17.62        15.62         1.81 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT 
      123.85        87.32         3.98         8.22        10.49        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AV 
       20.02         9.67         8.28        10.55       140.81        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       48.53        76.60        15.68        24.66         0.10         0.53 
TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B7 
        0.66         0.82         1.22        12.89        15.68         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       12.43        15.88        22.45        16.47        12.82         5.52 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BU 
       19.79         1.97        14.96        12.13        37.15         6.87 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P 
        5.69         6.84        27.45         6.87         2.66         6.28 
TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        6.38         9.30         6.71         4.01         7.13         3.48 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        4.08         6.48        61.94        30.61         5.69        26.93 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
       17.26         7.04         2.24        15.81        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GV-A3JX 
       17.75         2.66         3.12        20.98         7.66         6.15 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       11.54         1.51         8.75         2.50         6.48        10.52 
TCGA-K4-A5RJ TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN 
        1.74         6.38         6.35         3.45        13.48        16.67 
TCGA-XF-A8HE 
       97.45 

  AMP PEAK 27(17Q11.2) MUTATED AMP PEAK 27(17Q11.2) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK 27(17Q11.2) MUTATED AMP PEAK 27(17Q11.2) WILD-TYPE 
                        130.88                         140.81 
  AMP PEAK 27(17Q11.2) MUTATED AMP PEAK 27(17Q11.2) WILD-TYPE 
                          7.82                           8.91 
[1] "0.1 - 130.9 (7.8)" "0.1 - 140.8 (8.9)"
[1] "hr=" "1.4"
D27V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 27(17Q11.2) MUTATED          0       0       31        27       36
  AMP PEAK 27(17Q11.2) WILD-TYPE        1       2       37        45       31
D27V3, multiclass
           clus
vv          AMP PEAK 27(17Q11.2) MUTATED AMP PEAK 27(17Q11.2) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              0                              2
  STAGE II                            31                             37
  STAGE III                           27                             45
  STAGE IV                            36                             31
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  AMP PEAK 27(17Q11.2) MUTATED         30 44 14
  AMP PEAK 27(17Q11.2) WILD-TYPE       32 57 18
D27V4, multiclass
          clus
vv         AMP PEAK 27(17Q11.2) MUTATED AMP PEAK 27(17Q11.2) WILD-TYPE
  T0+T1+T2                           30                             32
  T3                                 44                             57
  T4                                 14                             18
[1] 3 2
[1] 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(17Q11.2) MUTATED   50 11 24  2
  AMP PEAK 27(17Q11.2) WILD-TYPE 80 11 14  5
D27V5, multiclass
    clus
vv   AMP PEAK 27(17Q11.2) MUTATED AMP PEAK 27(17Q11.2) WILD-TYPE
  N0                           50                             80
  N1                           11                             11
  N2                           24                             14
  N3                            2                              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                             M0 M1 MX
  AMP PEAK 27(17Q11.2) MUTATED   42  2 51
  AMP PEAK 27(17Q11.2) WILD-TYPE 64  3 51
D27V6, multiclass
    clus
vv   AMP PEAK 27(17Q11.2) MUTATED AMP PEAK 27(17Q11.2) WILD-TYPE
  M0                           42                             64
  M1                            2                              3
  MX                           51                             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"
D27V7, binary
                                cls
clus                              0  1
  AMP PEAK 27(17Q11.2) MUTATED   21 75
  AMP PEAK 27(17Q11.2) WILD-TYPE 29 89
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(17Q11.2) MUTATED     21   75
  AMP PEAK 27(17Q11.2) WILD-TYPE   29   89
        clus
vv       AMP PEAK 27(17Q11.2) MUTATED AMP PEAK 27(17Q11.2) WILD-TYPE
  FEMALE                           21                             29
  MALE                             75                             89
[1] 2 2
[1] FALSE
D27V8, continuous
D27V9, continuous
D27V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 27(17Q11.2) MUTATED       9                         4    77
  AMP PEAK 27(17Q11.2) WILD-TYPE    13                         7    93
D27V11, multiclass
                           clus
vv                          AMP PEAK 27(17Q11.2) MUTATED
  ASIAN                                                9
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               77
                           clus
vv                          AMP PEAK 27(17Q11.2) WILD-TYPE
  ASIAN                                                 13
  BLACK OR AFRICAN AMERICAN                              7
  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"

Clustering(28) Variable = AMP PEAK 28(17Q12) MUTATION ANALYSIS
D28V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 28(17Q12) MUTATED   54 31
  AMP PEAK 28(17Q12) WILD-TYPE 97 26
  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE 
                          85                          123 
  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE 
                          31                           26 
$`AMP PEAK 28(17Q12) MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20O 
       40.08         2.66         6.74        12.39         6.58        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X 
       17.88        19.50         5.06        14.96         8.35         8.25 
TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A47X 
        3.65         2.07        28.70         8.98         0.46         0.10 
TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        7.20        16.31         1.84         2.14        31.40        18.41 
TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IS 
      112.44        10.59         7.79        87.32         7.82        50.27 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ 
       48.00        17.98        67.36        30.67        43.59        15.35 
TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-FD-A3B5 TCGA-FD-A3B6 
        0.49         0.59         0.56         1.38         8.94         6.87 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43P 
        4.01        45.93        24.30        13.18        46.78        14.93 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5C1 TCGA-FD-A62O 
       14.93         3.62        13.38         5.36        49.68         4.83 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 
       50.66         9.30         6.71         4.11         2.20        15.19 
TCGA-FT-A3EE TCGA-G2-A3IE TCGA-GC-A3BM TCGA-GD-A3OP TCGA-GU-A42P TCGA-GU-A42R 
        3.25        20.12         2.89         2.10         6.41        11.31 
TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
        4.41         5.69         7.63         7.79         4.14         6.67 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WU 
        6.41        19.07         1.51         6.74        38.60         3.45 
TCGA-K4-A3WV TCGA-K4-A6FZ TCGA-MV-A51V TCGA-PQ-A6FI TCGA-XF-A8HD TCGA-XF-A8HF 
        4.67         1.81        13.48        12.23        88.93        56.19 
TCGA-XF-A8HG 
       15.35 

$`AMP PEAK 28(17Q12) WILD-TYPE`
TCGA-BL-A13I TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V 
        7.33        11.93        19.04        32.84        14.89         5.06 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42E 
       17.16         5.59         4.67        12.82        15.42         9.99 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
       28.41         1.94        23.01         0.43         0.69         0.13 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO 
        0.07         0.10         0.07         0.10        12.92         4.90 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1AA TCGA-DK-A1AB 
        5.46         5.19         9.34         2.53        19.00         8.91 
TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I4 
      130.88        16.14        17.62        15.62         1.81       123.85 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU 
        2.20         3.98         8.22        10.49        21.30        20.02 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AV TCGA-DK-A6AW 
        9.67         8.28        10.55       140.81        64.18        48.53 
TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       76.60        15.68        32.28        26.17        24.66         0.10 
TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 
        0.53         0.66         0.82         1.22        12.89        15.68 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       12.43        11.93        15.88        22.45        16.47        12.82 
TCGA-FD-A3SO TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43Y 
        5.52        19.79         1.97        22.98        14.96        12.13 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       37.15        11.01         6.87         5.69         6.84        27.45 
TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TG TCGA-FD-A6TI 
        6.87         2.66         6.28         6.38         2.66         4.01 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
        7.13         3.48         4.08         6.48        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY 
        5.69        26.93        35.24        17.26         7.04         0.85 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
        1.12         2.66         7.73         3.12        20.98         2.20 
TCGA-GU-A42Q TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A4AB 
        7.66         6.41         6.15        11.54         8.75         2.50 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R 
        6.48        10.52         1.74         4.27         6.38         6.35 
TCGA-LT-A5Z6 TCGA-PQ-A6FN TCGA-XF-A8HE 
        3.45        16.67        97.45 

  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE 
                        0.10                         0.07 
  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE 
                      112.44                       140.81 
  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE 
                        8.35                         8.75 
[1] "0.1 - 112.4 (8.3)" "0.1 - 140.8 (8.8)"
[1] "hr=" "1.6"
D28V2, continuous
                              vv
clus                           STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 28(17Q12) MUTATED          0       1       28        27       30
  AMP PEAK 28(17Q12) WILD-TYPE        1       1       40        45       37
D28V3, multiclass
           clus
vv          AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE
  STAGE 0A                           0                            1
  STAGE I                            1                            1
  STAGE II                          28                           40
  STAGE III                         27                           45
  STAGE IV                          30                           37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1+T2 T3 T4
  AMP PEAK 28(17Q12) MUTATED         30 35 16
  AMP PEAK 28(17Q12) WILD-TYPE       32 66 16
D28V4, multiclass
          clus
vv         AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE
  T0+T1+T2                         30                           32
  T3                               35                           66
  T4                               16                           16
[1] 3 2
[1] 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(17Q12) MUTATED   49  9 20  2
  AMP PEAK 28(17Q12) WILD-TYPE 81 13 18  5
D28V5, multiclass
    clus
vv   AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE
  N0                         49                           81
  N1                          9                           13
  N2                         20                           18
  N3                          2                            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                           M0 M1 MX
  AMP PEAK 28(17Q12) MUTATED   39  2 47
  AMP PEAK 28(17Q12) WILD-TYPE 67  3 55
D28V6, multiclass
    clus
vv   AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE
  M0                         39                           67
  M1                          2                            3
  MX                         47                           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"
D28V7, binary
                              cls
clus                            0  1
  AMP PEAK 28(17Q12) MUTATED   21 67
  AMP PEAK 28(17Q12) WILD-TYPE 29 97
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 28(17Q12) MUTATED     21   67
  AMP PEAK 28(17Q12) WILD-TYPE   29   97
        clus
vv       AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE
  FEMALE                         21                           29
  MALE                           67                           97
[1] 2 2
[1] FALSE
D28V8, continuous
D28V9, continuous
D28V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 28(17Q12) MUTATED       8                         4    70
  AMP PEAK 28(17Q12) WILD-TYPE    14                         7   100
D28V11, multiclass
                           clus
vv                          AMP PEAK 28(17Q12) MUTATED
  ASIAN                                              8
  BLACK OR AFRICAN AMERICAN                          4
  WHITE                                             70
                           clus
vv                          AMP PEAK 28(17Q12) WILD-TYPE
  ASIAN                                               14
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                              100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = AMP PEAK 29(19Q12) MUTATION ANALYSIS
D29V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 29(19Q12) MUTATED   61 23
  AMP PEAK 29(19Q12) WILD-TYPE 90 34
  AMP PEAK 29(19Q12) MUTATED AMP PEAK 29(19Q12) WILD-TYPE 
                          84                          124 
  AMP PEAK 29(19Q12) MUTATED AMP PEAK 29(19Q12) WILD-TYPE 
                          23                           34 
$`AMP PEAK 29(19Q12) MUTATED`
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20V 
        2.66         6.74        19.04        32.84        12.16         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A42C 
        8.35         8.25        17.16         5.59         3.65        28.70 
TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47X 
        9.99         1.94        23.01         0.46         0.43         0.10 
TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AB 
        5.46        16.31         2.53        31.40        18.41         8.91 
TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3X1 
      112.44         1.81       123.85        87.32         3.98        48.00 
TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ 
       64.18        67.36        15.68        30.67        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B8 
       26.17         0.49         0.56         1.22        12.89        12.43 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       24.30        22.45        19.79         1.97        22.98        14.93 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62P 
       14.93         3.62         6.84        27.45         6.87         6.28 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EF 
        2.66         2.20        15.19         4.08         3.25        61.94 
TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       35.24        20.12         0.85         4.50        15.91        14.07 
TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ 
        1.12         7.73        11.31         4.41         6.41         5.69 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS 
        7.63         7.79        19.07         6.74        38.60         8.75 
TCGA-K4-A4AB TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-MV-A51V TCGA-XF-A8HF TCGA-XF-A8HG 
        2.50         1.74         4.27        13.48        56.19        15.35 

$`AMP PEAK 29(19Q12) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20P 
       40.08         7.33        12.39         6.58        11.93        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A3PH TCGA-BT-A3PJ 
       19.50         5.06        14.89        14.96         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0EZ TCGA-CF-A27C TCGA-CF-A47S 
        2.07        15.42        28.41         8.98         0.69         0.13 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO 
        0.07         0.10         0.07         0.10        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA 
        7.20         5.19         1.84         9.34         2.14        19.00 
TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 
      130.88        16.14        17.62        15.62        10.59         7.79 
TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
        2.20         7.82         8.22        10.49        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 
       20.02         9.67         8.28        10.55       140.81        17.98 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       48.53        76.60        32.28        24.66         0.10         0.53 
TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A3B4 TCGA-FD-A3B5 
        0.59         0.66         1.38         0.82        15.68         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SM 
        6.87         4.01        11.93        15.88        45.93        16.47 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43S TCGA-FD-A43Y 
       12.82         5.52        13.18        46.78        14.96        12.13 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       13.38        37.15        11.01         6.87         5.36         5.69 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC 
       49.68         2.66         4.83         6.38        50.66         9.30 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A61P 
        6.71         4.11         4.01         7.13         3.48         6.48 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-GC-A3BM 
       30.61         5.69        26.93        17.26         7.04         2.89 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ 
        2.24        15.81        17.75         2.66         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GV-A3JX TCGA-GV-A3QI 
       20.98         2.20         6.41         7.66         6.15         4.14 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-K4-A3WU TCGA-K4-A3WV 
        6.67         6.41        11.54         1.51         3.45         4.67 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 
        6.48        10.52         1.81         6.38         6.35         3.45 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE 
       12.23        16.67        88.93        97.45 

  AMP PEAK 29(19Q12) MUTATED AMP PEAK 29(19Q12) WILD-TYPE 
                        0.10                         0.07 
  AMP PEAK 29(19Q12) MUTATED AMP PEAK 29(19Q12) WILD-TYPE 
                      123.85                       140.81 
  AMP PEAK 29(19Q12) MUTATED AMP PEAK 29(19Q12) WILD-TYPE 
                        9.45                         8.02 
[1] "0.1 - 123.8 (9.4)" "0.1 - 140.8 (8.0)"
[1] "hr=" "1.2"
D29V2, continuous
                              vv
clus                           STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 29(19Q12) MUTATED          0       0       25        25       33
  AMP PEAK 29(19Q12) WILD-TYPE        1       2       43        47       34
D29V3, multiclass
           clus
vv          AMP PEAK 29(19Q12) MUTATED AMP PEAK 29(19Q12) WILD-TYPE
  STAGE 0A                           0                            1
  STAGE I                            0                            2
  STAGE II                          25                           43
  STAGE III                         25                           47
  STAGE IV                          33                           34
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1+T2 T3 T4
  AMP PEAK 29(19Q12) MUTATED         23 39 15
  AMP PEAK 29(19Q12) WILD-TYPE       39 62 17
D29V4, multiclass
          clus
vv         AMP PEAK 29(19Q12) MUTATED AMP PEAK 29(19Q12) WILD-TYPE
  T0+T1+T2                         23                           39
  T3                               39                           62
  T4                               15                           17
[1] 3 2
[1] 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(19Q12) MUTATED   45  9 20  3
  AMP PEAK 29(19Q12) WILD-TYPE 85 13 18  4
D29V5, multiclass
    clus
vv   AMP PEAK 29(19Q12) MUTATED AMP PEAK 29(19Q12) WILD-TYPE
  N0                         45                           85
  N1                          9                           13
  N2                         20                           18
  N3                          3                            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                           M0 M1 MX
  AMP PEAK 29(19Q12) MUTATED   43  2 40
  AMP PEAK 29(19Q12) WILD-TYPE 63  3 62
D29V6, multiclass
    clus
vv   AMP PEAK 29(19Q12) MUTATED AMP PEAK 29(19Q12) WILD-TYPE
  M0                         43                           63
  M1                          2                            3
  MX                         40                           62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                              cls
clus                            0  1
  AMP PEAK 29(19Q12) MUTATED   20 66
  AMP PEAK 29(19Q12) WILD-TYPE 30 98
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 29(19Q12) MUTATED     20   66
  AMP PEAK 29(19Q12) WILD-TYPE   30   98
        clus
vv       AMP PEAK 29(19Q12) MUTATED AMP PEAK 29(19Q12) WILD-TYPE
  FEMALE                         20                           30
  MALE                           66                           98
[1] 2 2
[1] FALSE
D29V8, continuous
D29V9, continuous
D29V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 29(19Q12) MUTATED       9                         3    68
  AMP PEAK 29(19Q12) WILD-TYPE    13                         8   102
D29V11, multiclass
                           clus
vv                          AMP PEAK 29(19Q12) MUTATED
  ASIAN                                              9
  BLACK OR AFRICAN AMERICAN                          3
  WHITE                                             68
                           clus
vv                          AMP PEAK 29(19Q12) WILD-TYPE
  ASIAN                                               13
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                              102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = AMP PEAK 30(19Q13.43) MUTATION ANALYSIS
D30V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 30(19Q13.43) MUTATED   57 23
  AMP PEAK 30(19Q13.43) WILD-TYPE 94 34
  AMP PEAK 30(19Q13.43) MUTATED AMP PEAK 30(19Q13.43) WILD-TYPE 
                             80                             128 
  AMP PEAK 30(19Q13.43) MUTATED AMP PEAK 30(19Q13.43) WILD-TYPE 
                             23                              34 
$`AMP PEAK 30(19Q13.43) MUTATED`
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20V TCGA-BT-A20X 
        2.66         6.74        19.04        32.84         5.06         8.25 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ 
        5.59         3.65        12.82        28.70         9.99         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47X TCGA-CU-A0YR 
        1.94        23.01         0.46         0.43         0.10         7.20 
TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AB 
        5.46        16.31         2.53        31.40        18.41         8.91 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
      130.88       112.44       123.85         2.20         3.98         7.82 
TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 
        9.67        17.98        64.18        67.36        15.68        30.67 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A7DV 
       43.59        15.35         0.49         0.59         0.56         1.22 
TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3SL TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43U 
       12.89         8.94        22.45         1.97        22.98        14.93 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BT TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A6TH 
        3.62        12.13        11.01         6.84        27.45         2.20 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-A3IE 
       15.19         4.08         3.25        61.94        35.24        20.12 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS 
       15.91        14.07         1.12         7.73         3.12        20.98 
TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       11.31         4.41         6.41         5.69         7.63         7.79 
TCGA-GV-A3QI TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A4AB TCGA-K4-A6MB 
        4.14        19.07         6.74        38.60         2.50         4.27 
TCGA-XF-A8HF TCGA-XF-A8HG 
       56.19        15.35 

$`AMP PEAK 30(19Q13.43) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O 
       40.08         7.33        12.39         6.58        11.93        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W 
       17.88        19.50         5.06        14.89        14.96         8.35 
TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42F TCGA-CF-A27C 
       17.16         4.67         2.07        15.42        28.41         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN 
        0.13         0.07         0.10         0.07         0.10        12.92 
TCGA-CU-A0YO TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA 
        4.90         5.19         1.84         9.34         2.14        19.00 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       87.32         8.22        10.49        50.27        21.30        20.02 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 
        8.28        10.55       140.81        48.00        48.53        76.60 
TCGA-DK-A6B5 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KF 
       32.28        26.17        24.66         0.10         0.53         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
        1.38         0.82        15.68         6.87         4.01        12.43 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN 
       11.93        15.88        45.93        24.30        16.47        12.82 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43S 
        5.52        13.18        46.78        19.79        14.93        14.96 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5C0 
       13.38        37.15         6.87         5.36         5.69         6.87 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       49.68         2.66         4.83         6.28         6.38        50.66 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z9 
        9.30         6.71         4.11         2.66         4.01         7.13 
TCGA-FJ-A3ZE TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES 
        3.48         6.48        30.61         5.69        26.93        17.26 
TCGA-G2-A3IB TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
        7.04         0.85         2.89         2.24        15.81         4.50 
TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q 
       17.75         2.66         2.10         2.20         6.41         7.66 
TCGA-GV-A3JX TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-K4-A3WS 
        6.15         6.67         6.41        11.54         1.51         8.75 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
        3.45         4.67         6.48        10.52         1.74         1.81 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        6.38         6.35         3.45        13.48        12.23        16.67 
TCGA-XF-A8HD TCGA-XF-A8HE 
       88.93        97.45 

  AMP PEAK 30(19Q13.43) MUTATED AMP PEAK 30(19Q13.43) WILD-TYPE 
                           0.10                            0.07 
  AMP PEAK 30(19Q13.43) MUTATED AMP PEAK 30(19Q13.43) WILD-TYPE 
                         130.88                          140.81 
  AMP PEAK 30(19Q13.43) MUTATED AMP PEAK 30(19Q13.43) WILD-TYPE 
                           8.96                            8.25 
[1] "0.1 - 130.9 (9.0)" "0.1 - 140.8 (8.2)"
[1] "hr=" "1"  
D30V2, continuous
                                 vv
clus                              STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 30(19Q13.43) MUTATED          0       0       21        25       33
  AMP PEAK 30(19Q13.43) WILD-TYPE        1       2       47        47       34
D30V3, multiclass
           clus
vv          AMP PEAK 30(19Q13.43) MUTATED AMP PEAK 30(19Q13.43) WILD-TYPE
  STAGE 0A                              0                               1
  STAGE I                               0                               2
  STAGE II                             21                              47
  STAGE III                            25                              47
  STAGE IV                             33                              34
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1+T2 T3 T4
  AMP PEAK 30(19Q13.43) MUTATED         18 38 16
  AMP PEAK 30(19Q13.43) WILD-TYPE       44 63 16
D30V4, multiclass
          clus
vv         AMP PEAK 30(19Q13.43) MUTATED AMP PEAK 30(19Q13.43) WILD-TYPE
  T0+T1+T2                            18                              44
  T3                                  38                              63
  T4                                  16                              16
[1] 3 2
[1] 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(19Q13.43) MUTATED   39 11 18  4
  AMP PEAK 30(19Q13.43) WILD-TYPE 91 11 20  3
D30V5, multiclass
    clus
vv   AMP PEAK 30(19Q13.43) MUTATED AMP PEAK 30(19Q13.43) WILD-TYPE
  N0                            39                              91
  N1                            11                              11
  N2                            18                              20
  N3                             4                               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                              M0 M1 MX
  AMP PEAK 30(19Q13.43) MUTATED   42  3 37
  AMP PEAK 30(19Q13.43) WILD-TYPE 64  2 65
D30V6, multiclass
    clus
vv   AMP PEAK 30(19Q13.43) MUTATED AMP PEAK 30(19Q13.43) WILD-TYPE
  M0                            42                              64
  M1                             3                               2
  MX                            37                              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"
D30V7, binary
                                 cls
clus                                0   1
  AMP PEAK 30(19Q13.43) MUTATED    20  62
  AMP PEAK 30(19Q13.43) WILD-TYPE  30 102
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 30(19Q13.43) MUTATED     20   62
  AMP PEAK 30(19Q13.43) WILD-TYPE   30  102
        clus
vv       AMP PEAK 30(19Q13.43) MUTATED AMP PEAK 30(19Q13.43) WILD-TYPE
  FEMALE                            20                              30
  MALE                              62                             102
[1] 2 2
[1] FALSE
D30V8, continuous
D30V9, continuous
D30V10, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 30(19Q13.43) MUTATED       8                         3    66
  AMP PEAK 30(19Q13.43) WILD-TYPE    14                         8   104
D30V11, multiclass
                           clus
vv                          AMP PEAK 30(19Q13.43) MUTATED
  ASIAN                                                 8
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                66
                           clus
vv                          AMP PEAK 30(19Q13.43) WILD-TYPE
  ASIAN                                                  14
  BLACK OR AFRICAN AMERICAN                               8
  WHITE                                                 104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = AMP PEAK 31(20Q11.21) MUTATION ANALYSIS
D31V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 31(20Q11.21) MUTATED   95 41
  AMP PEAK 31(20Q11.21) WILD-TYPE 56 16
  AMP PEAK 31(20Q11.21) MUTATED AMP PEAK 31(20Q11.21) WILD-TYPE 
                            136                              72 
  AMP PEAK 31(20Q11.21) MUTATED AMP PEAK 31(20Q11.21) WILD-TYPE 
                             41                              16 
$`AMP PEAK 31(20Q11.21) MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N 
       40.08         2.66         6.74         6.58        19.04        32.84 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W 
       17.88        19.50         5.06        14.89         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
        8.25         3.65         2.07        28.70         9.99        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S 
        8.98         1.94        23.01         0.46         0.43         0.13 
TCGA-CF-A47T TCGA-CF-A47X TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        0.07         0.10        12.92         4.90         7.20         5.46 
TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD 
        1.84         2.14        31.40        18.41       130.88       112.44 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
        1.81        10.59         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU 
        3.98         7.82         8.22        10.49        50.27        20.02 
TCGA-DK-A3IV TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 
        9.67        10.55        48.00        17.98        64.18        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       15.68        32.28        30.67        43.59        15.35        26.17 
TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B6 
        0.49         0.59         0.56         1.22        12.89         6.87 
TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SP 
        4.01        11.93        45.93        24.30        22.45        13.18 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43X 
       46.78        19.79         1.97        22.98        14.93         3.62 
TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O 
       13.38        11.01        27.45         6.87        49.68         4.83 
TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI 
        6.38         9.30         6.71         4.11         2.20         4.01 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
       15.19         3.48         3.25         6.48        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        5.69        35.24         0.85         2.89         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 
        4.50        15.91        14.07         1.12         2.66         7.73 
TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV 
        2.10        20.98         2.20         7.66        11.31         4.41 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
        6.41         6.15         5.69         7.63         7.79         4.14 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU 
        6.41        19.07         6.74        38.60         8.75         3.45 
TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
        4.67         6.48         1.81         3.45        13.48        12.23 
TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
       16.67        88.93        56.19        15.35 

$`AMP PEAK 31(20Q11.21) WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20U TCGA-BT-A2LA 
        7.33        12.39        11.93        12.16        14.96        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-CF-A27C TCGA-CF-A47V 
        5.59         4.67        12.82        15.42         0.69         0.10 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 
        0.07         0.10         5.19        16.31         9.34         2.53 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IT 
       19.00         8.91        16.14        17.62        15.62        21.30 
TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-E7-A3X6 TCGA-E7-A3Y1 
        8.28       140.81        48.53        76.60        24.66         0.10 
TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A3B4 TCGA-FD-A3B5 
        0.53         0.66         1.38         0.82        15.68         8.94 
TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A43S 
       12.43        15.88        16.47        12.82         5.52        14.96 
TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       14.93        12.13        37.15         6.87         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TG TCGA-FJ-A3Z9 
        6.84         2.66         6.28        50.66         2.66         7.13 
TCGA-FJ-A3ZF TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3WC 
        4.08        26.93        17.26         7.04        20.12        17.75 
TCGA-GD-A3OQ TCGA-GU-A42P TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-K4-A4AB 
        3.12         6.41         6.67        11.54         1.51         2.50 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-XF-A8HE 
       10.52         1.74         4.27         6.38         6.35        97.45 

  AMP PEAK 31(20Q11.21) MUTATED AMP PEAK 31(20Q11.21) WILD-TYPE 
                           0.07                            0.07 
  AMP PEAK 31(20Q11.21) MUTATED AMP PEAK 31(20Q11.21) WILD-TYPE 
                         130.88                          140.81 
  AMP PEAK 31(20Q11.21) MUTATED AMP PEAK 31(20Q11.21) WILD-TYPE 
                          8.300                           8.925 
[1] "0.1 - 130.9 (8.3)" "0.1 - 140.8 (8.9)"
[1] "hr=" "1.2"
D31V2, continuous
                                 vv
clus                              STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 31(20Q11.21) MUTATED          0       1       46        44       46
  AMP PEAK 31(20Q11.21) WILD-TYPE        1       1       22        28       21
D31V3, multiclass
           clus
vv          AMP PEAK 31(20Q11.21) MUTATED AMP PEAK 31(20Q11.21) WILD-TYPE
  STAGE 0A                              0                               1
  STAGE I                               1                               1
  STAGE II                             46                              22
  STAGE III                            44                              28
  STAGE IV                             46                              21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1+T2 T3 T4
  AMP PEAK 31(20Q11.21) MUTATED         41 65 20
  AMP PEAK 31(20Q11.21) WILD-TYPE       21 36 12
D31V4, multiclass
          clus
vv         AMP PEAK 31(20Q11.21) MUTATED AMP PEAK 31(20Q11.21) WILD-TYPE
  T0+T1+T2                            41                              21
  T3                                  65                              36
  T4                                  20                              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  AMP PEAK 31(20Q11.21) MUTATED   81 13 28  6
  AMP PEAK 31(20Q11.21) WILD-TYPE 49  9 10  1
D31V5, multiclass
    clus
vv   AMP PEAK 31(20Q11.21) MUTATED AMP PEAK 31(20Q11.21) WILD-TYPE
  N0                            81                              49
  N1                            13                               9
  N2                            28                              10
  N3                             6                               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                              M0 M1 MX
  AMP PEAK 31(20Q11.21) MUTATED   68  4 67
  AMP PEAK 31(20Q11.21) WILD-TYPE 38  1 35
D31V6, multiclass
    clus
vv   AMP PEAK 31(20Q11.21) MUTATED AMP PEAK 31(20Q11.21) WILD-TYPE
  M0                            68                              38
  M1                             4                               1
  MX                            67                              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"
D31V7, binary
                                 cls
clus                                0   1
  AMP PEAK 31(20Q11.21) MUTATED    34 106
  AMP PEAK 31(20Q11.21) WILD-TYPE  16  58
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 31(20Q11.21) MUTATED     34  106
  AMP PEAK 31(20Q11.21) WILD-TYPE   16   58
        clus
vv       AMP PEAK 31(20Q11.21) MUTATED AMP PEAK 31(20Q11.21) WILD-TYPE
  FEMALE                            34                              16
  MALE                             106                              58
[1] 2 2
[1] FALSE
D31V8, continuous
D31V9, continuous
D31V10, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 31(20Q11.21) MUTATED      12                         6   112
  AMP PEAK 31(20Q11.21) WILD-TYPE    10                         5    58
D31V11, multiclass
                           clus
vv                          AMP PEAK 31(20Q11.21) MUTATED
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                               112
                           clus
vv                          AMP PEAK 31(20Q11.21) WILD-TYPE
  ASIAN                                                  10
  BLACK OR AFRICAN AMERICAN                               5
  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"

Clustering(32) Variable = AMP PEAK 32(22Q11.23) MUTATION ANALYSIS
D32V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 32(22Q11.23) MUTATED    29  13
  AMP PEAK 32(22Q11.23) WILD-TYPE 122  44
  AMP PEAK 32(22Q11.23) MUTATED AMP PEAK 32(22Q11.23) WILD-TYPE 
                             42                             166 
  AMP PEAK 32(22Q11.23) MUTATED AMP PEAK 32(22Q11.23) WILD-TYPE 
                             13                              44 
$`AMP PEAK 32(22Q11.23) MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A3PJ TCGA-C4-A0F6 
       40.08         2.66         8.35         5.59        12.82        23.01 
TCGA-CU-A0YR TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IS 
        7.20        31.40       112.44        87.32         8.22        50.27 
TCGA-DK-A3IU TCGA-DK-A3WX TCGA-E7-A4IJ TCGA-E7-A541 TCGA-FD-A3B6 TCGA-FD-A3B7 
       20.02        10.55         0.49         0.59         6.87         4.01 
TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A43P TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A62O 
       22.45        12.82        14.93        11.01         5.36         4.83 
TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-GC-A3BM TCGA-GC-A3I6 
       61.94        35.24        17.26        20.12         2.89         2.24 
TCGA-GC-A3RD TCGA-GD-A2C5 TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI 
       14.07         7.73         4.41         5.69         7.79         4.14 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-HQ-A2OE TCGA-K4-A6MB TCGA-LT-A5Z6 TCGA-XF-A8HD 
        6.67         6.41        38.60         4.27         3.45        88.93 

$`AMP PEAK 32(22Q11.23) WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         6.74        12.39         6.58        11.93        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH 
       14.96         5.06         8.25        17.16         3.65         4.67 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        2.07        15.42        28.70         9.99        28.41         8.98 
TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        1.94         0.46         0.43         0.69         0.13         0.07 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO 
        0.10         0.07         0.10         0.10        12.92         4.90 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        5.46         5.19        16.31         1.84         9.34         2.53 
TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE 
        2.14        18.41        19.00         8.91       130.88        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV 
        2.20         3.98         7.82        10.49        21.30         9.67 
TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
        8.28       140.81        48.00        17.98        64.18        48.53 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC 
       76.60        67.36        15.68        32.28        30.67        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KE 
       15.35        26.17        24.66         0.10         0.53         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 
        0.66         1.38         0.82         1.22        12.89        15.68 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        8.94        12.43        11.93        15.88        45.93        24.30 
TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       16.47         5.52        13.18        46.78        19.79         1.97 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       22.98        14.96        14.93         3.62        12.13        13.38 
TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       37.15         6.87         5.69         6.84        27.45         6.87 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC 
       49.68         2.66         6.28         6.38        50.66         9.30 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 
        6.71         4.11         2.66         2.20         4.01        15.19 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ 
        7.13         3.48         4.08         3.25         6.48        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3VY TCGA-GC-A3OO TCGA-GC-A3RB 
        5.69        26.93         7.04         0.85        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ 
       15.91        17.75         1.12         2.66         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JW 
       20.98         2.20         6.41         7.66        11.31         6.41 
TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
        6.15         7.63        19.07        11.54         1.51         6.74 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        8.75         3.45         4.67         2.50         6.48        10.52 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI 
        1.74         1.81         6.38         6.35        13.48        12.23 
TCGA-PQ-A6FN TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       16.67        97.45        56.19        15.35 

  AMP PEAK 32(22Q11.23) MUTATED AMP PEAK 32(22Q11.23) WILD-TYPE 
                           0.49                            0.07 
  AMP PEAK 32(22Q11.23) MUTATED AMP PEAK 32(22Q11.23) WILD-TYPE 
                         112.44                          140.81 
  AMP PEAK 32(22Q11.23) MUTATED AMP PEAK 32(22Q11.23) WILD-TYPE 
                          8.285                           8.830 
[1] "0.5 - 112.4 (8.3)" "0.1 - 140.8 (8.8)"
[1] "hr=" "1"  
D32V2, continuous
                                 vv
clus                              STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 32(22Q11.23) MUTATED          0       1       14        15       12
  AMP PEAK 32(22Q11.23) WILD-TYPE        1       1       54        57       55
D32V3, multiclass
           clus
vv          AMP PEAK 32(22Q11.23) MUTATED AMP PEAK 32(22Q11.23) WILD-TYPE
  STAGE 0A                              0                               1
  STAGE I                               1                               1
  STAGE II                             14                              54
  STAGE III                            15                              57
  STAGE IV                             12                              55
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1+T2 T3 T4
  AMP PEAK 32(22Q11.23) MUTATED         13 20  5
  AMP PEAK 32(22Q11.23) WILD-TYPE       49 81 27
D32V4, multiclass
          clus
vv         AMP PEAK 32(22Q11.23) MUTATED AMP PEAK 32(22Q11.23) WILD-TYPE
  T0+T1+T2                            13                              49
  T3                                  20                              81
  T4                                   5                              27
[1] 3 2
[1] 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 32(22Q11.23) MUTATED    23   4   8   2
  AMP PEAK 32(22Q11.23) WILD-TYPE 107  18  30   5
D32V5, multiclass
    clus
vv   AMP PEAK 32(22Q11.23) MUTATED AMP PEAK 32(22Q11.23) WILD-TYPE
  N0                            23                             107
  N1                             4                              18
  N2                             8                              30
  N3                             2                               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                              M0 M1 MX
  AMP PEAK 32(22Q11.23) MUTATED   23  1 19
  AMP PEAK 32(22Q11.23) WILD-TYPE 83  4 83
D32V6, multiclass
    clus
vv   AMP PEAK 32(22Q11.23) MUTATED AMP PEAK 32(22Q11.23) WILD-TYPE
  M0                            23                              83
  M1                             1                               4
  MX                            19                              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"
D32V7, binary
                                 cls
clus                                0   1
  AMP PEAK 32(22Q11.23) MUTATED     7  36
  AMP PEAK 32(22Q11.23) WILD-TYPE  43 128
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 32(22Q11.23) MUTATED      7   36
  AMP PEAK 32(22Q11.23) WILD-TYPE   43  128
        clus
vv       AMP PEAK 32(22Q11.23) MUTATED AMP PEAK 32(22Q11.23) WILD-TYPE
  FEMALE                             7                              43
  MALE                              36                             128
[1] 2 2
[1] FALSE
D32V8, continuous
D32V9, continuous
D32V10, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 32(22Q11.23) MUTATED       2                         2    37
  AMP PEAK 32(22Q11.23) WILD-TYPE    20                         9   133
D32V11, multiclass
                           clus
vv                          AMP PEAK 32(22Q11.23) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                37
                           clus
vv                          AMP PEAK 32(22Q11.23) WILD-TYPE
  ASIAN                                                  20
  BLACK OR AFRICAN AMERICAN                               9
  WHITE                                                 133
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = DEL PEAK  1(1P36.11) MUTATION ANALYSIS
D33V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.11) MUTATED    28  13
  DEL PEAK  1(1P36.11) WILD-TYPE 123  44
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            41                            167 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            13                             44 
$`DEL PEAK  1(1P36.11) MUTATED`
TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20T TCGA-BT-A2LD TCGA-BT-A42B TCGA-BT-A42E 
        6.58        19.04        14.89         3.65        15.42         9.99 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47X TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A5W6 
        0.46         0.43         0.10         7.20         5.46         1.84 
TCGA-DK-A1AE TCGA-DK-A2I2 TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3WX TCGA-DK-A6B6 
       16.14         7.79        10.49        21.30        10.55        30.67 
TCGA-E5-A2PC TCGA-FD-A3B5 TCGA-FD-A3SO TCGA-FD-A43Y TCGA-FD-A5BU TCGA-FD-A5C1 
       43.59         8.94         5.52        12.13         6.87        49.68 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FJ-A3ZE TCGA-G2-A2EL TCGA-GV-A3JV TCGA-GV-A3QI 
        4.11         2.66         3.48        26.93         4.41         4.14 
TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A5RJ TCGA-K4-A6MB 
       11.54         8.75         4.67         6.48         1.74         4.27 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-XF-A8HF TCGA-XF-A8HG 
        3.45        13.48        12.23        56.19        15.35 

$`DEL PEAK  1(1P36.11) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74        12.39        11.93 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       32.84        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH 
        5.06         8.35         8.25        17.16         5.59         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
       12.82         2.07        28.70        28.41         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       23.01         0.69         0.13         0.07         0.10         0.07 
TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E 
        0.10        12.92         4.90         5.19        16.31         9.34 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
        2.53         2.14        31.40        18.41        19.00         8.91 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      130.88       112.44        17.62        15.62         1.81        10.59 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20         3.98         7.82         8.22 
TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 
       50.27        20.02         9.67         8.28       140.81        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        48.53        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       32.28        15.35        26.17        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        0.53         0.59         0.56         0.66         1.38         0.82 
TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
        1.22        12.89        15.68         6.87         4.01        12.43 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       11.93        15.88        45.93        24.30        22.45        16.47 
TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
       12.82        13.18        46.78        19.79         1.97        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       14.93        14.96        14.93         3.62        13.38        37.15 
TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       11.01         5.36         5.69         6.84        27.45         6.87 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC 
        2.66         4.83         6.28         6.38        50.66         9.30 
TCGA-FD-A6TD TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF 
        6.71         2.20         4.01        15.19         7.13         4.08 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO 
        3.25         6.48        61.94        30.61         5.69        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 
       17.26         7.04        20.12         0.85         2.89         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75         1.12 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
        2.66         7.73         2.10         3.12        20.98         2.20 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
        6.41         7.66        11.31         6.41         6.15         5.69 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO 
        7.63         7.79         6.67         6.41        19.07         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A6FZ 
        6.74        38.60         3.45         2.50        10.52         1.81 
TCGA-K4-A83P TCGA-LC-A66R TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE 
        6.38         6.35        16.67        88.93        97.45 

  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                         56.19                         140.81 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                          7.79                           8.91 
[1] "0.1 - 56.2 (7.8)"  "0.1 - 140.8 (8.9)"
[1] "hr=" "1.4"
D33V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  1(1P36.11) MUTATED          1       0       11        15       14
  DEL PEAK  1(1P36.11) WILD-TYPE        0       2       57        57       53
D33V3, multiclass
           clus
vv          DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  STAGE 0A                             1                              0
  STAGE I                              0                              2
  STAGE II                            11                             57
  STAGE III                           15                             57
  STAGE IV                            14                             53
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  DEL PEAK  1(1P36.11) MUTATED         12 24  3
  DEL PEAK  1(1P36.11) WILD-TYPE       50 77 29
D33V4, multiclass
          clus
vv         DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  T0+T1+T2                           12                             50
  T3                                 24                             77
  T4                                  3                             29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK  1(1P36.11) MUTATED    27   8   3   3
  DEL PEAK  1(1P36.11) WILD-TYPE 103  14  35   4
D33V5, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                           27                            103
  N1                            8                             14
  N2                            3                             35
  N3                            3                              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                             M0 M1 MX
  DEL PEAK  1(1P36.11) MUTATED   18  1 24
  DEL PEAK  1(1P36.11) WILD-TYPE 88  4 78
D33V6, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  M0                           18                             88
  M1                            1                              4
  MX                           24                             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"
D33V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED     8  35
  DEL PEAK  1(1P36.11) WILD-TYPE  42 129
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      8   35
  DEL PEAK  1(1P36.11) WILD-TYPE   42  129
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  FEMALE                            8                             42
  MALE                             35                            129
[1] 2 2
[1] FALSE
D33V8, continuous
D33V9, continuous
D33V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.11) MUTATED       4                         2    35
  DEL PEAK  1(1P36.11) WILD-TYPE    18                         9   135
D33V11, multiclass
                           clus
vv                          DEL PEAK  1(1P36.11) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               35
                           clus
vv                          DEL PEAK  1(1P36.11) WILD-TYPE
  ASIAN                                                 18
  BLACK OR AFRICAN AMERICAN                              9
  WHITE                                                135
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = DEL PEAK  2(1Q32.1) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1Q32.1) MUTATED    28  12
  DEL PEAK  2(1Q32.1) WILD-TYPE 123  45
  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE 
                           40                           168 
  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE 
                           12                            45 
$`DEL PEAK  2(1Q32.1) MUTATED`
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-CF-A1HS 
       32.84        14.89         8.35        12.82         2.07         0.43 
TCGA-CU-A0YO TCGA-CU-A3YL TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM 
        4.90        16.31         1.81        87.32         2.20         7.82 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3X1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E7-A4IJ 
       10.49        50.27        48.00        15.68        30.67         0.49 
TCGA-E7-A4XJ TCGA-FD-A3SL TCGA-FD-A3SR TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A62S 
        0.53        22.45        19.79         6.87         6.28         6.38 
TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-G2-A2EK TCGA-G2-A3IE TCGA-G2-A3VY 
        4.11         2.20        15.19         5.69        20.12         0.85 
TCGA-GC-A3RC TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A40E TCGA-GV-A6ZA 
       15.91         6.41         5.69         7.79         6.41        11.54 
TCGA-K4-A3WU TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-XF-A8HF 
        3.45         3.45        13.48        56.19 

$`DEL PEAK  2(1Q32.1) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       11.93        19.04        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
       14.96         5.06         8.25        17.16         5.59         3.65 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        4.67        15.42        28.70         9.99        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        1.94        23.01         0.46         0.69         0.13         0.07 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YR 
        0.10         0.07         0.10         0.10        12.92         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.46         5.19         1.84         9.34         2.53         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       31.40        18.41        19.00         8.91       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       16.14        17.62        15.62        10.59         7.79       123.85 
TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
        3.98         8.22        21.30        20.02         9.67         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       10.55       140.81        17.98        64.18        48.53        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       67.36        32.28        43.59        15.35        26.17        24.66 
TCGA-E7-A3Y1 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        0.10         0.59         0.56         0.66         1.38         0.82 
TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        1.22        12.89        15.68         8.94         6.87         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM 
       12.43        11.93        15.88        45.93        24.30        16.47 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N 
       12.82         5.52        13.18        46.78         1.97        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       14.93        14.96        14.93         3.62        12.13        13.38 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       37.15        11.01         6.87         5.36         5.69         6.84 
TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TC 
       27.45        49.68         2.66         4.83        50.66         9.30 
TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        6.71         2.66         4.01         7.13         3.48         4.08 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO 
        3.25         6.48        61.94        30.61        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       17.26         7.04         2.89         2.24        15.81         4.50 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP 
       14.07        17.75         1.12         2.66         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
        3.12        20.98         2.20         6.41         7.66        11.31 
TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G 
        4.41         6.15         7.63         4.14         6.67        19.07 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AB 
        1.51         6.74        38.60         8.75         4.67         2.50 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        6.48        10.52         1.74         1.81         4.27         6.38 
TCGA-LC-A66R TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG 
        6.35        12.23        16.67        88.93        97.45        15.35 

  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE 
                         0.43                          0.07 
  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE 
                        87.32                        140.81 
  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE 
                        7.805                         8.925 
[1] "0.4 - 87.3 (7.8)"  "0.1 - 140.8 (8.9)"
[1] "hr=" "1.2"
D34V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  2(1Q32.1) MUTATED          1       0       15        10       13
  DEL PEAK  2(1Q32.1) WILD-TYPE        0       2       53        62       54
D34V3, multiclass
           clus
vv          DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             0                             2
  STAGE II                           15                            53
  STAGE III                          10                            62
  STAGE IV                           13                            54
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  DEL PEAK  2(1Q32.1) MUTATED         10 17  6
  DEL PEAK  2(1Q32.1) WILD-TYPE       52 84 26
D34V4, multiclass
          clus
vv         DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE
  T0+T1+T2                          10                            52
  T3                                17                            84
  T4                                 6                            26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  2(1Q32.1) MUTATED    18   3   9   2
  DEL PEAK  2(1Q32.1) WILD-TYPE 112  19  29   5
D34V5, multiclass
    clus
vv   DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE
  N0                          18                           112
  N1                           3                            19
  N2                           9                            29
  N3                           2                             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                            M0 M1 MX
  DEL PEAK  2(1Q32.1) MUTATED   19  1 19
  DEL PEAK  2(1Q32.1) WILD-TYPE 87  4 83
D34V6, multiclass
    clus
vv   DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE
  M0                          19                            87
  M1                           1                             4
  MX                          19                            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"
D34V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1Q32.1) MUTATED     4  36
  DEL PEAK  2(1Q32.1) WILD-TYPE  46 128
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1Q32.1) MUTATED      4   36
  DEL PEAK  2(1Q32.1) WILD-TYPE   46  128
        clus
vv       DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE
  FEMALE                           4                            46
  MALE                            36                           128
[1] 2 2
[1] FALSE
D34V8, continuous
D34V9, continuous
D34V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1Q32.1) MUTATED       4                         1    33
  DEL PEAK  2(1Q32.1) WILD-TYPE    18                        10   137
D34V11, multiclass
                           clus
vv                          DEL PEAK  2(1Q32.1) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              33
                           clus
vv                          DEL PEAK  2(1Q32.1) WILD-TYPE
  ASIAN                                                18
  BLACK OR AFRICAN AMERICAN                            10
  WHITE                                               137
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = DEL PEAK  3(2Q22.1) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2Q22.1) MUTATED    45  18
  DEL PEAK  3(2Q22.1) WILD-TYPE 106  39
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           63                           145 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           18                            39 
$`DEL PEAK  3(2Q22.1) MUTATED`
TCGA-BL-A13I TCGA-BT-A20P TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LA 
        7.33        17.88        14.89         5.06         8.35        17.16 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A47X TCGA-CU-A0YN 
        4.67        12.82         8.98        23.01         0.10        12.92 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A2HX TCGA-DK-A2I1 
        5.46         5.19         2.53        18.41         1.81        10.59 
TCGA-DK-A3IK TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 
        2.20        50.27         9.67        17.98        64.18        67.36 
TCGA-DK-A6B6 TCGA-E5-A4U1 TCGA-E7-A541 TCGA-FD-A3B5 TCGA-FD-A3N6 TCGA-FD-A3SJ 
       30.67        26.17         0.59         8.94        15.88        24.30 
TCGA-FD-A3SR TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N 
       19.79        13.38         5.36        27.45         6.87         2.66 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF 
        4.11         2.66         2.20         4.08         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A3VY TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A6I1 
       30.61        26.93         0.85        15.81        14.07         2.66 
TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GV-A3JV TCGA-GV-A3JW 
        2.10        20.98         2.20         7.66         4.41         6.41 
TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A5RJ TCGA-K4-A6FZ 
        5.69         6.67         3.45         6.48         1.74         1.81 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-XF-A8HG 
        3.45        13.48        15.35 

$`DEL PEAK  3(2Q22.1) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         2.66         6.74        12.39         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       19.04        32.84        12.16        19.50         5.06        14.96 
TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
        8.25         5.59         3.65         2.07        15.42        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        9.99        28.41         1.94         0.46         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YO 
        0.13         0.07         0.10         0.07         0.10         4.90 
TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 
        7.20        16.31         1.84         9.34         2.14        31.40 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00         8.91       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IM 
       15.62         7.79       123.85        87.32         3.98         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX 
        8.22        10.49        21.30        20.02         8.28        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 
      140.81        48.00        48.53        76.60        15.68        32.28 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       43.59        15.35        24.66         0.10         0.49         0.53 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 
        0.56         0.66         1.38         0.82         1.22        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3NA 
       15.68         6.87         4.01        12.43        11.93        45.93 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       22.45        16.47        12.82         5.52        13.18        46.78 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
        1.97        22.98        14.93        14.96        14.93         3.62 
TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY 
       12.13        37.15        11.01         6.87         5.69         6.84 
TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC 
       49.68         4.83         6.28         6.38        50.66         9.30 
TCGA-FD-A6TD TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE 
        6.71         4.01        15.19         7.13         3.48         3.25 
TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3BM 
        5.69        35.24        17.26         7.04        20.12         2.89 
TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 
        2.24         4.50        15.91        17.75         1.12         7.73 
TCGA-GD-A3OQ TCGA-GU-A42P TCGA-GU-A42R TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH 
        3.12         6.41        11.31         6.15         7.63         7.79 
TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
        4.14         6.41        19.07        11.54         1.51         6.74 
TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A6MB 
       38.60         8.75         4.67         2.50        10.52         4.27 
TCGA-K4-A83P TCGA-LC-A66R TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE 
        6.38         6.35        12.23        16.67        88.93        97.45 
TCGA-XF-A8HF 
       56.19 

  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                        67.36                        140.81 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                         7.66                          8.91 
[1] "0.1 - 67.4 (7.7)"  "0.1 - 140.8 (8.9)"
[1] "hr=" "1.2"
D35V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  3(2Q22.1) MUTATED          0       0       24        18       23
  DEL PEAK  3(2Q22.1) WILD-TYPE        1       2       44        54       44
D35V3, multiclass
           clus
vv          DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  STAGE 0A                            0                             1
  STAGE I                             0                             2
  STAGE II                           24                            44
  STAGE III                          18                            54
  STAGE IV                           23                            44
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  DEL PEAK  3(2Q22.1) MUTATED         19 31  6
  DEL PEAK  3(2Q22.1) WILD-TYPE       43 70 26
D35V4, multiclass
          clus
vv         DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  T0+T1+T2                          19                            43
  T3                                31                            70
  T4                                 6                            26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK  3(2Q22.1) MUTATED   35  6 16  2
  DEL PEAK  3(2Q22.1) WILD-TYPE 95 16 22  5
D35V5, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  N0                          35                            95
  N1                           6                            16
  N2                          16                            22
  N3                           2                             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                            M0 M1 MX
  DEL PEAK  3(2Q22.1) MUTATED   34  1 29
  DEL PEAK  3(2Q22.1) WILD-TYPE 72  4 73
D35V6, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  M0                          34                            72
  M1                           1                             4
  MX                          29                            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"
D35V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED    19  46
  DEL PEAK  3(2Q22.1) WILD-TYPE  31 118
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     19   46
  DEL PEAK  3(2Q22.1) WILD-TYPE   31  118
        clus
vv       DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  FEMALE                          19                            31
  MALE                            46                           118
[1] 2 2
[1] FALSE
D35V8, continuous
D35V9, continuous
D35V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(2Q22.1) MUTATED       6                         3    52
  DEL PEAK  3(2Q22.1) WILD-TYPE    16                         8   118
D35V11, multiclass
                           clus
vv                          DEL PEAK  3(2Q22.1) MUTATED
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              52
                           clus
vv                          DEL PEAK  3(2Q22.1) WILD-TYPE
  ASIAN                                                16
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                               118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = DEL PEAK  4(2Q37.1) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  4(2Q37.1) MUTATED   75 30
  DEL PEAK  4(2Q37.1) WILD-TYPE 76 27
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                          105                           103 
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                           30                            27 
$`DEL PEAK  4(2Q37.1) MUTATED`
TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20V 
        2.66        19.04        32.84        19.50        14.89         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C 
        8.35         8.25        17.16         4.67        15.42        28.70 
TCGA-BT-A42E TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47X TCGA-CU-A0YN 
        9.99         8.98         0.46         0.43         0.10        12.92 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A5 
        7.20         5.46         5.19        16.31         1.84         2.14 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A3IK 
      130.88       112.44        15.62         1.81        10.59         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        3.98         7.82        50.27        21.30        20.02         9.67 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 
       17.98        64.18        48.53        67.36        32.28        30.67 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE 
       15.35        26.17        24.66         0.49         0.59         0.56 
TCGA-E7-A7DV TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SN 
        1.22        15.68         8.94        11.93        24.30        12.82 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BY 
       19.79         1.97         3.62        13.38         5.36         6.84 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       27.45         6.87         2.66         9.30         6.71         4.11 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EK 
        2.66         2.20         4.08         6.48        61.94         5.69 
TCGA-G2-A2EL TCGA-G2-A3VY TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       26.93         0.85        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A3OP TCGA-GU-A42P TCGA-GV-A3JV TCGA-GV-A3JW 
       17.75         1.12         2.10         6.41         4.41         6.41 
TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G 
        6.15         7.63         7.79         4.14         6.67        19.07 
TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC 
       11.54        38.60         8.75         3.45         4.67         6.48 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-LC-A66R TCGA-LT-A5Z6 
       10.52         1.74         1.81         4.27         6.35         3.45 
TCGA-MV-A51V TCGA-PQ-A6FN TCGA-XF-A8HG 
       13.48        16.67        15.35 

$`DEL PEAK  4(2Q37.1) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         6.74        12.39         6.58        11.93 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A2LB TCGA-BT-A2LD 
       12.16        17.88         5.06        14.96         5.59         3.65 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C 
       12.82         2.07        28.41         1.94        23.01         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YO 
        0.13         0.07         0.10         0.07         0.10         4.90 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
        9.34         2.53        31.40        18.41        19.00         8.91 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IN 
       16.14        17.62         7.79       123.85        87.32         8.22 
TCGA-DK-A3IQ TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6B0 
       10.49         8.28        10.55       140.81        48.00        76.60 
TCGA-DK-A6B2 TCGA-E5-A2PC TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A677 
       15.68        43.59         0.10         0.53         0.66         1.38 
TCGA-E7-A678 TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 
        0.82        12.89         6.87         4.01        12.43        15.88 
TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       45.93        22.45        16.47         5.52        13.18        46.78 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BS 
       22.98        14.93        14.96        14.93        12.13        37.15 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P 
       11.01         6.87         5.69        49.68         4.83         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        6.38        50.66         4.01        15.19         7.13         3.48 
TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
        3.25        30.61        35.24        17.26         7.04        20.12 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS 
        2.89         2.24         2.66         7.73         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JZ TCGA-GV-A40E TCGA-H4-A2HO 
        2.20         7.66        11.31         5.69         6.41         1.51 
TCGA-H4-A2HQ TCGA-K4-A4AB TCGA-K4-A83P TCGA-PQ-A6FI TCGA-XF-A8HD TCGA-XF-A8HE 
        6.74         2.50         6.38        12.23        88.93        97.45 
TCGA-XF-A8HF 
       56.19 

  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                       130.88                        140.81 
  DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE 
                         8.25                          9.34 
[1] "0.1 - 130.9 (8.2)" "0.1 - 140.8 (9.3)"
[1] "hr=" "1.2"
D36V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  4(2Q37.1) MUTATED          1       0       37        30       37
  DEL PEAK  4(2Q37.1) WILD-TYPE        0       2       31        42       30
D36V3, multiclass
           clus
vv          DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             0                             2
  STAGE II                           37                            31
  STAGE III                          30                            42
  STAGE IV                           37                            30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  DEL PEAK  4(2Q37.1) MUTATED         34 48 16
  DEL PEAK  4(2Q37.1) WILD-TYPE       28 53 16
D36V4, multiclass
          clus
vv         DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  T0+T1+T2                          34                            28
  T3                                48                            53
  T4                                16                            16
[1] 3 2
[1] 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(2Q37.1) MUTATED   63 10 25  2
  DEL PEAK  4(2Q37.1) WILD-TYPE 67 12 13  5
D36V5, multiclass
    clus
vv   DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  N0                          63                            67
  N1                          10                            12
  N2                          25                            13
  N3                           2                             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                            M0 M1 MX
  DEL PEAK  4(2Q37.1) MUTATED   54  1 52
  DEL PEAK  4(2Q37.1) WILD-TYPE 52  4 50
D36V6, multiclass
    clus
vv   DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  M0                          54                            52
  M1                           1                             4
  MX                          52                            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"
D36V7, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.1) MUTATED   20 88
  DEL PEAK  4(2Q37.1) WILD-TYPE 30 76
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.1) MUTATED     20   88
  DEL PEAK  4(2Q37.1) WILD-TYPE   30   76
        clus
vv       DEL PEAK  4(2Q37.1) MUTATED DEL PEAK  4(2Q37.1) WILD-TYPE
  FEMALE                          20                            30
  MALE                            88                            76
[1] 2 2
[1] FALSE
D36V8, continuous
D36V9, continuous
D36V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q37.1) MUTATED      11                         4    85
  DEL PEAK  4(2Q37.1) WILD-TYPE    11                         7    85
D36V11, multiclass
                           clus
vv                          DEL PEAK  4(2Q37.1) MUTATED
  ASIAN                                              11
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              85
                           clus
vv                          DEL PEAK  4(2Q37.1) WILD-TYPE
  ASIAN                                                11
  BLACK OR AFRICAN AMERICAN                             7
  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"

Clustering(37) Variable = DEL PEAK  5(3P21.31) MUTATION ANALYSIS
D37V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  5(3P21.31) MUTATED    47  18
  DEL PEAK  5(3P21.31) WILD-TYPE 104  39
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                            65                            143 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                            18                             39 
$`DEL PEAK  5(3P21.31) MUTATED`
TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A42C 
        6.74        19.04        14.89         5.06         8.25        28.70 
TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A47X TCGA-CU-A0YN 
        9.99         8.98         1.94         0.43         0.10        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1AB 
        4.90         7.20         5.46        16.31        31.40         8.91 
TCGA-DK-A2I2 TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A6AV 
        7.79         7.82        10.49        10.55        48.00        64.18 
TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B4 TCGA-FD-A3B6 
       32.28        43.59         0.59         1.22        15.68         6.87 
TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A43Y TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.93        24.30        12.13         5.36         6.84        27.45 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TG TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EJ 
       49.68         6.28         2.66         3.48        61.94        30.61 
TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 
       26.93        17.26         7.04         0.85         2.89         2.24 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        4.50        17.75         1.12         2.20         7.66        11.31 
TCGA-GV-A3JW TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WV 
        6.41        11.54         6.74        38.60         8.75         4.67 
TCGA-K4-A4AC TCGA-LC-A66R TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD 
        6.48         6.35        12.23        16.67        88.93 

$`DEL PEAK  5(3P21.31) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66        12.39         6.58        11.93 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       32.84        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
        8.35        17.16         5.59         3.65         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C 
        2.07        15.42        28.41        23.01         0.46         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A3QU 
        0.13         0.07         0.10         0.07         0.10         5.19 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AA 
        1.84         9.34         2.53         2.14        18.41        19.00 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
      130.88       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN 
       10.59       123.85        87.32         2.20         3.98         8.22 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY 
       50.27        21.30        20.02         9.67         8.28       140.81 
TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 
       17.98        48.53        76.60        67.36        15.68        30.67 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        26.17        24.66         0.10         0.49         0.53 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A3B3 TCGA-FD-A3B5 
        0.56         0.66         1.38         0.82        12.89         8.94 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM 
        4.01        12.43        15.88        45.93        22.45        16.47 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       12.82         5.52        13.18        46.78        19.79         1.97 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR 
       22.98        14.93        14.96        14.93         3.62        13.38 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A62N 
       37.15        11.01         6.87         5.69         6.87         2.66 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        4.83         6.38        50.66         9.30         6.71         4.11 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A3EE 
        2.20         4.01        15.19         7.13         4.08         3.25 
TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3IE TCGA-GC-A3OO TCGA-GC-A3RC 
        6.48         5.69        35.24        20.12        15.81        15.91 
TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
       14.07         2.66         7.73         2.10         3.12        20.98 
TCGA-GU-A42P TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        6.41         4.41         6.15         5.69         7.63         7.79 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-K4-A3WU 
        4.14         6.67         6.41        19.07         1.51         3.45 
TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        2.50        10.52         1.74         1.81         4.27         6.38 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
        3.45        13.48        97.45        56.19        15.35 

  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                         88.93                         140.81 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                          8.75                           8.35 
[1] "0.1 - 88.9 (8.8)"  "0.1 - 140.8 (8.3)"
[1] "hr=" "1"  
D37V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  5(3P21.31) MUTATED          1       0       21        22       19
  DEL PEAK  5(3P21.31) WILD-TYPE        0       2       47        50       48
D37V3, multiclass
           clus
vv          DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  STAGE 0A                             1                              0
  STAGE I                              0                              2
  STAGE II                            21                             47
  STAGE III                           22                             50
  STAGE IV                            19                             48
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  DEL PEAK  5(3P21.31) MUTATED         19 28  9
  DEL PEAK  5(3P21.31) WILD-TYPE       43 73 23
D37V4, multiclass
          clus
vv         DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  T0+T1+T2                           19                             43
  T3                                 28                             73
  T4                                  9                             23
[1] 3 2
[1] 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(3P21.31) MUTATED   41  6  9  3
  DEL PEAK  5(3P21.31) WILD-TYPE 89 16 29  4
D37V5, multiclass
    clus
vv   DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  N0                           41                             89
  N1                            6                             16
  N2                            9                             29
  N3                            3                              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                             M0 M1 MX
  DEL PEAK  5(3P21.31) MUTATED   30  3 31
  DEL PEAK  5(3P21.31) WILD-TYPE 76  2 71
D37V6, multiclass
    clus
vv   DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  M0                           30                             76
  M1                            3                              2
  MX                           31                             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"
D37V7, binary
                                cls
clus                               0   1
  DEL PEAK  5(3P21.31) MUTATED    19  46
  DEL PEAK  5(3P21.31) WILD-TYPE  31 118
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3P21.31) MUTATED     19   46
  DEL PEAK  5(3P21.31) WILD-TYPE   31  118
        clus
vv       DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  FEMALE                           19                             31
  MALE                             46                            118
[1] 2 2
[1] FALSE
D37V8, continuous
D37V9, continuous
D37V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(3P21.31) MUTATED       4                         5    51
  DEL PEAK  5(3P21.31) WILD-TYPE    18                         6   119
D37V11, multiclass
                           clus
vv                          DEL PEAK  5(3P21.31) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               51
                           clus
vv                          DEL PEAK  5(3P21.31) WILD-TYPE
  ASIAN                                                 18
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                119
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = DEL PEAK  6(3P14.2) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(3P14.2) MUTATED    47  16
  DEL PEAK  6(3P14.2) WILD-TYPE 104  41
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           63                           145 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           16                            41 
$`DEL PEAK  6(3P14.2) MUTATED`
TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A42B TCGA-BT-A42C 
       14.89         5.06         8.35         8.25        15.42        28.70 
TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A0YR 
        9.99         8.98         1.94         0.43        12.92         7.20 
TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A2I2 TCGA-DK-A3IM 
        5.46        16.31        31.40         8.91         7.79         7.82 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A6B5 TCGA-E5-A2PC 
       10.49        50.27        10.55        48.00        32.28        43.59 
TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3SJ 
        0.59         1.22        15.68         6.87        11.93        24.30 
TCGA-FD-A3SN TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ 
       12.82        22.98        12.13         5.36         6.84        27.45 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TG TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EJ 
       49.68         6.28         2.66         3.48        61.94        30.61 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3I6 TCGA-GC-A3RB 
       17.26         7.04        20.12         0.85         2.24         4.50 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GV-A3JW TCGA-GV-A6ZA 
       17.75         1.12         2.20         7.66         6.41        11.54 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A6MB 
        6.74        38.60         8.75         4.67         6.48         4.27 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD 
       12.23        16.67        88.93 

$`DEL PEAK  6(3P14.2) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       11.93        19.04        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        5.06        14.96        17.16         5.59         3.65         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C 
       12.82         2.07        28.41        23.01         0.46         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
        0.13         0.07         0.10         0.07         0.10         0.10 
TCGA-CU-A0YO TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        4.90         5.19         1.84         9.34         2.53         2.14 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       18.41        19.00       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
       15.62         1.81        10.59       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
        3.98         8.22        21.30        20.02         9.67         8.28 
TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
      140.81        17.98        64.18        48.53        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       15.68        30.67        15.35        26.17        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        0.49         0.53         0.56         0.66         1.38         0.82 
TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA 
       12.89         8.94         4.01        12.43        15.88        45.93 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       22.45        16.47         5.52        13.18        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR 
        1.97        14.93        14.96        14.93         3.62        13.38 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A62N 
       37.15        11.01         6.87         5.69         6.87         2.66 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        4.83         6.38        50.66         9.30         6.71         4.11 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A3EE 
        2.20         4.01        15.19         7.13         4.08         3.25 
TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-GC-A3BM TCGA-GC-A3OO 
        6.48         5.69        26.93        35.24         2.89        15.81 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       15.91        14.07         2.66         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ 
       20.98         6.41        11.31         4.41         6.15         5.69 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
        7.63         7.79         4.14         6.67         6.41        19.07 
TCGA-H4-A2HO TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
        1.51         3.45         2.50        10.52         1.74         1.81 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-XF-A8HE TCGA-XF-A8HF 
        6.38         6.35         3.45        13.48        97.45        56.19 
TCGA-XF-A8HG 
       15.35 

  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                         0.43                          0.07 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                        88.93                        140.81 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                         8.98                          7.79 
[1] "0.4 - 88.9 (9.0)"  "0.1 - 140.8 (7.8)"
[1] "hr=" "1.2"
D38V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  6(3P14.2) MUTATED          1       0       18        22       21
  DEL PEAK  6(3P14.2) WILD-TYPE        0       2       50        50       46
D38V3, multiclass
           clus
vv          DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             0                             2
  STAGE II                           18                            50
  STAGE III                          22                            50
  STAGE IV                           21                            46
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  DEL PEAK  6(3P14.2) MUTATED         17 31  8
  DEL PEAK  6(3P14.2) WILD-TYPE       45 70 24
D38V4, multiclass
          clus
vv         DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  T0+T1+T2                          17                            45
  T3                                31                            70
  T4                                 8                            24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK  6(3P14.2) MUTATED   39  8  7  4
  DEL PEAK  6(3P14.2) WILD-TYPE 91 14 31  3
D38V5, multiclass
    clus
vv   DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  N0                          39                            91
  N1                           8                            14
  N2                           7                            31
  N3                           4                             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                            M0 M1 MX
  DEL PEAK  6(3P14.2) MUTATED   27  3 33
  DEL PEAK  6(3P14.2) WILD-TYPE 79  2 69
D38V6, multiclass
    clus
vv   DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  M0                          27                            79
  M1                           3                             2
  MX                          33                            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"
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P14.2) MUTATED    18  46
  DEL PEAK  6(3P14.2) WILD-TYPE  32 118
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED     18   46
  DEL PEAK  6(3P14.2) WILD-TYPE   32  118
        clus
vv       DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  FEMALE                          18                            32
  MALE                            46                           118
[1] 2 2
[1] FALSE
D38V8, continuous
D38V9, continuous
D38V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(3P14.2) MUTATED       2                         5    52
  DEL PEAK  6(3P14.2) WILD-TYPE    20                         6   118
D38V11, multiclass
                           clus
vv                          DEL PEAK  6(3P14.2) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              52
                           clus
vv                          DEL PEAK  6(3P14.2) WILD-TYPE
  ASIAN                                                20
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                               118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = DEL PEAK  7(3P13) MUTATION ANALYSIS
D39V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  7(3P13) MUTATED    44  14
  DEL PEAK  7(3P13) WILD-TYPE 107  43
  DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE 
                         58                         150 
  DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE 
                         14                          43 
$`DEL PEAK  7(3P13) MUTATED`
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A42B 
       32.84        14.89         5.06         8.35         8.25        15.42 
TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CU-A0YN TCGA-CU-A0YR 
       28.70         9.99         8.98         1.94        12.92         7.20 
TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A2I2 TCGA-DK-A3IM 
        5.46        16.31        31.40         8.91         7.79         7.82 
TCGA-DK-A3IQ TCGA-DK-A3WX TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A541 
       10.49        10.55        32.28        43.59         0.49         0.59 
TCGA-E7-A7DV TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SN 
        1.22        15.68         6.87        11.93        24.30        12.82 
TCGA-FD-A43Y TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA 
       12.13         5.36         6.84        49.68         6.28        50.66 
TCGA-FD-A6TG TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A3IB 
        2.66         3.48        61.94        30.61         5.69         7.04 
TCGA-G2-A3VY TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A6C6 
        0.85         2.24         4.50        17.75         1.12         2.20 
TCGA-GV-A3JW TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AC 
        6.41         6.74        38.60         8.75         4.67         6.48 
TCGA-LC-A66R TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD 
        6.35        12.23        16.67        88.93 

$`DEL PEAK  7(3P13) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       11.93        19.04        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
       14.96        17.16         5.59         3.65         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        2.07        28.41        23.01         0.46         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
        0.13         0.07         0.10         0.07         0.10         0.10 
TCGA-CU-A0YO TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        4.90         5.19         1.84         9.34         2.53         2.14 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       18.41        19.00       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
       15.62         1.81        10.59       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        3.98         8.22        50.27        21.30        20.02         9.67 
TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
        8.28       140.81        48.00        17.98        64.18        48.53 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 
       76.60        67.36        15.68        30.67        15.35        26.17 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
       24.66         0.10         0.53         0.56         0.66         1.38 
TCGA-E7-A678 TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 
        0.82        12.89         8.94         4.01        12.43        15.88 
TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       45.93        22.45        16.47         5.52        13.18        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79         1.97        22.98        14.93        14.96        14.93 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
        3.62        13.38        37.15        11.01         6.87         5.69 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TC 
       27.45         6.87         2.66         4.83         6.38         9.30 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        6.71         4.11         2.20         4.01        15.19         7.13 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
        4.08         3.25         6.48        26.93        35.24        17.26 
TCGA-G2-A3IE TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 
       20.12         2.89        15.81        15.91        14.07         2.66 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A42Q 
        7.73         2.10         3.12        20.98         6.41         7.66 
TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       11.31         4.41         6.15         5.69         7.63         7.79 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
        4.14         6.67         6.41        19.07        11.54         1.51 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
        3.45         2.50        10.52         1.74         1.81         4.27 
TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
        6.38         3.45        13.48        97.45        56.19        15.35 

  DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE 
                       0.49                        0.07 
  DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE 
                      88.93                      140.81 
  DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE 
                       8.55                        8.61 
[1] "0.5 - 88.9 (8.6)"  "0.1 - 140.8 (8.6)"
[1] "hr=" "1.2"
D39V2, continuous
                             vv
clus                          STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  7(3P13) MUTATED          0       0       17        20       21
  DEL PEAK  7(3P13) WILD-TYPE        1       2       51        52       46
D39V3, multiclass
           clus
vv          DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE
  STAGE 0A                          0                           1
  STAGE I                           0                           2
  STAGE II                         17                          51
  STAGE III                        20                          52
  STAGE IV                         21                          46
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1+T2 T3 T4
  DEL PEAK  7(3P13) MUTATED         16 26  9
  DEL PEAK  7(3P13) WILD-TYPE       46 75 23
D39V4, multiclass
          clus
vv         DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE
  T0+T1+T2                        16                          46
  T3                              26                          75
  T4                               9                          23
[1] 3 2
[1] 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(3P13) MUTATED   34  6  9  4
  DEL PEAK  7(3P13) WILD-TYPE 96 16 29  3
D39V5, multiclass
    clus
vv   DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE
  N0                        34                          96
  N1                         6                          16
  N2                         9                          29
  N3                         4                           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                          M0 M1 MX
  DEL PEAK  7(3P13) MUTATED   24  3 31
  DEL PEAK  7(3P13) WILD-TYPE 82  2 71
D39V6, multiclass
    clus
vv   DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE
  M0                        24                          82
  M1                         3                           2
  MX                        31                          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"
D39V7, binary
                             cls
clus                            0   1
  DEL PEAK  7(3P13) MUTATED    15  44
  DEL PEAK  7(3P13) WILD-TYPE  35 120
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3P13) MUTATED     15   44
  DEL PEAK  7(3P13) WILD-TYPE   35  120
        clus
vv       DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE
  FEMALE                        15                          35
  MALE                          44                         120
[1] 2 2
[1] FALSE
D39V8, continuous
D39V9, continuous
D39V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(3P13) MUTATED       2                         5    45
  DEL PEAK  7(3P13) WILD-TYPE    20                         6   125
D39V11, multiclass
                           clus
vv                          DEL PEAK  7(3P13) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         5
  WHITE                                            45
                           clus
vv                          DEL PEAK  7(3P13) WILD-TYPE
  ASIAN                                              20
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                             125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(40) Variable = DEL PEAK  8(4Q22.1) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  8(4Q22.1) MUTATED   64 23
  DEL PEAK  8(4Q22.1) WILD-TYPE 87 34
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                           87                           121 
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                           23                            34 
$`DEL PEAK  8(4Q22.1) MUTATED`
TCGA-BL-A13I TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A2LD 
        7.33         5.06        14.96         5.06         5.59         3.65 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0F0 
        4.67        12.82        15.42        28.70        28.41         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47V TCGA-CU-A0YN TCGA-CU-A0YO 
       23.01         0.46         0.43         0.10        12.92         4.90 
TCGA-CU-A0YR TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 
        7.20         2.53        18.41       112.44         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
        7.79        87.32         2.20         7.82         8.22        10.49 
TCGA-DK-A3IT TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       21.30        17.98        64.18        15.68        32.28        30.67 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A541 TCGA-FD-A3B3 
       43.59        15.35        26.17        24.66         0.59        12.89 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SO TCGA-FD-A43Y 
        6.87         4.01        24.30        22.45         5.52        12.13 
TCGA-FD-A5BR TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
       13.38         6.84        49.68         2.66         4.83         6.28 
TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
        6.38         9.30         2.66         2.20        15.19         4.08 
TCGA-G2-A2EF TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-GC-A3BM 
       61.94        26.93        35.24        17.26         7.04         2.89 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A6C6 TCGA-GU-A42Q 
       15.81         4.50         2.66         7.73         2.20         7.66 
TCGA-GV-A3JV TCGA-GV-A3QH TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A3WV 
        4.41         7.79        11.54         6.74         8.75         4.67 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-PQ-A6FI 
        6.48        10.52         1.74         1.81         4.27        12.23 
TCGA-PQ-A6FN TCGA-XF-A8HF TCGA-XF-A8HG 
       16.67        56.19        15.35 

$`DEL PEAK  8(4Q22.1) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         2.66         6.74        12.39         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T 
       19.04        32.84        12.16        17.88        19.50        14.89 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PK TCGA-BT-A42E TCGA-C4-A0EZ 
        8.35         8.25        17.16         2.07         9.99         8.98 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
        0.69         0.13         0.07         0.07         0.10         0.10 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 
        5.46         5.19        16.31         1.84         9.34         2.14 
TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF 
       31.40        19.00         8.91       130.88        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV 
       15.62       123.85         3.98        50.27        20.02         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 
        8.28        10.55       140.81        48.00        48.53        76.60 
TCGA-DK-A6B1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF 
       67.36         0.10         0.49         0.53         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 
        1.38         0.82         1.22        15.68         8.94        12.43 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP 
       11.93        15.88        45.93        16.47        12.82        13.18 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79         1.97        22.98        14.93        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
       14.93         3.62        37.15        11.01         6.87         5.36 
TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TE 
        5.69        27.45         6.87        50.66         6.71         4.11 
TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ 
        4.01         7.13         3.48         3.25         6.48        30.61 
TCGA-G2-A2EK TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD 
        5.69        20.12         0.85         2.24        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42P 
       17.75         1.12         2.10         3.12        20.98         6.41 
TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI 
       11.31         6.41         6.15         5.69         7.63         4.14 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WU 
        6.67         6.41        19.07         1.51        38.60         3.45 
TCGA-K4-A4AB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-XF-A8HD 
        2.50         6.38         6.35         3.45        13.48        88.93 
TCGA-XF-A8HE 
       97.45 

  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                       112.44                        140.81 
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                         7.82                          8.94 
[1] "0.1 - 112.4 (7.8)" "0.1 - 140.8 (8.9)"
[1] "hr=" "1"  
D40V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  8(4Q22.1) MUTATED          1       0       27        29       30
  DEL PEAK  8(4Q22.1) WILD-TYPE        0       2       41        43       37
D40V3, multiclass
           clus
vv          DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             0                             2
  STAGE II                           27                            41
  STAGE III                          29                            43
  STAGE IV                           30                            37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  DEL PEAK  8(4Q22.1) MUTATED         25 47  9
  DEL PEAK  8(4Q22.1) WILD-TYPE       37 54 23
D40V4, multiclass
          clus
vv         DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  T0+T1+T2                          25                            37
  T3                                47                            54
  T4                                 9                            23
[1] 3 2
[1] 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(4Q22.1) MUTATED   53 10 19  2
  DEL PEAK  8(4Q22.1) WILD-TYPE 77 12 19  5
D40V5, multiclass
    clus
vv   DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  N0                          53                            77
  N1                          10                            12
  N2                          19                            19
  N3                           2                             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                            M0 M1 MX
  DEL PEAK  8(4Q22.1) MUTATED   45  2 42
  DEL PEAK  8(4Q22.1) WILD-TYPE 61  3 60
D40V6, multiclass
    clus
vv   DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  M0                          45                            61
  M1                           2                             3
  MX                          42                            60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q22.1) MUTATED    25  64
  DEL PEAK  8(4Q22.1) WILD-TYPE  25 100
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.1) MUTATED     25   64
  DEL PEAK  8(4Q22.1) WILD-TYPE   25  100
        clus
vv       DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  FEMALE                          25                            25
  MALE                            64                           100
[1] 2 2
[1] FALSE
D40V8, continuous
D40V9, continuous
D40V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(4Q22.1) MUTATED       7                         5    71
  DEL PEAK  8(4Q22.1) WILD-TYPE    15                         6    99
D40V11, multiclass
                           clus
vv                          DEL PEAK  8(4Q22.1) MUTATED
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              71
                           clus
vv                          DEL PEAK  8(4Q22.1) WILD-TYPE
  ASIAN                                                15
  BLACK OR AFRICAN AMERICAN                             6
  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"

Clustering(41) Variable = DEL PEAK  9(4Q34.2) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  9(4Q34.2) MUTATED   73 22
  DEL PEAK  9(4Q34.2) WILD-TYPE 78 35
  DEL PEAK  9(4Q34.2) MUTATED DEL PEAK  9(4Q34.2) WILD-TYPE 
                           95                           113 
  DEL PEAK  9(4Q34.2) MUTATED DEL PEAK  9(4Q34.2) WILD-TYPE 
                           22                            35 
$`DEL PEAK  9(4Q34.2) MUTATED`
TCGA-BL-A13J TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W 
        2.66        32.84         5.06        14.89         5.06         8.35 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        5.59         3.65         4.67        15.42        28.70         9.99 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S TCGA-CU-A0YN 
       28.41         1.94         0.46         0.43         0.13        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE 
        4.90         7.20         2.53        18.41       112.44        16.14 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM 
        1.81        10.59         7.79        87.32         2.20         7.82 
TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
        8.22        21.30        64.18        15.68        32.28        30.67 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A541 TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 
       43.59        15.35         0.59        12.89         6.87         4.01 
TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A5BR 
       22.45        12.82         5.52        22.98        12.13        13.38 
TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
        6.84        49.68         2.66         4.83         6.28         6.38 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       50.66         9.30         6.71         4.11         2.66         2.20 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A2EF TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE 
       15.19         4.08        61.94        26.93         7.04        20.12 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC 
        0.85         2.89        15.81         4.50        15.91        17.75 
TCGA-GD-A2C5 TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW 
        7.73         2.20         7.66        11.31         4.41         6.41 
TCGA-GV-A3QH TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS 
        7.79        19.07        11.54         6.74        38.60         8.75 
TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
        4.67         6.48        10.52         1.74         1.81         4.27 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-XF-A8HF TCGA-XF-A8HG 
        3.45        13.48        16.67        56.19        15.35 

$`DEL PEAK  9(4Q34.2) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         6.74        12.39         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20X 
       19.04        12.16        17.88        19.50        14.96         8.25 
TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A27C 
       17.16        12.82         2.07         8.98        23.01         0.69 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A3KJ 
        0.07         0.10         0.07         0.10         0.10         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 
        5.19        16.31         1.84         9.34         2.14        31.40 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I4 
       19.00         8.91       130.88        17.62        15.62       123.85 
TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
        3.98        10.49        50.27        20.02         9.67         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 
       10.55       140.81        48.00        17.98        48.53        76.60 
TCGA-DK-A6B1 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       67.36        26.17        24.66         0.10         0.49         0.53 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B4 
        0.56         0.66         1.38         0.82         1.22        15.68 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        8.94        12.43        11.93        15.88        45.93        24.30 
TCGA-FD-A3SM TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       16.47        13.18        46.78        19.79         1.97        14.93 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       14.96        14.93         3.62        37.15        11.01         6.87 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A6TI TCGA-FJ-A3Z9 
        5.36         5.69        27.45         6.87         4.01         7.13 
TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO 
        3.48         3.25         6.48        30.61         5.69        35.24 
TCGA-G2-A2ES TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OP 
       17.26         2.24        14.07         1.12         2.66         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42P TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        3.12        20.98         6.41         6.15         5.69         7.63 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HO TCGA-K4-A3WU TCGA-K4-A4AB 
        4.14         6.67         6.41         1.51         3.45         2.50 
TCGA-K4-A83P TCGA-LC-A66R TCGA-PQ-A6FI TCGA-XF-A8HD TCGA-XF-A8HE 
        6.38         6.35        12.23        88.93        97.45 

  DEL PEAK  9(4Q34.2) MUTATED DEL PEAK  9(4Q34.2) WILD-TYPE 
                         0.13                          0.07 
  DEL PEAK  9(4Q34.2) MUTATED DEL PEAK  9(4Q34.2) WILD-TYPE 
                       112.44                        140.81 
  DEL PEAK  9(4Q34.2) MUTATED DEL PEAK  9(4Q34.2) WILD-TYPE 
                         7.82                          8.98 
[1] "0.1 - 112.4 (7.8)" "0.1 - 140.8 (9.0)"
[1] "hr=" "1.3"
D41V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  9(4Q34.2) MUTATED          1       0       30        30       33
  DEL PEAK  9(4Q34.2) WILD-TYPE        0       2       38        42       34
D41V3, multiclass
           clus
vv          DEL PEAK  9(4Q34.2) MUTATED DEL PEAK  9(4Q34.2) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             0                             2
  STAGE II                           30                            38
  STAGE III                          30                            42
  STAGE IV                           33                            34
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  DEL PEAK  9(4Q34.2) MUTATED         25 50 10
  DEL PEAK  9(4Q34.2) WILD-TYPE       37 51 22
D41V4, multiclass
          clus
vv         DEL PEAK  9(4Q34.2) MUTATED DEL PEAK  9(4Q34.2) WILD-TYPE
  T0+T1+T2                          25                            37
  T3                                50                            51
  T4                                10                            22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK  9(4Q34.2) MUTATED   55 11 21  1
  DEL PEAK  9(4Q34.2) WILD-TYPE 75 11 17  6
D41V5, multiclass
    clus
vv   DEL PEAK  9(4Q34.2) MUTATED DEL PEAK  9(4Q34.2) WILD-TYPE
  N0                          55                            75
  N1                          11                            11
  N2                          21                            17
  N3                           1                             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"
                               vv
clus                            M0 M1 MX
  DEL PEAK  9(4Q34.2) MUTATED   42  2 52
  DEL PEAK  9(4Q34.2) WILD-TYPE 64  3 50
D41V6, multiclass
    clus
vv   DEL PEAK  9(4Q34.2) MUTATED DEL PEAK  9(4Q34.2) WILD-TYPE
  M0                          42                            64
  M1                           2                             3
  MX                          52                            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"
D41V7, binary
                               cls
clus                             0  1
  DEL PEAK  9(4Q34.2) MUTATED   22 75
  DEL PEAK  9(4Q34.2) WILD-TYPE 28 89
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q34.2) MUTATED     22   75
  DEL PEAK  9(4Q34.2) WILD-TYPE   28   89
        clus
vv       DEL PEAK  9(4Q34.2) MUTATED DEL PEAK  9(4Q34.2) WILD-TYPE
  FEMALE                          22                            28
  MALE                            75                            89
[1] 2 2
[1] FALSE
D41V8, continuous
D41V9, continuous
D41V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(4Q34.2) MUTATED       8                         5    77
  DEL PEAK  9(4Q34.2) WILD-TYPE    14                         6    93
D41V11, multiclass
                           clus
vv                          DEL PEAK  9(4Q34.2) MUTATED
  ASIAN                                               8
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              77
                           clus
vv                          DEL PEAK  9(4Q34.2) WILD-TYPE
  ASIAN                                                14
  BLACK OR AFRICAN AMERICAN                             6
  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"

Clustering(42) Variable = DEL PEAK 10(5Q11.2) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 10(5Q11.2) MUTATED   72 31
  DEL PEAK 10(5Q11.2) WILD-TYPE 79 26
  DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE 
                          103                           105 
  DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE 
                           31                            26 
$`DEL PEAK 10(5Q11.2) MUTATED`
TCGA-BL-A0C8 TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20T 
       40.08         6.58        19.04        32.84         5.06        14.89 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        5.06         8.35        17.16         5.59         3.65         4.67 
TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       12.82        15.42         9.99        23.01         0.46         0.43 
TCGA-CU-A3QU TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I4 
        5.19         2.14        18.41       112.44        10.59       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20         3.98         7.82         8.22        10.49 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WX TCGA-DK-A3X1 
       50.27        21.30        20.02         9.67        10.55        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ 
       17.98        64.18        15.68        32.28        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B5 
       26.17        24.66         0.49         0.59         1.22         8.94 
TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SP 
        6.87        11.93        24.30        22.45        16.47        13.18 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BY 
       19.79         1.97        14.93        13.38         5.36         6.84 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TC 
       27.45         6.87         2.66         4.83         6.38         9.30 
TCGA-FD-A6TG TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF 
        2.66        15.19         3.48         4.08         6.48        61.94 
TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3VY TCGA-GC-A3OO TCGA-GC-A3YS TCGA-GC-A6I1 
       26.93         7.04         0.85        15.81         1.12         2.66 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GV-A3JW TCGA-GV-A3JX 
        7.73         2.10         2.20         6.41         6.41         6.15 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        7.63         7.79         4.14         6.41        19.07        11.54 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        6.74        38.60         3.45         4.67         2.50         6.48 
TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-MV-A51V TCGA-PQ-A6FN TCGA-XF-A8HF 
       10.52         1.81         4.27        13.48        16.67        56.19 
TCGA-XF-A8HG 
       15.35 

$`DEL PEAK 10(5Q11.2) WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20O 
        7.33         2.66         6.74        12.39        11.93        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A3PK TCGA-BT-A42C 
       17.88        19.50        14.96         8.25         2.07        28.70 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
       28.41         8.98         1.94         0.69         0.13         0.07 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO 
        0.10         0.07         0.10         0.10        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        7.20         5.46        16.31         1.84         9.34         2.53 
TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF 
       31.40        19.00         8.91       130.88        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A6AW 
       15.62         1.81         7.79         8.28       140.81        48.53 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KE 
       76.60        67.36        30.67         0.10         0.53         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B7 
        0.66         1.38         0.82        12.89        15.68         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SQ 
       12.43        15.88        45.93        12.82         5.52        46.78 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS 
       22.98        14.93        14.96         3.62        12.13        37.15 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA 
       11.01         6.87         5.69        49.68         6.28        50.66 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FT-A3EE 
        6.71         4.11         2.20         4.01         7.13         3.25 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-GC-A3BM 
       30.61         5.69        35.24        17.26        20.12         2.89 
TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GD-A3OQ 
        2.24         4.50        15.91        14.07        17.75         3.12 
TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QK 
       20.98         7.66        11.31         4.41         5.69         6.67 
TCGA-H4-A2HO TCGA-K4-A3WS TCGA-K4-A5RJ TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 
        1.51         8.75         1.74         6.38         6.35         3.45 
TCGA-PQ-A6FI TCGA-XF-A8HD TCGA-XF-A8HE 
       12.23        88.93        97.45 

  DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE 
                         0.43                          0.07 
  DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE 
                       123.85                        140.81 
  DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE 
                         8.94                          8.28 
[1] "0.4 - 123.8 (8.9)" "0.1 - 140.8 (8.3)"
[1] "hr=" "1.2"
D42V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 10(5Q11.2) MUTATED          1       1       30        32       39
  DEL PEAK 10(5Q11.2) WILD-TYPE        0       1       38        40       28
D42V3, multiclass
           clus
vv          DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             1                             1
  STAGE II                           30                            38
  STAGE III                          32                            40
  STAGE IV                           39                            28
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  DEL PEAK 10(5Q11.2) MUTATED         31 50 15
  DEL PEAK 10(5Q11.2) WILD-TYPE       31 51 17
D42V4, multiclass
          clus
vv         DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE
  T0+T1+T2                          31                            31
  T3                                50                            51
  T4                                15                            17
[1] 3 2
[1] 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(5Q11.2) MUTATED   55 13 23  5
  DEL PEAK 10(5Q11.2) WILD-TYPE 75  9 15  2
D42V5, multiclass
    clus
vv   DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE
  N0                          55                            75
  N1                          13                             9
  N2                          23                            15
  N3                           5                             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                            M0 M1 MX
  DEL PEAK 10(5Q11.2) MUTATED   47  4 54
  DEL PEAK 10(5Q11.2) WILD-TYPE 59  1 48
D42V6, multiclass
    clus
vv   DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE
  M0                          47                            59
  M1                           4                             1
  MX                          54                            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"
D42V7, binary
                               cls
clus                             0  1
  DEL PEAK 10(5Q11.2) MUTATED   25 81
  DEL PEAK 10(5Q11.2) WILD-TYPE 25 83
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q11.2) MUTATED     25   81
  DEL PEAK 10(5Q11.2) WILD-TYPE   25   83
        clus
vv       DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE
  FEMALE                          25                            25
  MALE                            81                            83
[1] 2 2
[1] FALSE
D42V8, continuous
D42V9, continuous
D42V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(5Q11.2) MUTATED       8                         6    85
  DEL PEAK 10(5Q11.2) WILD-TYPE    14                         5    85
D42V11, multiclass
                           clus
vv                          DEL PEAK 10(5Q11.2) MUTATED
  ASIAN                                               8
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                              85
                           clus
vv                          DEL PEAK 10(5Q11.2) WILD-TYPE
  ASIAN                                                14
  BLACK OR AFRICAN AMERICAN                             5
  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"

Clustering(43) Variable = DEL PEAK 11(5Q35.1) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 11(5Q35.1) MUTATED   70 27
  DEL PEAK 11(5Q35.1) WILD-TYPE 81 30
  DEL PEAK 11(5Q35.1) MUTATED DEL PEAK 11(5Q35.1) WILD-TYPE 
                           97                           111 
  DEL PEAK 11(5Q35.1) MUTATED DEL PEAK 11(5Q35.1) WILD-TYPE 
                           27                            30 
$`DEL PEAK 11(5Q35.1) MUTATED`
TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20W 
        6.58        19.04        32.84         5.06         5.06         8.35 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        3.65         4.67        12.82        15.42        28.70         9.99 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AA 
       23.01         0.46         5.19         2.53         2.14        19.00 
TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IN 
      112.44        10.59       123.85        87.32         3.98         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A6AV 
       10.49        50.27        21.30        10.55        48.00        64.18 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A541 
       15.68        32.28        43.59        24.66         0.49         0.59 
TCGA-E7-A7DV TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ 
        1.22         8.94         6.87        11.93        45.93        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A3SS 
       22.45        16.47        12.82        13.18        19.79         1.97 
TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       14.93        13.38         5.36         6.84        27.45         6.87 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG 
        4.83         6.38        50.66         9.30         6.71         2.66 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EL 
       15.19         3.48         4.08         6.48        61.94        26.93 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
        7.04        20.12         0.85        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 
       14.07         1.12         2.66         7.73         2.10         2.20 
TCGA-GU-A42P TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        6.41         6.41         6.15         5.69         7.63         7.79 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WU 
        6.41        19.07        11.54         6.74        38.60         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-MV-A51V TCGA-PQ-A6FN TCGA-XF-A8HF 
        2.50         6.48        10.52        13.48        16.67        56.19 
TCGA-XF-A8HG 
       15.35 

$`DEL PEAK 11(5Q35.1) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74        12.39        11.93 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20X 
       12.16        17.88        19.50        14.89        14.96         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PK TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
       17.16         5.59         2.07        28.41         8.98         1.94 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69         0.13         0.07         0.10         0.07 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        0.10         0.10        12.92         4.90         7.20         5.46 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AB 
       16.31         1.84         9.34        31.40        18.41         8.91 
TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 
      130.88        16.14        17.62        15.62         1.81         7.79 
TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY 
        2.20         7.82        20.02         9.67         8.28       140.81 
TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A4TZ 
       17.98        48.53        76.60        67.36        30.67        15.35 
TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
       26.17         0.10         0.53         0.56         0.66         1.38 
TCGA-E7-A678 TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 
        0.82        12.89        15.68         4.01        12.43        15.88 
TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X 
        5.52        46.78        22.98        14.93        14.96         3.62 
TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C1 
       12.13        37.15        11.01         6.87         5.69        49.68 
TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z9 
        2.66         6.28         4.11         2.20         4.01         7.13 
TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-GC-A3BM 
        3.25        30.61         5.69        35.24        17.26         2.89 
TCGA-GC-A3I6 TCGA-GC-A3WC TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R 
        2.24        17.75         3.12        20.98         7.66        11.31 
TCGA-GV-A3JV TCGA-GV-A3QI TCGA-GV-A3QK TCGA-H4-A2HO TCGA-K4-A3WS TCGA-K4-A3WV 
        4.41         4.14         6.67         1.51         8.75         4.67 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 
        1.74         1.81         4.27         6.38         6.35         3.45 
TCGA-PQ-A6FI TCGA-XF-A8HD TCGA-XF-A8HE 
       12.23        88.93        97.45 

  DEL PEAK 11(5Q35.1) MUTATED DEL PEAK 11(5Q35.1) WILD-TYPE 
                         0.46                          0.07 
  DEL PEAK 11(5Q35.1) MUTATED DEL PEAK 11(5Q35.1) WILD-TYPE 
                       123.85                        140.81 
  DEL PEAK 11(5Q35.1) MUTATED DEL PEAK 11(5Q35.1) WILD-TYPE 
                         9.99                          7.82 
[1] "0.5 - 123.8 (10.0)" "0.1 - 140.8 (7.8)" 
[1] "hr=" "1.1"
D43V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 11(5Q35.1) MUTATED          1       0       30        30       37
  DEL PEAK 11(5Q35.1) WILD-TYPE        0       2       38        42       30
D43V3, multiclass
           clus
vv          DEL PEAK 11(5Q35.1) MUTATED DEL PEAK 11(5Q35.1) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             0                             2
  STAGE II                           30                            38
  STAGE III                          30                            42
  STAGE IV                           37                            30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  DEL PEAK 11(5Q35.1) MUTATED         29 45 15
  DEL PEAK 11(5Q35.1) WILD-TYPE       33 56 17
D43V4, multiclass
          clus
vv         DEL PEAK 11(5Q35.1) MUTATED DEL PEAK 11(5Q35.1) WILD-TYPE
  T0+T1+T2                          29                            33
  T3                                45                            56
  T4                                15                            17
[1] 3 2
[1] 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(5Q35.1) MUTATED   53 11 21  6
  DEL PEAK 11(5Q35.1) WILD-TYPE 77 11 17  1
D43V5, multiclass
    clus
vv   DEL PEAK 11(5Q35.1) MUTATED DEL PEAK 11(5Q35.1) WILD-TYPE
  N0                          53                            77
  N1                          11                            11
  N2                          21                            17
  N3                           6                             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                            M0 M1 MX
  DEL PEAK 11(5Q35.1) MUTATED   41  4 54
  DEL PEAK 11(5Q35.1) WILD-TYPE 65  1 48
D43V6, multiclass
    clus
vv   DEL PEAK 11(5Q35.1) MUTATED DEL PEAK 11(5Q35.1) WILD-TYPE
  M0                          41                            65
  M1                           4                             1
  MX                          54                            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"
D43V7, binary
                               cls
clus                             0  1
  DEL PEAK 11(5Q35.1) MUTATED   21 79
  DEL PEAK 11(5Q35.1) WILD-TYPE 29 85
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q35.1) MUTATED     21   79
  DEL PEAK 11(5Q35.1) WILD-TYPE   29   85
        clus
vv       DEL PEAK 11(5Q35.1) MUTATED DEL PEAK 11(5Q35.1) WILD-TYPE
  FEMALE                          21                            29
  MALE                            79                            85
[1] 2 2
[1] FALSE
D43V8, continuous
D43V9, continuous
D43V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(5Q35.1) MUTATED       6                         6    82
  DEL PEAK 11(5Q35.1) WILD-TYPE    16                         5    88
D43V11, multiclass
                           clus
vv                          DEL PEAK 11(5Q35.1) MUTATED
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                              82
                           clus
vv                          DEL PEAK 11(5Q35.1) WILD-TYPE
  ASIAN                                                16
  BLACK OR AFRICAN AMERICAN                             5
  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"

Clustering(44) Variable = DEL PEAK 12(6P25.3) MUTATION ANALYSIS
D44V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(6P25.3) MUTATED    36  17
  DEL PEAK 12(6P25.3) WILD-TYPE 115  40
  DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE 
                           53                           155 
  DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE 
                           17                            40 
$`DEL PEAK 12(6P25.3) MUTATED`
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        5.06         8.25        17.16         5.59         3.65         4.67 
TCGA-CU-A0YR TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE 
        7.20         1.84        31.40         8.91       130.88        16.14 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IT 
        1.81        10.59         7.79       123.85         3.98        21.30 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 
       48.00        17.98        67.36        30.67        15.35        26.17 
TCGA-E7-A4IJ TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SL 
        0.49        15.68         6.87         4.01        45.93        22.45 
TCGA-FD-A3SN TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A62O TCGA-FD-A62P TCGA-FJ-A3Z7 
       12.82        14.93         5.36         4.83         6.28        15.19 
TCGA-FJ-A3ZF TCGA-G2-A2EO TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GV-A3JZ TCGA-GV-A3QF 
        4.08        35.24         2.10        20.98         5.69         7.63 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HQ TCGA-K4-A4AB 
        7.79         4.14         6.67         6.41         6.74         2.50 
TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-XF-A8HG 
        1.81         3.45        13.48        12.23        15.35 

$`DEL PEAK 12(6P25.3) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       11.93        19.04        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A3PJ TCGA-BT-A3PK 
        5.06        14.89        14.96         8.35        12.82         2.07 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
       15.42        28.70         9.99        28.41         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
       23.01         0.46         0.43         0.69         0.13         0.07 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO 
        0.10         0.07         0.10         0.10        12.92         4.90 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.46         5.19        16.31         9.34         2.53         2.14 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I6 
       18.41        19.00       112.44        17.62        15.62        87.32 
TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU 
        2.20         7.82         8.22        10.49        50.27        20.02 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AV TCGA-DK-A6AW 
        9.67         8.28        10.55       140.81        64.18        48.53 
TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 
       76.60        15.68        32.28        43.59        24.66         0.10 
TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        0.53         0.59         0.56         0.66         1.38         0.82 
TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        1.22        12.89         8.94        12.43        11.93        15.88 
TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       24.30        16.47         5.52        13.18        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y 
        1.97        22.98        14.93        14.96         3.62        12.13 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY 
       13.38        37.15        11.01         6.87         5.69         6.84 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TA 
       27.45         6.87        49.68         2.66         6.38        50.66 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
        9.30         6.71         4.11         2.66         2.20         4.01 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
        7.13         3.48         3.25         6.48        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
        5.69        26.93        17.26         7.04        20.12         0.85 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
        2.89         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A6C6 
       17.75         1.12         2.66         7.73         3.12         2.20 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
        6.41         7.66        11.31         4.41         6.41         6.15 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU 
       19.07        11.54         1.51        38.60         8.75         3.45 
TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P 
        4.67         6.48        10.52         1.74         4.27         6.38 
TCGA-LC-A66R TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        6.35        16.67        88.93        97.45        56.19 

  DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE 
                         0.49                          0.07 
  DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE 
                       130.88                        140.81 
  DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE 
                         7.79                          8.94 
[1] "0.5 - 130.9 (7.8)" "0.1 - 140.8 (8.9)"
[1] "hr=" "1.2"
D44V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 12(6P25.3) MUTATED          0       0       14        19       21
  DEL PEAK 12(6P25.3) WILD-TYPE        1       2       54        53       46
D44V3, multiclass
           clus
vv          DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE
  STAGE 0A                            0                             1
  STAGE I                             0                             2
  STAGE II                           14                            54
  STAGE III                          19                            53
  STAGE IV                           21                            46
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  DEL PEAK 12(6P25.3) MUTATED         11 23 13
  DEL PEAK 12(6P25.3) WILD-TYPE       51 78 19
D44V4, multiclass
          clus
vv         DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE
  T0+T1+T2                          11                            51
  T3                                23                            78
  T4                                13                            19
[1] 3 2
[1] 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(6P25.3) MUTATED    27   2  15   2
  DEL PEAK 12(6P25.3) WILD-TYPE 103  20  23   5
D44V5, multiclass
    clus
vv   DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE
  N0                          27                           103
  N1                           2                            20
  N2                          15                            23
  N3                           2                             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                            M0 M1 MX
  DEL PEAK 12(6P25.3) MUTATED   27  2 25
  DEL PEAK 12(6P25.3) WILD-TYPE 79  3 77
D44V6, multiclass
    clus
vv   DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE
  M0                          27                            79
  M1                           2                             3
  MX                          25                            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"
D44V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(6P25.3) MUTATED    16  38
  DEL PEAK 12(6P25.3) WILD-TYPE  34 126
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6P25.3) MUTATED     16   38
  DEL PEAK 12(6P25.3) WILD-TYPE   34  126
        clus
vv       DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE
  FEMALE                          16                            34
  MALE                            38                           126
[1] 2 2
[1] FALSE
D44V8, continuous
D44V9, continuous
D44V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(6P25.3) MUTATED       2                         4    47
  DEL PEAK 12(6P25.3) WILD-TYPE    20                         7   123
D44V11, multiclass
                           clus
vv                          DEL PEAK 12(6P25.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              47
                           clus
vv                          DEL PEAK 12(6P25.3) WILD-TYPE
  ASIAN                                                20
  BLACK OR AFRICAN AMERICAN                             7
  WHITE                                               123
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(45) Variable = DEL PEAK 13(6Q21) MUTATION ANALYSIS
D45V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 13(6Q21) MUTATED   67 30
  DEL PEAK 13(6Q21) WILD-TYPE 84 27
  DEL PEAK 13(6Q21) MUTATED DEL PEAK 13(6Q21) WILD-TYPE 
                         97                         111 
  DEL PEAK 13(6Q21) MUTATED DEL PEAK 13(6Q21) WILD-TYPE 
                         30                          27 
$`DEL PEAK 13(6Q21) MUTATED`
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A2LD 
       19.04        32.84        14.89         5.06         5.59         3.65 
TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0F0 TCGA-CF-A1HR 
        4.67         2.07        15.42        28.70         1.94         0.46 
TCGA-CF-A27C TCGA-CF-A47X TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 
        0.69         0.10         5.19         1.84         2.53        31.40 
TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       18.41         8.91         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       87.32         2.20         3.98        10.49        50.27        21.30 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC 
       48.00        17.98        64.18        32.28        30.67        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE 
       15.35        26.17        24.66         0.49         0.59         0.56 
TCGA-E7-A7DV TCGA-FD-A3B5 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SQ 
        1.22         8.94        24.30        22.45        12.82        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BT 
       19.79         1.97        14.93        14.93        13.38        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        6.87         5.36         6.84        27.45         6.87        49.68 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG 
        4.83         6.28         6.38         9.30         4.11         2.66 
TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE 
        2.20        15.19         6.48        35.24        17.26        20.12 
TCGA-G2-A3VY TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GU-A42P 
        0.85         2.24        14.07         2.66         2.10         6.41 
TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A40E 
       11.31         6.41         6.15         7.63         7.79         6.41 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A4AB 
       19.07        11.54         6.74        38.60         4.67         2.50 
TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HF 
        1.81         3.45        13.48        16.67        88.93        56.19 
TCGA-XF-A8HG 
       15.35 

$`DEL PEAK 13(6Q21) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       11.93        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A42E TCGA-BT-A42F 
        8.35         8.25        17.16        12.82         9.99        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        8.98        23.01         0.43         0.13         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        0.07         0.10        12.92         4.90         7.20         5.46 
TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AD 
       16.31         9.34         2.14        19.00       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU 
       16.14        17.62        15.62         7.82         8.22        20.02 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 
        9.67         8.28        10.55       140.81        48.53        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A677 
       67.36        15.68         0.10         0.53         0.66         1.38 
TCGA-E7-A678 TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
        0.82        12.89        15.68         6.87         4.01        12.43 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP 
       11.93        15.88        45.93        16.47         5.52        13.18 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BX 
       22.98        14.96         3.62        12.13        37.15         5.69 
TCGA-FD-A62N TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        2.66        50.66         6.71         4.01         7.13         3.48 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        4.08         3.25        61.94        30.61         5.69        26.93 
TCGA-G2-A3IB TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC 
        7.04         2.89        15.81         4.50        15.91        17.75 
TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q 
        1.12         7.73         3.12        20.98         2.20         7.66 
TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A3QK TCGA-H4-A2HO TCGA-K4-A3WS 
        4.41         5.69         4.14         6.67         1.51         8.75 
TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P 
        3.45         6.48        10.52         1.74         4.27         6.38 
TCGA-LC-A66R TCGA-PQ-A6FI TCGA-XF-A8HE 
        6.35        12.23        97.45 

  DEL PEAK 13(6Q21) MUTATED DEL PEAK 13(6Q21) WILD-TYPE 
                       0.10                        0.07 
  DEL PEAK 13(6Q21) MUTATED DEL PEAK 13(6Q21) WILD-TYPE 
                     123.85                      140.81 
  DEL PEAK 13(6Q21) MUTATED DEL PEAK 13(6Q21) WILD-TYPE 
                       8.94                        8.28 
[1] "0.1 - 123.8 (8.9)" "0.1 - 140.8 (8.3)"
[1] "hr=" "1.2"
D45V2, continuous
                             vv
clus                          STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 13(6Q21) MUTATED          1       0       31        25       39
  DEL PEAK 13(6Q21) WILD-TYPE        0       2       37        47       28
D45V3, multiclass
           clus
vv          DEL PEAK 13(6Q21) MUTATED DEL PEAK 13(6Q21) WILD-TYPE
  STAGE 0A                          1                           0
  STAGE I                           0                           2
  STAGE II                         31                          37
  STAGE III                        25                          47
  STAGE IV                         39                          28
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1+T2 T3 T4
  DEL PEAK 13(6Q21) MUTATED         30 46 14
  DEL PEAK 13(6Q21) WILD-TYPE       32 55 18
D45V4, multiclass
          clus
vv         DEL PEAK 13(6Q21) MUTATED DEL PEAK 13(6Q21) WILD-TYPE
  T0+T1+T2                        30                          32
  T3                              46                          55
  T4                              14                          18
[1] 3 2
[1] 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(6Q21) MUTATED   49 10 25  3
  DEL PEAK 13(6Q21) WILD-TYPE 81 12 13  4
D45V5, multiclass
    clus
vv   DEL PEAK 13(6Q21) MUTATED DEL PEAK 13(6Q21) WILD-TYPE
  N0                        49                          81
  N1                        10                          12
  N2                        25                          13
  N3                         3                           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                          M0 M1 MX
  DEL PEAK 13(6Q21) MUTATED   42  2 54
  DEL PEAK 13(6Q21) WILD-TYPE 64  3 48
D45V6, multiclass
    clus
vv   DEL PEAK 13(6Q21) MUTATED DEL PEAK 13(6Q21) WILD-TYPE
  M0                        42                          64
  M1                         2                           3
  MX                        54                          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"
D45V7, binary
                             cls
clus                           0  1
  DEL PEAK 13(6Q21) MUTATED   27 72
  DEL PEAK 13(6Q21) WILD-TYPE 23 92
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q21) MUTATED     27   72
  DEL PEAK 13(6Q21) WILD-TYPE   23   92
        clus
vv       DEL PEAK 13(6Q21) MUTATED DEL PEAK 13(6Q21) WILD-TYPE
  FEMALE                        27                          23
  MALE                          72                          92
[1] 2 2
[1] FALSE
D45V8, continuous
D45V9, continuous
D45V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(6Q21) MUTATED       9                         6    78
  DEL PEAK 13(6Q21) WILD-TYPE    13                         5    92
D45V11, multiclass
                           clus
vv                          DEL PEAK 13(6Q21) MUTATED
  ASIAN                                             9
  BLACK OR AFRICAN AMERICAN                         6
  WHITE                                            78
                           clus
vv                          DEL PEAK 13(6Q21) WILD-TYPE
  ASIAN                                              13
  BLACK OR AFRICAN AMERICAN                           5
  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"

Clustering(46) Variable = DEL PEAK 14(6Q27) MUTATION ANALYSIS
D46V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 14(6Q27) MUTATED   68 29
  DEL PEAK 14(6Q27) WILD-TYPE 83 28
  DEL PEAK 14(6Q27) MUTATED DEL PEAK 14(6Q27) WILD-TYPE 
                         97                         111 
  DEL PEAK 14(6Q27) MUTATED DEL PEAK 14(6Q27) WILD-TYPE 
                         29                          28 
$`DEL PEAK 14(6Q27) MUTATED`
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
       19.04        32.84         5.06         5.59         3.65         4.67 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A47X TCGA-CU-A0YR 
        2.07        28.70         1.94         0.46         0.10         7.20 
TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A1AD 
        5.19         1.84         2.53        31.40         8.91       112.44 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
        1.81        10.59         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X1 
        3.98         8.22        10.49        50.27        21.30        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ 
       17.98        64.18        32.28        30.67        43.59        15.35 
TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A7DV TCGA-FD-A3B5 TCGA-FD-A3SL TCGA-FD-A3SN 
        0.49         0.56         1.22         8.94        22.45        12.82 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BT 
       46.78        19.79         1.97        12.13        13.38        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        6.87         5.36         6.84        27.45         6.87        49.68 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TE 
        4.83         6.28         6.38        50.66         9.30         4.11 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A2ES 
        2.66         2.20        15.19         6.48        35.24        17.26 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A6I1 
       20.12         0.85         2.24         4.50        14.07         2.66 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GU-A42P TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3JX 
        7.73         2.10         6.41        11.31         6.41         6.15 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G 
        5.69         7.63         7.79         4.14         6.41        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A54R 
       11.54         6.74        38.60         8.75         2.50        10.52 
TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HF 
        1.81         3.45        13.48        16.67        88.93        56.19 
TCGA-XF-A8HG 
       15.35 

$`DEL PEAK 14(6Q27) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       11.93        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A42B 
       14.96         8.35         8.25        17.16        12.82        15.42 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C 
        9.99        28.41         8.98        23.01         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN 
        0.13         0.07         0.10         0.07         0.10        12.92 
TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A7 
        4.90         5.46        16.31         9.34         2.14        18.41 
TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IM 
       19.00       130.88        16.14        17.62        15.62         7.82 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW 
       20.02         9.67         8.28        10.55       140.81        48.53 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       76.60        67.36        15.68        26.17        24.66         0.10 
TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A3B3 
        0.53         0.59         0.66         1.38         0.82        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       15.68         6.87         4.01        12.43        11.93        15.88 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N 
       45.93        24.30        16.47         5.52        13.18        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BX 
       14.93        14.96        14.93         3.62        37.15         5.69 
TCGA-FD-A62N TCGA-FD-A6TD TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        2.66         6.71         4.01         7.13         3.48         4.08 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB 
        3.25        61.94        30.61         5.69        26.93         7.04 
TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A3OQ 
        2.89        15.81        15.91        17.75         1.12         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GV-A3JV TCGA-GV-A3QK TCGA-H4-A2HO 
       20.98         2.20         7.66         4.41         6.67         1.51 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P 
        3.45         4.67         6.48         1.74         4.27         6.38 
TCGA-LC-A66R TCGA-PQ-A6FI TCGA-XF-A8HE 
        6.35        12.23        97.45 

  DEL PEAK 14(6Q27) MUTATED DEL PEAK 14(6Q27) WILD-TYPE 
                       0.10                        0.07 
  DEL PEAK 14(6Q27) MUTATED DEL PEAK 14(6Q27) WILD-TYPE 
                     123.85                      140.81 
  DEL PEAK 14(6Q27) MUTATED DEL PEAK 14(6Q27) WILD-TYPE 
                       7.79                        9.34 
[1] "0.1 - 123.8 (7.8)" "0.1 - 140.8 (9.3)"
[1] "hr=" "1.1"
D46V2, continuous
                             vv
clus                          STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 14(6Q27) MUTATED          1       0       27        30       39
  DEL PEAK 14(6Q27) WILD-TYPE        0       2       41        42       28
D46V3, multiclass
           clus
vv          DEL PEAK 14(6Q27) MUTATED DEL PEAK 14(6Q27) WILD-TYPE
  STAGE 0A                          1                           0
  STAGE I                           0                           2
  STAGE II                         27                          41
  STAGE III                        30                          42
  STAGE IV                         39                          28
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1+T2 T3 T4
  DEL PEAK 14(6Q27) MUTATED         26 48 16
  DEL PEAK 14(6Q27) WILD-TYPE       36 53 16
D46V4, multiclass
          clus
vv         DEL PEAK 14(6Q27) MUTATED DEL PEAK 14(6Q27) WILD-TYPE
  T0+T1+T2                        26                          36
  T3                              48                          53
  T4                              16                          16
[1] 3 2
[1] 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(6Q27) MUTATED   50  8 26  4
  DEL PEAK 14(6Q27) WILD-TYPE 80 14 12  3
D46V5, multiclass
    clus
vv   DEL PEAK 14(6Q27) MUTATED DEL PEAK 14(6Q27) WILD-TYPE
  N0                        50                          80
  N1                         8                          14
  N2                        26                          12
  N3                         4                           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                          M0 M1 MX
  DEL PEAK 14(6Q27) MUTATED   41  2 55
  DEL PEAK 14(6Q27) WILD-TYPE 65  3 47
D46V6, multiclass
    clus
vv   DEL PEAK 14(6Q27) MUTATED DEL PEAK 14(6Q27) WILD-TYPE
  M0                        41                          65
  M1                         2                           3
  MX                        55                          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"
D46V7, binary
                             cls
clus                           0  1
  DEL PEAK 14(6Q27) MUTATED   26 73
  DEL PEAK 14(6Q27) WILD-TYPE 24 91
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(6Q27) MUTATED     26   73
  DEL PEAK 14(6Q27) WILD-TYPE   24   91
        clus
vv       DEL PEAK 14(6Q27) MUTATED DEL PEAK 14(6Q27) WILD-TYPE
  FEMALE                        26                          24
  MALE                          73                          91
[1] 2 2
[1] FALSE
D46V8, continuous
D46V9, continuous
D46V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(6Q27) MUTATED       8                         5    80
  DEL PEAK 14(6Q27) WILD-TYPE    14                         6    90
D46V11, multiclass
                           clus
vv                          DEL PEAK 14(6Q27) MUTATED
  ASIAN                                             8
  BLACK OR AFRICAN AMERICAN                         5
  WHITE                                            80
                           clus
vv                          DEL PEAK 14(6Q27) WILD-TYPE
  ASIAN                                              14
  BLACK OR AFRICAN AMERICAN                           6
  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"

Clustering(47) Variable = DEL PEAK 15(7Q36.3) MUTATION ANALYSIS
D47V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(7Q36.3) MUTATED    23   7
  DEL PEAK 15(7Q36.3) WILD-TYPE 128  50
  DEL PEAK 15(7Q36.3) MUTATED DEL PEAK 15(7Q36.3) WILD-TYPE 
                           30                           178 
  DEL PEAK 15(7Q36.3) MUTATED DEL PEAK 15(7Q36.3) WILD-TYPE 
                            7                            50 
$`DEL PEAK 15(7Q36.3) MUTATED`
TCGA-BT-A20N TCGA-BT-A20X TCGA-CF-A1HS TCGA-CF-A47X TCGA-DK-A2I4 TCGA-DK-A3IK 
       32.84         8.25         0.43         0.10       123.85         2.20 
TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-FD-A3N6 TCGA-FD-A3NA 
        7.82        10.49        15.35        26.17        15.88        45.93 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A6TE TCGA-FJ-A3ZF TCGA-GC-A3I6 
        6.84        27.45         6.87         4.11         4.08         2.24 
TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GV-A3JV TCGA-GV-A3QF 
        4.50        14.07         1.12         2.66         4.41         7.63 
TCGA-K4-A3WS TCGA-K4-A6MB TCGA-LC-A66R TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD 
        8.75         4.27         6.35        12.23        16.67        88.93 

$`DEL PEAK 15(7Q36.3) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       11.93        19.04        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB 
       14.89        14.96         5.06         8.35        17.16         5.59 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
        3.65         4.67        12.82         2.07        15.42        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
        9.99        28.41         8.98         1.94        23.01         0.46 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
        0.69         0.13         0.07         0.10         0.07         0.10 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       12.92         4.90         7.20         5.46         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        1.84         9.34         2.53         2.14        31.40        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00         8.91       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IL 
       15.62         1.81        10.59         7.79        87.32         3.98 
TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
        8.22        50.27        21.30        20.02         9.67         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       10.55       140.81        48.00        17.98        64.18        48.53 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC 
       76.60        67.36        15.68        32.28        30.67        43.59 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE 
       24.66         0.10         0.49         0.53         0.59         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 
        0.66         1.38         0.82         1.22        12.89        15.68 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3SJ 
        8.94         6.87         4.01        12.43        11.93        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       22.45        16.47        12.82         5.52        13.18        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79         1.97        22.98        14.93        14.96        14.93 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
        3.62        12.13        13.38        37.15        11.01         6.87 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
        5.36         5.69        49.68         2.66         4.83         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TH 
        6.38        50.66         9.30         6.71         2.66         2.20 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P 
        4.01        15.19         7.13         3.48         3.25         6.48 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       61.94        30.61         5.69        26.93        35.24        17.26 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RC 
        7.04        20.12         0.85         2.89        15.81        15.91 
TCGA-GC-A3WC TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       17.75         7.73         2.10         3.12        20.98         2.20 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
        6.41         7.66        11.31         6.41         6.15         5.69 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        7.79         4.14         6.67         6.41        19.07        11.54 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        1.51         6.74        38.60         3.45         4.67         2.50 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LT-A5Z6 
        6.48        10.52         1.74         1.81         6.38         3.45 
TCGA-MV-A51V TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       13.48        97.45        56.19        15.35 

  DEL PEAK 15(7Q36.3) MUTATED DEL PEAK 15(7Q36.3) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK 15(7Q36.3) MUTATED DEL PEAK 15(7Q36.3) WILD-TYPE 
                       123.85                        140.81 
  DEL PEAK 15(7Q36.3) MUTATED DEL PEAK 15(7Q36.3) WILD-TYPE 
                        7.725                         8.960 
[1] "0.1 - 123.8 (7.7)" "0.1 - 140.8 (9.0)"
[1] "hr=" "1.1"
D47V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 15(7Q36.3) MUTATED          0       0        6        12       11
  DEL PEAK 15(7Q36.3) WILD-TYPE        1       2       62        60       56
D47V3, multiclass
           clus
vv          DEL PEAK 15(7Q36.3) MUTATED DEL PEAK 15(7Q36.3) WILD-TYPE
  STAGE 0A                            0                             1
  STAGE I                             0                             2
  STAGE II                            6                            62
  STAGE III                          12                            60
  STAGE IV                           11                            56
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  DEL PEAK 15(7Q36.3) MUTATED          6 20  3
  DEL PEAK 15(7Q36.3) WILD-TYPE       56 81 29
D47V4, multiclass
          clus
vv         DEL PEAK 15(7Q36.3) MUTATED DEL PEAK 15(7Q36.3) WILD-TYPE
  T0+T1+T2                           6                            56
  T3                                20                            81
  T4                                 3                            29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 15(7Q36.3) MUTATED    19   4   7   0
  DEL PEAK 15(7Q36.3) WILD-TYPE 111  18  31   7
D47V5, multiclass
    clus
vv   DEL PEAK 15(7Q36.3) MUTATED DEL PEAK 15(7Q36.3) WILD-TYPE
  N0                          19                           111
  N1                           4                            18
  N2                           7                            31
  N3                           0                             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"
                               vv
clus                            M0 M1 MX
  DEL PEAK 15(7Q36.3) MUTATED   12  0 18
  DEL PEAK 15(7Q36.3) WILD-TYPE 94  5 84
D47V6, multiclass
    clus
vv   DEL PEAK 15(7Q36.3) MUTATED DEL PEAK 15(7Q36.3) WILD-TYPE
  M0                          12                            94
  M1                           0                             5
  MX                          18                            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"
D47V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(7Q36.3) MUTATED     7  23
  DEL PEAK 15(7Q36.3) WILD-TYPE  43 141
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(7Q36.3) MUTATED      7   23
  DEL PEAK 15(7Q36.3) WILD-TYPE   43  141
        clus
vv       DEL PEAK 15(7Q36.3) MUTATED DEL PEAK 15(7Q36.3) WILD-TYPE
  FEMALE                           7                            43
  MALE                            23                           141
[1] 2 2
[1] FALSE
D47V8, continuous
D47V9, continuous
D47V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(7Q36.3) MUTATED       2                         1    24
  DEL PEAK 15(7Q36.3) WILD-TYPE    20                        10   146
D47V11, multiclass
                           clus
vv                          DEL PEAK 15(7Q36.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              24
                           clus
vv                          DEL PEAK 15(7Q36.3) WILD-TYPE
  ASIAN                                                20
  BLACK OR AFRICAN AMERICAN                            10
  WHITE                                               146
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = DEL PEAK 16(8P23.3) MUTATION ANALYSIS
D48V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 16(8P23.3) MUTATED   90 28
  DEL PEAK 16(8P23.3) WILD-TYPE 61 29
  DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE 
                          118                            90 
  DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE 
                           28                            29 
$`DEL PEAK 16(8P23.3) MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB 
       40.08         2.66        19.04         5.06         8.35         5.59 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
       12.82         2.07        28.70         9.99        28.41         8.98 
TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CU-A0YN TCGA-CU-A0YR 
        1.94         0.43         0.69         0.13        12.92         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AC 
        5.46         5.19         2.53         2.14        18.41       130.88 
TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
      112.44         1.81        10.59       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU 
        3.98         7.82         8.22        10.49        21.30        20.02 
TCGA-DK-A3IV TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A4TZ TCGA-E5-A4U1 
        9.67        64.18        15.68        32.28        15.35        26.17 
TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A7DV 
       24.66         0.49         0.59         0.56         1.38         1.22 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SJ 
       15.68         8.94         6.87         4.01        11.93        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43N 
       22.45        16.47         5.52        13.18        19.79        22.98 
TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY 
       14.93        12.13        13.38         6.87         5.69         6.84 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       27.45         6.87         2.66         6.28         6.38        50.66 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        9.30         6.71         4.11         2.20        15.19         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A3IE 
        3.48         4.08         6.48        61.94         5.69        20.12 
TCGA-G2-A3VY TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
        0.85         4.50        15.91        14.07        17.75         1.12 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P 
        7.73         2.10         3.12        20.98         2.20         6.41 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        6.15         5.69         7.79         6.41        19.07        11.54 
TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        6.74         8.75         3.45         4.67         2.50         6.48 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R 
       10.52         1.74         1.81         4.27         6.38         6.35 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-XF-A8HG 
        3.45        13.48        16.67        15.35 

$`DEL PEAK 16(8P23.3) WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N 
        7.33         6.74        12.39         6.58        11.93        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A42B TCGA-C4-A0F6 
        8.25        17.16         3.65         4.67        15.42        23.01 
TCGA-CF-A1HR TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
        0.46         0.07         0.10         0.07         0.10         0.10 
TCGA-CU-A0YO TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1AA 
        4.90        16.31         1.84         9.34        31.40        19.00 
TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A3IS 
        8.91        16.14        17.62        15.62         7.79        50.27 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW 
        8.28        10.55       140.81        48.00        17.98        48.53 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       76.60        67.36        30.67        43.59         0.10         0.53 
TCGA-E7-A5KF TCGA-E7-A678 TCGA-FD-A3B3 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA 
        0.66         0.82        12.89        12.43        15.88        45.93 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.82        46.78         1.97        14.96        14.93         3.62 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A6TG 
       37.15        11.01         5.36        49.68         4.83         2.66 
TCGA-FD-A6TI TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
        4.01         3.25        30.61        26.93        35.24        17.26 
TCGA-G2-A3IB TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A6I1 TCGA-GU-A42Q 
        7.04         2.89         2.24        15.81         2.66         7.66 
TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK 
       11.31         4.41         6.41         7.63         4.14         6.67 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-PQ-A6FI TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        1.51        38.60        12.23        88.93        97.45        56.19 

  DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE 
                         0.13                          0.07 
  DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE 
                       130.88                        140.81 
  DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE 
                        7.165                        12.045 
[1] "0.1 - 130.9 (7.2)"  "0.1 - 140.8 (12.0)"
[1] "hr=" "1.1"
D48V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 16(8P23.3) MUTATED          1       2       37        34       43
  DEL PEAK 16(8P23.3) WILD-TYPE        0       0       31        38       24
D48V3, multiclass
           clus
vv          DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             2                             0
  STAGE II                           37                            31
  STAGE III                          34                            38
  STAGE IV                           43                            24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  DEL PEAK 16(8P23.3) MUTATED         35 51 20
  DEL PEAK 16(8P23.3) WILD-TYPE       27 50 12
D48V4, multiclass
          clus
vv         DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE
  T0+T1+T2                          35                            27
  T3                                51                            50
  T4                                20                            12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 16(8P23.3) MUTATED   65 14 24  5
  DEL PEAK 16(8P23.3) WILD-TYPE 65  8 14  2
D48V5, multiclass
    clus
vv   DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE
  N0                          65                            65
  N1                          14                             8
  N2                          24                            14
  N3                           5                             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                            M0 M1 MX
  DEL PEAK 16(8P23.3) MUTATED   50  5 63
  DEL PEAK 16(8P23.3) WILD-TYPE 56  0 39
D48V6, multiclass
    clus
vv   DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE
  M0                          50                            56
  M1                           5                             0
  MX                          63                            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"
D48V7, binary
                               cls
clus                             0  1
  DEL PEAK 16(8P23.3) MUTATED   25 94
  DEL PEAK 16(8P23.3) WILD-TYPE 25 70
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(8P23.3) MUTATED     25   94
  DEL PEAK 16(8P23.3) WILD-TYPE   25   70
        clus
vv       DEL PEAK 16(8P23.3) MUTATED DEL PEAK 16(8P23.3) WILD-TYPE
  FEMALE                          25                            25
  MALE                            94                            70
[1] 2 2
[1] FALSE
D48V8, continuous
D48V9, continuous
D48V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(8P23.3) MUTATED       9                         9    93
  DEL PEAK 16(8P23.3) WILD-TYPE    13                         2    77
D48V11, multiclass
                           clus
vv                          DEL PEAK 16(8P23.3) MUTATED
  ASIAN                                               9
  BLACK OR AFRICAN AMERICAN                           9
  WHITE                                              93
                           clus
vv                          DEL PEAK 16(8P23.3) WILD-TYPE
  ASIAN                                                13
  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"

Clustering(49) Variable = DEL PEAK 17(8P12) MUTATION ANALYSIS
D49V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 17(8P12) MUTATED   76 25
  DEL PEAK 17(8P12) WILD-TYPE 75 32
  DEL PEAK 17(8P12) MUTATED DEL PEAK 17(8P12) WILD-TYPE 
                        101                         107 
  DEL PEAK 17(8P12) MUTATED DEL PEAK 17(8P12) WILD-TYPE 
                         25                          32 
$`DEL PEAK 17(8P12) MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB 
       40.08         2.66        19.04         5.06         8.35         5.59 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
        3.65        12.82         2.07        28.70         9.99        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CU-A0YN 
        8.98         1.94         0.43         0.69         0.13        12.92 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1AC TCGA-DK-A1AD 
        7.20         5.46        16.31         2.53       130.88       112.44 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IM 
        1.81        10.59       123.85        87.32         3.98         7.82 
TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 
        8.22        21.30         9.67        64.18        15.68        32.28 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE 
       15.35        26.17        24.66         0.49         0.59         0.56 
TCGA-E7-A677 TCGA-E7-A7DV TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        1.38         1.22        15.68         8.94         6.87         4.01 
TCGA-FD-A3N5 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A43N 
       11.93        22.45        16.47        12.82         5.52        22.98 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       12.13        13.38         6.87         5.69         6.84        27.45 
TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TH 
        6.87         2.66         6.28         9.30         4.11         2.20 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A3IE 
       15.19         4.08         6.48        61.94         5.69        20.12 
TCGA-G2-A3VY TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GD-A3OP 
        0.85         4.50        15.91        14.07        17.75         2.10 
TCGA-GD-A3OQ TCGA-GU-A42P TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        3.12         6.41         6.41         6.15         5.69         7.63 
TCGA-GV-A3QH TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-K4-A3WS 
        7.79         6.41        19.07        11.54         6.74         8.75 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
        3.45         2.50         6.48        10.52         1.74         1.81 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN 
        6.38         6.35         3.45        13.48        16.67 

$`DEL PEAK 17(8P12) WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N 
        7.33         6.74        12.39         6.58        11.93        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-C4-A0F6 TCGA-CF-A1HR 
        8.25        17.16         4.67        15.42        23.01         0.46 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YO 
        0.07         0.10         0.07         0.10         0.10         4.90 
TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        5.19         1.84         9.34         2.14        31.40        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 
       19.00         8.91        16.14        17.62        15.62         7.79 
TCGA-DK-A3IK TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX 
        2.20        10.49        50.27        20.02         8.28        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
      140.81        48.00        17.98        48.53        76.60        67.36 
TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A678 
       30.67        43.59         0.10         0.53         0.66         0.82 
TCGA-FD-A3B3 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SP 
       12.89        12.43        15.88        45.93        24.30        13.18 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       46.78        19.79         1.97        14.93        14.96        14.93 
TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5C1 TCGA-FD-A62O 
        3.62        37.15        11.01         5.36        49.68         4.83 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z9 
        6.38        50.66         6.71         2.66         4.01         7.13 
TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
        3.48         3.25        30.61        26.93        35.24        17.26 
TCGA-G2-A3IB TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3YS TCGA-GC-A6I1 
        7.04         2.89         2.24        15.81         1.12         2.66 
TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV 
        7.73        20.98         2.20         7.66        11.31         4.41 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A6MB 
        4.14         6.67         1.51        38.60         4.67         4.27 
TCGA-PQ-A6FI TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       12.23        88.93        97.45        56.19        15.35 

  DEL PEAK 17(8P12) MUTATED DEL PEAK 17(8P12) WILD-TYPE 
                       0.13                        0.07 
  DEL PEAK 17(8P12) MUTATED DEL PEAK 17(8P12) WILD-TYPE 
                     130.88                      140.81 
  DEL PEAK 17(8P12) MUTATED DEL PEAK 17(8P12) WILD-TYPE 
                       7.20                       11.31 
[1] "0.1 - 130.9 (7.2)"  "0.1 - 140.8 (11.3)"
[1] "hr=" "1"  
D49V2, continuous
                             vv
clus                          STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 17(8P12) MUTATED          1       1       34        29       36
  DEL PEAK 17(8P12) WILD-TYPE        0       1       34        43       31
D49V3, multiclass
           clus
vv          DEL PEAK 17(8P12) MUTATED DEL PEAK 17(8P12) WILD-TYPE
  STAGE 0A                          1                           0
  STAGE I                           1                           1
  STAGE II                         34                          34
  STAGE III                        29                          43
  STAGE IV                         36                          31
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1+T2 T3 T4
  DEL PEAK 17(8P12) MUTATED         30 42 20
  DEL PEAK 17(8P12) WILD-TYPE       32 59 12
D49V4, multiclass
          clus
vv         DEL PEAK 17(8P12) MUTATED DEL PEAK 17(8P12) WILD-TYPE
  T0+T1+T2                        30                          32
  T3                              42                          59
  T4                              20                          12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2 N3
  DEL PEAK 17(8P12) MUTATED   57 12 19  4
  DEL PEAK 17(8P12) WILD-TYPE 73 10 19  3
D49V5, multiclass
    clus
vv   DEL PEAK 17(8P12) MUTATED DEL PEAK 17(8P12) WILD-TYPE
  N0                        57                          73
  N1                        12                          10
  N2                        19                          19
  N3                         4                           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                          M0 M1 MX
  DEL PEAK 17(8P12) MUTATED   46  4 52
  DEL PEAK 17(8P12) WILD-TYPE 60  1 50
D49V6, multiclass
    clus
vv   DEL PEAK 17(8P12) MUTATED DEL PEAK 17(8P12) WILD-TYPE
  M0                        46                          60
  M1                         4                           1
  MX                        52                          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"
D49V7, binary
                             cls
clus                           0  1
  DEL PEAK 17(8P12) MUTATED   21 82
  DEL PEAK 17(8P12) WILD-TYPE 29 82
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(8P12) MUTATED     21   82
  DEL PEAK 17(8P12) WILD-TYPE   29   82
        clus
vv       DEL PEAK 17(8P12) MUTATED DEL PEAK 17(8P12) WILD-TYPE
  FEMALE                        21                          29
  MALE                          82                          82
[1] 2 2
[1] FALSE
D49V8, continuous
D49V9, continuous
D49V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(8P12) MUTATED      10                         7    80
  DEL PEAK 17(8P12) WILD-TYPE    12                         4    90
D49V11, multiclass
                           clus
vv                          DEL PEAK 17(8P12) MUTATED
  ASIAN                                            10
  BLACK OR AFRICAN AMERICAN                         7
  WHITE                                            80
                           clus
vv                          DEL PEAK 17(8P12) WILD-TYPE
  ASIAN                                              12
  BLACK OR AFRICAN AMERICAN                           4
  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"

Clustering(50) Variable = DEL PEAK 18(8P11.21) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 18(8P11.21) MUTATED    38  14
  DEL PEAK 18(8P11.21) WILD-TYPE 113  43
  DEL PEAK 18(8P11.21) MUTATED DEL PEAK 18(8P11.21) WILD-TYPE 
                            52                            156 
  DEL PEAK 18(8P11.21) MUTATED DEL PEAK 18(8P11.21) WILD-TYPE 
                            14                             43 
$`DEL PEAK 18(8P11.21) MUTATED`
TCGA-BL-A0C8 TCGA-BT-A2LB TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0F0 TCGA-CF-A1HS 
       40.08         5.59         2.07        28.70         1.94         0.43 
TCGA-CF-A47S TCGA-CU-A0YR TCGA-DK-A1A5 TCGA-DK-A2HX TCGA-DK-A3IL TCGA-DK-A3IM 
        0.13         7.20         2.14         1.81         3.98         7.82 
TCGA-DK-A3IN TCGA-DK-A3IV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A4TZ TCGA-E5-A4U1 
        8.22         9.67        15.68        32.28        15.35        26.17 
TCGA-E7-A3X6 TCGA-E7-A541 TCGA-E7-A5KE TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
       24.66         0.59         0.56         8.94         6.87         4.01 
TCGA-FD-A3N5 TCGA-FD-A3SL TCGA-FD-A3SO TCGA-FD-A5BR TCGA-FD-A5BX TCGA-FD-A5BZ 
       11.93        22.45         5.52        13.38         5.69        27.45 
TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH 
        6.87         6.28         9.30         6.71         4.11         2.20 
TCGA-FJ-A3Z7 TCGA-G2-A2EF TCGA-G2-A2EK TCGA-GC-A3WC TCGA-GD-A2C5 TCGA-GD-A3OP 
       15.19        61.94         5.69        17.75         7.73         2.10 
TCGA-GD-A3OQ TCGA-GV-A3JW TCGA-GV-A40G TCGA-H4-A2HQ TCGA-K4-A3WV TCGA-K4-A54R 
        3.12         6.41        19.07         6.74         4.67        10.52 
TCGA-K4-A5RJ TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-PQ-A6FN 
        1.74         6.38         3.45        16.67 

$`DEL PEAK 18(8P11.21) WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
        7.33         2.66         6.74        12.39         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
       14.89        14.96         5.06         8.35         8.25        17.16 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
        3.65         4.67        12.82        15.42         9.99        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47T TCGA-CF-A47V 
        8.98        23.01         0.46         0.69         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ 
        0.07         0.10         0.10        12.92         4.90         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 
        5.19        16.31         1.84         9.34         2.53        31.40 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00         8.91       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       17.62        15.62        10.59         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW 
        2.20        10.49        50.27        21.30        20.02         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       10.55       140.81        48.00        17.98        64.18        48.53 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       76.60        67.36        30.67        43.59         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 
        0.53         0.66         1.38         0.82         1.22        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM 
       15.68        12.43        15.88        45.93        24.30        16.47 
TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
       12.82        13.18        46.78        19.79         1.97        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS 
       14.93        14.96        14.93         3.62        12.13        37.15 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62N 
       11.01         6.87         5.36         6.84        49.68         2.66 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z9 
        4.83         6.38        50.66         2.66         4.01         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EL 
        3.48         4.08         3.25         6.48        30.61        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM 
       35.24        17.26         7.04        20.12         0.85         2.89 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS 
        2.24        15.81         4.50        15.91        14.07         1.12 
TCGA-GC-A6I1 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
        2.66        20.98         2.20         6.41         7.66        11.31 
TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
        4.41         6.15         5.69         7.63         7.79         4.14 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WS 
        6.67         6.41        11.54         1.51        38.60         8.75 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-LC-A66R 
        3.45         2.50         6.48         1.81         4.27         6.35 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       13.48        12.23        88.93        97.45        56.19        15.35 

  DEL PEAK 18(8P11.21) MUTATED DEL PEAK 18(8P11.21) WILD-TYPE 
                          0.13                           0.07 
  DEL PEAK 18(8P11.21) MUTATED DEL PEAK 18(8P11.21) WILD-TYPE 
                         61.94                         140.81 
  DEL PEAK 18(8P11.21) MUTATED DEL PEAK 18(8P11.21) WILD-TYPE 
                         6.805                         10.520 
[1] "0.1 - 61.9 (6.8)"   "0.1 - 140.8 (10.5)"
[1] "hr=" "1.3"
D50V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 18(8P11.21) MUTATED          0       1       22         8       20
  DEL PEAK 18(8P11.21) WILD-TYPE        1       1       46        64       47
D50V3, multiclass
           clus
vv          DEL PEAK 18(8P11.21) MUTATED DEL PEAK 18(8P11.21) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              1                              1
  STAGE II                            22                             46
  STAGE III                            8                             64
  STAGE IV                            20                             47
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  DEL PEAK 18(8P11.21) MUTATED         20 17  9
  DEL PEAK 18(8P11.21) WILD-TYPE       42 84 23
D50V4, multiclass
          clus
vv         DEL PEAK 18(8P11.21) MUTATED DEL PEAK 18(8P11.21) WILD-TYPE
  T0+T1+T2                           20                             42
  T3                                 17                             84
  T4                                  9                             23
[1] 3 2
[1] 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(8P11.21) MUTATED    27   7  12   0
  DEL PEAK 18(8P11.21) WILD-TYPE 103  15  26   7
D50V5, multiclass
    clus
vv   DEL PEAK 18(8P11.21) MUTATED DEL PEAK 18(8P11.21) WILD-TYPE
  N0                           27                            103
  N1                            7                             15
  N2                           12                             26
  N3                            0                              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"
                                vv
clus                             M0 M1 MX
  DEL PEAK 18(8P11.21) MUTATED   20  2 30
  DEL PEAK 18(8P11.21) WILD-TYPE 86  3 72
D50V6, multiclass
    clus
vv   DEL PEAK 18(8P11.21) MUTATED DEL PEAK 18(8P11.21) WILD-TYPE
  M0                           20                             86
  M1                            2                              3
  MX                           30                             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"
D50V7, binary
                                cls
clus                               0   1
  DEL PEAK 18(8P11.21) MUTATED    13  39
  DEL PEAK 18(8P11.21) WILD-TYPE  37 125
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(8P11.21) MUTATED     13   39
  DEL PEAK 18(8P11.21) WILD-TYPE   37  125
        clus
vv       DEL PEAK 18(8P11.21) MUTATED DEL PEAK 18(8P11.21) WILD-TYPE
  FEMALE                           13                             37
  MALE                             39                            125
[1] 2 2
[1] FALSE
D50V8, continuous
D50V9, continuous
D50V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(8P11.21) MUTATED       3                         4    41
  DEL PEAK 18(8P11.21) WILD-TYPE    19                         7   129
D50V11, multiclass
                           clus
vv                          DEL PEAK 18(8P11.21) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               41
                           clus
vv                          DEL PEAK 18(8P11.21) WILD-TYPE
  ASIAN                                                 19
  BLACK OR AFRICAN AMERICAN                              7
  WHITE                                                129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(51) Variable = DEL PEAK 19(9P23) MUTATION ANALYSIS
D51V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 19(9P23) MUTATED   66 22
  DEL PEAK 19(9P23) WILD-TYPE 85 35
  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE 
                         88                         120 
  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE 
                         22                          35 
$`DEL PEAK 19(9P23) MUTATED`
TCGA-BL-A0C8 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20Q TCGA-BT-A20T 
       40.08        11.93        19.04        32.84        19.50        14.89 
TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E 
        8.35        17.16         5.59         2.07        28.70         9.99 
TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47X TCGA-CU-A0YO TCGA-CU-A3KJ 
        1.94         0.46         0.69         0.10         4.90         5.46 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1AA TCGA-DK-A1AB 
       16.31         1.84         9.34         2.53        19.00         8.91 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IN TCGA-DK-A3IQ 
       17.62        15.62        10.59         2.20         8.22        10.49 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       50.27        21.30        10.55        48.00        17.98        64.18 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A541 
       15.68        32.28        43.59        26.17        24.66         0.59 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3SM TCGA-FD-A3SN 
        0.56         0.66        15.68         8.94        16.47        12.82 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A5BR TCGA-FD-A5BV 
       46.78        19.79         1.97        22.98        13.38         5.36 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       27.45         6.87        49.68         4.83         6.28         6.38 
TCGA-FD-A6TA TCGA-FD-A6TG TCGA-FJ-A3ZE TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EO 
       50.66         2.66         3.48         6.48        30.61        35.24 
TCGA-G2-A3IB TCGA-G2-A3VY TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OQ 
        7.04         0.85        14.07         1.12         2.66         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GV-A3JW TCGA-GV-A3QH TCGA-GV-A3QK 
       20.98         2.20         7.66         6.41         7.79         6.67 
TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       11.54         6.74        38.60         8.75         3.45         4.67 
TCGA-K4-A4AB TCGA-K4-A6MB TCGA-PQ-A6FI TCGA-PQ-A6FN 
        2.50         4.27        12.23        16.67 

$`DEL PEAK 19(9P23) WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20O 
        7.33         2.66         6.74        12.39         6.58        12.16 
TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LD 
       17.88         5.06        14.96         5.06         8.25         3.65 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 
        4.67        12.82        15.42        28.41         8.98        23.01 
TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
        0.43         0.13         0.07         0.10         0.07         0.10 
TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3QU TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
       12.92         7.20         5.19         2.14        31.40        18.41 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 
      130.88       112.44        16.14         1.81         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       87.32         3.98         7.82        20.02         9.67         8.28 
TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A4TZ 
      140.81        48.53        76.60        67.36        30.67        15.35 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV 
        0.10         0.49         0.53         1.38         0.82         1.22 
TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       12.89         6.87         4.01        12.43        11.93        15.88 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43P 
       45.93        24.30        22.45         5.52        13.18        14.93 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        14.93         3.62        12.13        37.15        11.01 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A6TC TCGA-FD-A6TD 
        6.87         5.69         6.84         2.66         9.30         6.71 
TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF 
        4.11         2.20         4.01        15.19         7.13         4.08 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IE 
        3.25        61.94         5.69        26.93        17.26        20.12 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC 
        2.89         2.24        15.81         4.50        15.91        17.75 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GU-A42P TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JX 
        7.73         2.10         6.41        11.31         4.41         6.15 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO 
        5.69         7.63         4.14         6.41        19.07         1.51 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R 
        6.48        10.52         1.74         1.81         6.38         6.35 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
        3.45        13.48        88.93        97.45        56.19        15.35 

  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE 
                       0.10                        0.07 
  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE 
                      64.18                      140.81 
  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE 
                      9.665                       7.760 
[1] "0.1 - 64.2 (9.7)"  "0.1 - 140.8 (7.8)"
[1] "hr=" "1.3"
D51V2, continuous
                             vv
clus                          STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 19(9P23) MUTATED          1       1       28        30       29
  DEL PEAK 19(9P23) WILD-TYPE        0       1       40        42       38
D51V3, multiclass
           clus
vv          DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE
  STAGE 0A                          1                           0
  STAGE I                           1                           1
  STAGE II                         28                          40
  STAGE III                        30                          42
  STAGE IV                         29                          38
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1+T2 T3 T4
  DEL PEAK 19(9P23) MUTATED         27 45 12
  DEL PEAK 19(9P23) WILD-TYPE       35 56 20
D51V4, multiclass
          clus
vv         DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE
  T0+T1+T2                        27                          35
  T3                              45                          56
  T4                              12                          20
[1] 3 2
[1] 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(9P23) MUTATED   55  8 18  2
  DEL PEAK 19(9P23) WILD-TYPE 75 14 20  5
D51V5, multiclass
    clus
vv   DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE
  N0                        55                          75
  N1                         8                          14
  N2                        18                          20
  N3                         2                           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                          M0 M1 MX
  DEL PEAK 19(9P23) MUTATED   47  3 41
  DEL PEAK 19(9P23) WILD-TYPE 59  2 61
D51V6, multiclass
    clus
vv   DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE
  M0                        47                          59
  M1                         3                           2
  MX                        41                          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"
D51V7, binary
                             cls
clus                           0  1
  DEL PEAK 19(9P23) MUTATED   23 69
  DEL PEAK 19(9P23) WILD-TYPE 27 95
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(9P23) MUTATED     23   69
  DEL PEAK 19(9P23) WILD-TYPE   27   95
        clus
vv       DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE
  FEMALE                        23                          27
  MALE                          69                          95
[1] 2 2
[1] FALSE
D51V8, continuous
D51V9, continuous
D51V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(9P23) MUTATED      11                         5    68
  DEL PEAK 19(9P23) WILD-TYPE    11                         6   102
D51V11, multiclass
                           clus
vv                          DEL PEAK 19(9P23) MUTATED
  ASIAN                                            11
  BLACK OR AFRICAN AMERICAN                         5
  WHITE                                            68
                           clus
vv                          DEL PEAK 19(9P23) WILD-TYPE
  ASIAN                                              11
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                             102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = DEL PEAK 20(9P21.3) MUTATION ANALYSIS
D52V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 20(9P21.3) MUTATED   85 34
  DEL PEAK 20(9P21.3) WILD-TYPE 66 23
  DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE 
                          119                            89 
  DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE 
                           34                            23 
$`DEL PEAK 20(9P21.3) MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66        12.39         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U 
       19.04        32.84        17.88        19.50        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PK TCGA-BT-A42B 
        5.06         8.35         8.25         5.59         2.07        15.42 
TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C 
       28.70         9.99         1.94        23.01         0.46         0.69 
TCGA-CF-A47T TCGA-CF-A47X TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 
        0.07         0.10         4.90         5.46        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE 
        9.34         2.53         2.14        19.00         8.91        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IN TCGA-DK-A3IQ 
       17.62        15.62        10.59         2.20         8.22        10.49 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A3X2 
       50.27        21.30         8.28        10.55        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       64.18        15.68        32.28        43.59        26.17        24.66 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-FD-A3B5 TCGA-FD-A3N6 
        0.59         0.56         0.66         1.38         8.94        15.88 
TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       45.93        16.47        12.82        13.18        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
        1.97        22.98        14.93         3.62        12.13        13.38 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        6.87         5.36         5.69        27.45         6.87        49.68 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TG 
        4.83         6.28         6.38        50.66         6.71         2.66 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-A3IB 
       15.19         3.48         6.48        61.94        35.24         7.04 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 
       20.12         0.85         2.89        14.07         1.12         2.66 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JW 
        3.12        20.98         2.20         7.66        11.31         6.41 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HQ 
        7.63         7.79         6.67         6.41        11.54         6.74 
TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
       38.60         8.75         3.45         4.67         2.50         6.48 
TCGA-K4-A6MB TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HE TCGA-XF-A8HF 
        4.27        12.23        16.67        97.45        56.19 

$`DEL PEAK 20(9P21.3) WILD-TYPE`
TCGA-BL-A3JM TCGA-BT-A20O TCGA-BT-A20R TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH 
        6.74        12.16         5.06        17.16         3.65         4.67 
TCGA-BT-A3PJ TCGA-BT-A42F TCGA-C4-A0EZ TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47V 
       12.82        28.41         8.98         0.43         0.13         0.10 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3QU TCGA-DK-A1A6 
        0.07         0.10        12.92         7.20         5.19        31.40 
TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 
       18.41       130.88       112.44         1.81         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WY 
       87.32         3.98         7.82        20.02         9.67       140.81 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E7-A3Y1 
       48.53        76.60        67.36        30.67        15.35         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 
        0.49         0.53         0.82         1.22        12.89        15.68 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SL 
        6.87         4.01        12.43        11.93        24.30        22.45 
TCGA-FD-A3SO TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BY 
        5.52        14.93        14.96        37.15        11.01         6.84 
TCGA-FD-A62N TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z9 
        2.66         9.30         4.11         2.20         4.01         7.13 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES 
        4.08         3.25        30.61         5.69        26.93        17.26 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GD-A2C5 
        2.24        15.81         4.50        15.91        17.75         7.73 
TCGA-GD-A3OP TCGA-GU-A42P TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QI 
        2.10         6.41         4.41         6.15         5.69         4.14 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P 
       19.07         1.51        10.52         1.74         1.81         6.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-XF-A8HD TCGA-XF-A8HG 
        6.35         3.45        13.48        88.93        15.35 

  DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE 
                        97.45                        140.81 
  DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE 
                         8.94                          7.73 
[1] "0.1 - 97.5 (8.9)"  "0.1 - 140.8 (7.7)"
[1] "hr=" "1"  
D52V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 20(9P21.3) MUTATED          1       1       40        41       37
  DEL PEAK 20(9P21.3) WILD-TYPE        0       1       28        31       30
D52V3, multiclass
           clus
vv          DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             1                             1
  STAGE II                           40                            28
  STAGE III                          41                            31
  STAGE IV                           37                            30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  DEL PEAK 20(9P21.3) MUTATED         36 57 19
  DEL PEAK 20(9P21.3) WILD-TYPE       26 44 13
D52V4, multiclass
          clus
vv         DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE
  T0+T1+T2                          36                            26
  T3                                57                            44
  T4                                19                            13
[1] 3 2
[1] 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(9P21.3) MUTATED   75 10 24  2
  DEL PEAK 20(9P21.3) WILD-TYPE 55 12 14  5
D52V5, multiclass
    clus
vv   DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE
  N0                          75                            55
  N1                          10                            12
  N2                          24                            14
  N3                           2                             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                            M0 M1 MX
  DEL PEAK 20(9P21.3) MUTATED   60  3 59
  DEL PEAK 20(9P21.3) WILD-TYPE 46  2 43
D52V6, multiclass
    clus
vv   DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE
  M0                          60                            46
  M1                           3                             2
  MX                          59                            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"
D52V7, binary
                               cls
clus                             0  1
  DEL PEAK 20(9P21.3) MUTATED   30 93
  DEL PEAK 20(9P21.3) WILD-TYPE 20 71
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(9P21.3) MUTATED     30   93
  DEL PEAK 20(9P21.3) WILD-TYPE   20   71
        clus
vv       DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE
  FEMALE                          30                            20
  MALE                            93                            71
[1] 2 2
[1] FALSE
D52V8, continuous
D52V9, continuous
D52V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(9P21.3) MUTATED      13                         7    94
  DEL PEAK 20(9P21.3) WILD-TYPE     9                         4    76
D52V11, multiclass
                           clus
vv                          DEL PEAK 20(9P21.3) MUTATED
  ASIAN                                              13
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              94
                           clus
vv                          DEL PEAK 20(9P21.3) WILD-TYPE
  ASIAN                                                 9
  BLACK OR AFRICAN AMERICAN                             4
  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"

Clustering(53) Variable = DEL PEAK 21(9Q33.2) MUTATION ANALYSIS
D53V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 21(9Q33.2) MUTATED   55 25
  DEL PEAK 21(9Q33.2) WILD-TYPE 96 32
  DEL PEAK 21(9Q33.2) MUTATED DEL PEAK 21(9Q33.2) WILD-TYPE 
                           80                           128 
  DEL PEAK 21(9Q33.2) MUTATED DEL PEAK 21(9Q33.2) WILD-TYPE 
                           25                            32 
$`DEL PEAK 21(9Q33.2) MUTATED`
TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T 
        2.66         6.58        32.84        17.88        19.50        14.89 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A42C TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C 
        5.59         3.65        28.70        23.01         0.46         0.69 
TCGA-CF-A47S TCGA-CF-A47V TCGA-CF-A47X TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU 
        0.13         0.10         0.10         4.90         5.46         5.19 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AD 
        1.84         9.34         2.14        31.40        19.00       112.44 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3WX 
       17.62        15.62        10.49        50.27        21.30        10.55 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       17.98        64.18        32.28        43.59        26.17        24.66 
TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A7DV TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        0.59         0.66         1.22         8.94         6.87         4.01 
TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43X 
       16.47        46.78        19.79         1.97        22.98         3.62 
TCGA-FD-A43Y TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P 
       12.13        27.45         6.87        49.68         4.83         6.28 
TCGA-FD-A6TA TCGA-FD-A6TG TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2EL 
       50.66         2.66        15.19         6.48         5.69        26.93 
TCGA-G2-A2EO TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A2C5 
       35.24         0.85         2.89        14.07         2.66         7.73 
TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GV-A3JV TCGA-GV-A3QH TCGA-GV-A40G TCGA-GV-A6ZA 
        2.10         2.20         4.41         7.79        19.07        11.54 
TCGA-HQ-A2OE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-MV-A51V TCGA-PQ-A6FN 
       38.60         3.45         4.67         2.50        13.48        16.67 
TCGA-XF-A8HF TCGA-XF-A8HG 
       56.19        15.35 

$`DEL PEAK 21(9Q33.2) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J 
       40.08         7.33         6.74        12.39        11.93        19.04 
TCGA-BT-A20O TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
       12.16         5.06        14.96         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E 
       17.16         4.67        12.82         2.07        15.42         9.99 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A47T TCGA-CF-A47W 
       28.41         8.98         1.94         0.43         0.07         0.07 
TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A7 
        0.10        12.92         7.20        16.31         2.53        18.41 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
        8.91       130.88        16.14         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20         3.98         7.82         8.22 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW 
       20.02         9.67         8.28       140.81        48.00        48.53 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E7-A3Y1 
       76.60        67.36        15.68        30.67        15.35         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A3B3 
        0.49         0.53         0.56         1.38         0.82        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
       15.68        12.43        11.93        15.88        45.93        24.30 
TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43P TCGA-FD-A43S 
       22.45        12.82         5.52        13.18        14.93        14.96 
TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
       14.93        13.38        37.15        11.01         6.87         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TD 
        5.69         6.84         2.66         6.38         9.30         6.71 
TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        4.11         2.20         4.01         7.13         3.48         4.08 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
        3.25        61.94        30.61        17.26         7.04        20.12 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS 
        2.24        15.81         4.50        15.91        17.75         1.12 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JW 
        3.12        20.98         6.41         7.66        11.31         6.41 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
        6.15         5.69         7.63         4.14         6.67         6.41 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ 
        1.51         6.74         8.75         6.48        10.52         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI 
        1.81         4.27         6.38         6.35         3.45        12.23 
TCGA-XF-A8HD TCGA-XF-A8HE 
       88.93        97.45 

  DEL PEAK 21(9Q33.2) MUTATED DEL PEAK 21(9Q33.2) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK 21(9Q33.2) MUTATED DEL PEAK 21(9Q33.2) WILD-TYPE 
                       112.44                        140.81 
  DEL PEAK 21(9Q33.2) MUTATED DEL PEAK 21(9Q33.2) WILD-TYPE 
                        9.915                         8.265 
[1] "0.1 - 112.4 (9.9)" "0.1 - 140.8 (8.3)"
[1] "hr=" "1.1"
D53V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 21(9Q33.2) MUTATED          1       0       24        27       28
  DEL PEAK 21(9Q33.2) WILD-TYPE        0       2       44        45       39
D53V3, multiclass
           clus
vv          DEL PEAK 21(9Q33.2) MUTATED DEL PEAK 21(9Q33.2) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             0                             2
  STAGE II                           24                            44
  STAGE III                          27                            45
  STAGE IV                           28                            39
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  DEL PEAK 21(9Q33.2) MUTATED         25 41 12
  DEL PEAK 21(9Q33.2) WILD-TYPE       37 60 20
D53V4, multiclass
          clus
vv         DEL PEAK 21(9Q33.2) MUTATED DEL PEAK 21(9Q33.2) WILD-TYPE
  T0+T1+T2                          25                            37
  T3                                41                            60
  T4                                12                            20
[1] 3 2
[1] 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(9Q33.2) MUTATED   50  8 20  2
  DEL PEAK 21(9Q33.2) WILD-TYPE 80 14 18  5
D53V5, multiclass
    clus
vv   DEL PEAK 21(9Q33.2) MUTATED DEL PEAK 21(9Q33.2) WILD-TYPE
  N0                          50                            80
  N1                           8                            14
  N2                          20                            18
  N3                           2                             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                            M0 M1 MX
  DEL PEAK 21(9Q33.2) MUTATED   43  1 38
  DEL PEAK 21(9Q33.2) WILD-TYPE 63  4 64
D53V6, multiclass
    clus
vv   DEL PEAK 21(9Q33.2) MUTATED DEL PEAK 21(9Q33.2) WILD-TYPE
  M0                          43                            63
  M1                           1                             4
  MX                          38                            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"
D53V7, binary
                               cls
clus                             0  1
  DEL PEAK 21(9Q33.2) MUTATED   16 67
  DEL PEAK 21(9Q33.2) WILD-TYPE 34 97
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(9Q33.2) MUTATED     16   67
  DEL PEAK 21(9Q33.2) WILD-TYPE   34   97
        clus
vv       DEL PEAK 21(9Q33.2) MUTATED DEL PEAK 21(9Q33.2) WILD-TYPE
  FEMALE                          16                            34
  MALE                            67                            97
[1] 2 2
[1] FALSE
D53V8, continuous
D53V9, continuous
D53V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(9Q33.2) MUTATED      11                         2    63
  DEL PEAK 21(9Q33.2) WILD-TYPE    11                         9   107
D53V11, multiclass
                           clus
vv                          DEL PEAK 21(9Q33.2) MUTATED
  ASIAN                                              11
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              63
                           clus
vv                          DEL PEAK 21(9Q33.2) WILD-TYPE
  ASIAN                                                11
  BLACK OR AFRICAN AMERICAN                             9
  WHITE                                               107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = DEL PEAK 22(10P12.1) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 22(10P12.1) MUTATED    28   9
  DEL PEAK 22(10P12.1) WILD-TYPE 123  48
  DEL PEAK 22(10P12.1) MUTATED DEL PEAK 22(10P12.1) WILD-TYPE 
                            37                            171 
  DEL PEAK 22(10P12.1) MUTATED DEL PEAK 22(10P12.1) WILD-TYPE 
                             9                             48 
$`DEL PEAK 22(10P12.1) MUTATED`
TCGA-BT-A20U TCGA-BT-A2LA TCGA-BT-A42C TCGA-C4-A0F0 TCGA-CF-A27C TCGA-CU-A0YR 
       14.96        17.16        28.70         1.94         0.69         7.20 
TCGA-CU-A3KJ TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A3IS TCGA-DK-A6AV TCGA-E5-A2PC 
        5.46         1.81         7.79        50.27        64.18        43.59 
TCGA-E5-A4TZ TCGA-E7-A541 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3N5 
       15.35         0.59        15.68         8.94         4.01        11.93 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A5BY TCGA-FD-A6TD 
       19.79         1.97        22.98        12.13         6.84         6.71 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-G2-A2EL TCGA-G2-A3IB TCGA-GC-A3BM 
       15.19         3.48         4.08        26.93         7.04         2.89 
TCGA-GC-A3RC TCGA-GV-A40G TCGA-H4-A2HQ TCGA-K4-A3WU TCGA-MV-A51V TCGA-PQ-A6FI 
       15.91        19.07         6.74         3.45        13.48        12.23 
TCGA-XF-A8HE 
       97.45 

$`DEL PEAK 22(10P12.1) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       11.93        19.04        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB 
        5.06        14.89         5.06         8.35         8.25         5.59 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E 
        3.65         4.67        12.82         2.07        15.42         9.99 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S 
       28.41         8.98        23.01         0.46         0.43         0.13 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN 
        0.07         0.10         0.07         0.10         0.10        12.92 
TCGA-CU-A0YO TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        4.90         5.19        16.31         1.84         9.34         2.53 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        31.40        18.41        19.00         8.91       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I4 
      112.44        16.14        17.62        15.62        10.59       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20         3.98         7.82         8.22        10.49 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        20.02         9.67         8.28        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       48.00        17.98        48.53        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       32.28        30.67        26.17        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV 
        0.53         0.56         0.66         1.38         0.82         1.22 
TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
       12.89         6.87        12.43        15.88        45.93        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       22.45        16.47        12.82         5.52        13.18        46.78 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       14.93        14.96        14.93         3.62        13.38        37.15 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 
       11.01         6.87         5.36         5.69        27.45         6.87 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       49.68         2.66         4.83         6.28         6.38        50.66 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z9 
        9.30         4.11         2.66         2.20         4.01         7.13 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO 
        3.25         6.48        61.94        30.61         5.69        35.24 
TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       17.26        20.12         0.85         2.24        15.81         4.50 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP 
       14.07        17.75         1.12         2.66         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
        3.12        20.98         2.20         6.41         7.66        11.31 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        4.41         6.41         6.15         5.69         7.63         7.79 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE 
        4.14         6.67         6.41        11.54         1.51        38.60 
TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ 
        8.75         4.67         2.50         6.48        10.52         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FN 
        1.81         4.27         6.38         6.35         3.45        16.67 
TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
       88.93        56.19        15.35 

  DEL PEAK 22(10P12.1) MUTATED DEL PEAK 22(10P12.1) WILD-TYPE 
                          0.59                           0.07 
  DEL PEAK 22(10P12.1) MUTATED DEL PEAK 22(10P12.1) WILD-TYPE 
                         97.45                         140.81 
  DEL PEAK 22(10P12.1) MUTATED DEL PEAK 22(10P12.1) WILD-TYPE 
                         11.93                           8.28 
[1] "0.6 - 97.5 (11.9)" "0.1 - 140.8 (8.3)"
[1] "hr=" "1.2"
D54V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 22(10P12.1) MUTATED          0       0       12        13       11
  DEL PEAK 22(10P12.1) WILD-TYPE        1       2       56        59       56
D54V3, multiclass
           clus
vv          DEL PEAK 22(10P12.1) MUTATED DEL PEAK 22(10P12.1) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              0                              2
  STAGE II                            12                             56
  STAGE III                           13                             59
  STAGE IV                            11                             56
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  DEL PEAK 22(10P12.1) MUTATED         12 12  7
  DEL PEAK 22(10P12.1) WILD-TYPE       50 89 25
D54V4, multiclass
          clus
vv         DEL PEAK 22(10P12.1) MUTATED DEL PEAK 22(10P12.1) WILD-TYPE
  T0+T1+T2                           12                             50
  T3                                 12                             89
  T4                                  7                             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 22(10P12.1) MUTATED    25   2   5   3
  DEL PEAK 22(10P12.1) WILD-TYPE 105  20  33   4
D54V5, multiclass
    clus
vv   DEL PEAK 22(10P12.1) MUTATED DEL PEAK 22(10P12.1) WILD-TYPE
  N0                           25                            105
  N1                            2                             20
  N2                            5                             33
  N3                            3                              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                             M0 M1 MX
  DEL PEAK 22(10P12.1) MUTATED   16  2 19
  DEL PEAK 22(10P12.1) WILD-TYPE 90  3 83
D54V6, multiclass
    clus
vv   DEL PEAK 22(10P12.1) MUTATED DEL PEAK 22(10P12.1) WILD-TYPE
  M0                           16                             90
  M1                            2                              3
  MX                           19                             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"
D54V7, binary
                                cls
clus                               0   1
  DEL PEAK 22(10P12.1) MUTATED     8  29
  DEL PEAK 22(10P12.1) WILD-TYPE  42 135
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(10P12.1) MUTATED      8   29
  DEL PEAK 22(10P12.1) WILD-TYPE   42  135
        clus
vv       DEL PEAK 22(10P12.1) MUTATED DEL PEAK 22(10P12.1) WILD-TYPE
  FEMALE                            8                             42
  MALE                             29                            135
[1] 2 2
[1] FALSE
D54V8, continuous
D54V9, continuous
D54V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(10P12.1) MUTATED       2                         6    27
  DEL PEAK 22(10P12.1) WILD-TYPE    20                         5   143
D54V11, multiclass
                           clus
vv                          DEL PEAK 22(10P12.1) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               27
                           clus
vv                          DEL PEAK 22(10P12.1) WILD-TYPE
  ASIAN                                                 20
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(55) Variable = DEL PEAK 23(10Q23.31) MUTATION ANALYSIS
D55V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 23(10Q23.31) MUTATED   62 24
  DEL PEAK 23(10Q23.31) WILD-TYPE 89 33
  DEL PEAK 23(10Q23.31) MUTATED DEL PEAK 23(10Q23.31) WILD-TYPE 
                             86                             122 
  DEL PEAK 23(10Q23.31) MUTATED DEL PEAK 23(10Q23.31) WILD-TYPE 
                             24                              33 
$`DEL PEAK 23(10Q23.31) MUTATED`
TCGA-BL-A0C8 TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       40.08        32.84         5.06        14.96         5.06         8.35 
TCGA-BT-A2LD TCGA-BT-A42B TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CU-A0YO 
        3.65        15.42         1.94        23.01         0.69         4.90 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AD 
        5.46         5.19         1.84         2.14        18.41       112.44 
TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        1.81         7.79        87.32         2.20         3.98         7.82 
TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A2PC 
        8.22        50.27         9.67        67.36        30.67        43.59 
TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 
       24.66         0.49         0.59         1.22         6.87         4.01 
TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       11.93        24.30        19.79         1.97        22.98        14.93 
TCGA-FD-A43U TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TD 
       14.93         6.84        27.45        49.68        50.66         6.71 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2EL 
       15.19         3.48         4.08         6.48         5.69        26.93 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RC TCGA-GC-A3RD 
        7.04        20.12         0.85         2.89        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GU-A42P TCGA-GV-A3JW TCGA-GV-A3JX 
       17.75         2.66         2.10         6.41         6.41         6.15 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40G TCGA-GV-A6ZA 
        5.69         7.63         7.79         4.14        19.07        11.54 
TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ 
        6.74         8.75         3.45         6.48        10.52         1.74 
TCGA-K4-A6FZ TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-XF-A8HD 
        1.81         6.35         3.45        13.48        12.23        88.93 
TCGA-XF-A8HE TCGA-XF-A8HF 
       97.45        56.19 

$`DEL PEAK 23(10Q23.31) WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
        7.33         2.66         6.74        12.39         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20X 
       19.04        12.16        17.88        19.50        14.89         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       17.16         5.59         4.67        12.82         2.07        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S 
        9.99        28.41         8.98         0.46         0.43         0.13 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN 
        0.07         0.10         0.07         0.10         0.10        12.92 
TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AA 
        7.20        16.31         9.34         2.53        31.40        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
        8.91       130.88        16.14        17.62        15.62        10.59 
TCGA-DK-A2I4 TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX 
      123.85        10.49        21.30        20.02         8.28        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
      140.81        48.00        17.98        64.18        48.53        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       15.68        32.28        15.35        26.17         0.10         0.53 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A3B3 TCGA-FD-A3B4 
        0.56         0.66         1.38         0.82        12.89        15.68 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM 
        8.94        12.43        15.88        45.93        22.45        16.47 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43S TCGA-FD-A43X 
       12.82         5.52        13.18        46.78        14.96         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
       12.13        13.38        37.15        11.01         6.87         5.36 
TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
        5.69         6.87         2.66         4.83         6.28         6.38 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z9 
        9.30         4.11         2.66         2.20         4.01         7.13 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A2ES TCGA-GC-A3I6 
        3.25        61.94        30.61        35.24        17.26         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS 
       15.81         4.50         1.12         7.73         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3QK TCGA-GV-A40E 
        2.20         7.66        11.31         4.41         6.67         6.41 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A6MB TCGA-K4-A83P 
        1.51        38.60         4.67         2.50         4.27         6.38 
TCGA-PQ-A6FN TCGA-XF-A8HG 
       16.67        15.35 

  DEL PEAK 23(10Q23.31) MUTATED DEL PEAK 23(10Q23.31) WILD-TYPE 
                           0.49                            0.07 
  DEL PEAK 23(10Q23.31) MUTATED DEL PEAK 23(10Q23.31) WILD-TYPE 
                         112.44                          140.81 
  DEL PEAK 23(10Q23.31) MUTATED DEL PEAK 23(10Q23.31) WILD-TYPE 
                          7.710                           9.665 
[1] "0.5 - 112.4 (7.7)" "0.1 - 140.8 (9.7)"
[1] "hr=" "1"  
D55V2, continuous
                                 vv
clus                              STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 23(10Q23.31) MUTATED          1       1       29        24       30
  DEL PEAK 23(10Q23.31) WILD-TYPE        0       1       39        48       37
D55V3, multiclass
           clus
vv          DEL PEAK 23(10Q23.31) MUTATED DEL PEAK 23(10Q23.31) WILD-TYPE
  STAGE 0A                              1                               0
  STAGE I                               1                               1
  STAGE II                             29                              39
  STAGE III                            24                              48
  STAGE IV                             30                              37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1+T2 T3 T4
  DEL PEAK 23(10Q23.31) MUTATED         26 36 12
  DEL PEAK 23(10Q23.31) WILD-TYPE       36 65 20
D55V4, multiclass
          clus
vv         DEL PEAK 23(10Q23.31) MUTATED DEL PEAK 23(10Q23.31) WILD-TYPE
  T0+T1+T2                            26                              36
  T3                                  36                              65
  T4                                  12                              20
[1] 3 2
[1] 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(10Q23.31) MUTATED   45  8 16  5
  DEL PEAK 23(10Q23.31) WILD-TYPE 85 14 22  2
D55V5, multiclass
    clus
vv   DEL PEAK 23(10Q23.31) MUTATED DEL PEAK 23(10Q23.31) WILD-TYPE
  N0                            45                              85
  N1                             8                              14
  N2                            16                              22
  N3                             5                               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                              M0 M1 MX
  DEL PEAK 23(10Q23.31) MUTATED   36  2 47
  DEL PEAK 23(10Q23.31) WILD-TYPE 70  3 55
D55V6, multiclass
    clus
vv   DEL PEAK 23(10Q23.31) MUTATED DEL PEAK 23(10Q23.31) WILD-TYPE
  M0                            36                              70
  M1                             2                               3
  MX                            47                              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"
D55V7, binary
                                 cls
clus                               0  1
  DEL PEAK 23(10Q23.31) MUTATED   19 67
  DEL PEAK 23(10Q23.31) WILD-TYPE 31 97
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 23(10Q23.31) MUTATED     19   67
  DEL PEAK 23(10Q23.31) WILD-TYPE   31   97
        clus
vv       DEL PEAK 23(10Q23.31) MUTATED DEL PEAK 23(10Q23.31) WILD-TYPE
  FEMALE                            19                              31
  MALE                              67                              97
[1] 2 2
[1] FALSE
D55V8, continuous
D55V9, continuous
D55V10, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(10Q23.31) MUTATED       3                         6    71
  DEL PEAK 23(10Q23.31) WILD-TYPE    19                         5    99
D55V11, multiclass
                           clus
vv                          DEL PEAK 23(10Q23.31) MUTATED
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                71
                           clus
vv                          DEL PEAK 23(10Q23.31) WILD-TYPE
  ASIAN                                                  19
  BLACK OR AFRICAN AMERICAN                               5
  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"

Clustering(56) Variable = DEL PEAK 24(11P15.5) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 24(11P15.5) MUTATED   68 30
  DEL PEAK 24(11P15.5) WILD-TYPE 83 27
  DEL PEAK 24(11P15.5) MUTATED DEL PEAK 24(11P15.5) WILD-TYPE 
                            98                            110 
  DEL PEAK 24(11P15.5) MUTATED DEL PEAK 24(11P15.5) WILD-TYPE 
                            30                             27 
$`DEL PEAK 24(11P15.5) MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20T 
       40.08         2.66        19.04        32.84         5.06        14.89 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
        5.06         8.35         4.67         2.07        15.42        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        8.98         1.94        23.01         0.46         0.43         0.69 
TCGA-CF-A47S TCGA-CF-A47X TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-CU-A72E 
        0.13         0.10         7.20         5.46         1.84         9.34 
TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A2HX 
        2.14        18.41         8.91       112.44        17.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
       10.59        87.32         2.20         3.98         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B5 
       10.49        50.27        21.30        17.98        64.18        32.28 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
       15.35        26.17        24.66         0.59         0.56         0.66 
TCGA-E7-A7DV TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN 
        1.22         8.94         4.01        24.30        22.45        12.82 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A5BV TCGA-FD-A5BZ 
       19.79         1.97        22.98        12.13         5.36        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TA 
        6.87        49.68         2.66         4.83         6.28        50.66 
TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FT-A61P 
        9.30         2.66         2.20        15.19         3.48         6.48 
TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RD 
       35.24        20.12         0.85         2.89         2.24        14.07 
TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        1.12         7.73         2.10         2.20         7.66        11.31 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        4.41         6.41         7.63         6.41        19.07        11.54 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A6MB TCGA-PQ-A6FI 
        6.74        38.60         8.75         4.67         4.27        12.23 
TCGA-XF-A8HF TCGA-XF-A8HG 
       56.19        15.35 

$`DEL PEAK 24(11P15.5) WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O 
        7.33         6.74        12.39         6.58        11.93        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       17.88        19.50        14.96         8.25        17.16         5.59 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42E TCGA-BT-A42F TCGA-CF-A47T TCGA-CF-A47V 
        3.65        12.82         9.99        28.41         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3QU TCGA-CU-A3YL 
        0.07         0.10        12.92         4.90         5.19        16.31 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AG 
        2.53        31.40        19.00       130.88        16.14        15.62 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
        7.79       123.85        20.02         9.67         8.28        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
      140.81        48.00        48.53        76.60        67.36        15.68 
TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A677 
       30.67        43.59         0.10         0.49         0.53         1.38 
TCGA-E7-A678 TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 
        0.82        12.89        15.68         6.87        12.43        11.93 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       15.88        45.93        16.47         5.52        13.18        46.78 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       14.93        14.96        14.93         3.62        13.38        37.15 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62S TCGA-FD-A6TD 
       11.01         6.87         5.69         6.84         6.38         6.71 
TCGA-FD-A6TE TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EF 
        4.11         4.01         7.13         4.08         3.25        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-GC-A3OO 
       30.61         5.69        26.93        17.26         7.04        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A3OS 
        4.50        15.91        17.75         2.66         3.12        20.98 
TCGA-GU-A42P TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
        6.41         6.15         5.69         7.79         4.14         6.67 
TCGA-H4-A2HO TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ 
        1.51         3.45         2.50         6.48        10.52         1.74 
TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN 
        1.81         6.38         6.35         3.45        13.48        16.67 
TCGA-XF-A8HD TCGA-XF-A8HE 
       88.93        97.45 

  DEL PEAK 24(11P15.5) MUTATED DEL PEAK 24(11P15.5) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 24(11P15.5) MUTATED DEL PEAK 24(11P15.5) WILD-TYPE 
                        112.44                         140.81 
  DEL PEAK 24(11P15.5) MUTATED DEL PEAK 24(11P15.5) WILD-TYPE 
                         8.020                         10.255 
[1] "0.1 - 112.4 (8.0)"  "0.1 - 140.8 (10.3)"
[1] "hr=" "1.4"
D56V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 24(11P15.5) MUTATED          1       1       29        25       42
  DEL PEAK 24(11P15.5) WILD-TYPE        0       1       39        47       25
D56V3, multiclass
           clus
vv          DEL PEAK 24(11P15.5) MUTATED DEL PEAK 24(11P15.5) WILD-TYPE
  STAGE 0A                             1                              0
  STAGE I                              1                              1
  STAGE II                            29                             39
  STAGE III                           25                             47
  STAGE IV                            42                             25
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  DEL PEAK 24(11P15.5) MUTATED         31 49 15
  DEL PEAK 24(11P15.5) WILD-TYPE       31 52 17
D56V4, multiclass
          clus
vv         DEL PEAK 24(11P15.5) MUTATED DEL PEAK 24(11P15.5) WILD-TYPE
  T0+T1+T2                           31                             31
  T3                                 49                             52
  T4                                 15                             17
[1] 3 2
[1] 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(11P15.5) MUTATED   52 10 28  3
  DEL PEAK 24(11P15.5) WILD-TYPE 78 12 10  4
D56V5, multiclass
    clus
vv   DEL PEAK 24(11P15.5) MUTATED DEL PEAK 24(11P15.5) WILD-TYPE
  N0                           52                             78
  N1                           10                             12
  N2                           28                             10
  N3                            3                              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                             M0 M1 MX
  DEL PEAK 24(11P15.5) MUTATED   50  4 47
  DEL PEAK 24(11P15.5) WILD-TYPE 56  1 55
D56V6, multiclass
    clus
vv   DEL PEAK 24(11P15.5) MUTATED DEL PEAK 24(11P15.5) WILD-TYPE
  M0                           50                             56
  M1                            4                              1
  MX                           47                             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"
D56V7, binary
                                cls
clus                              0  1
  DEL PEAK 24(11P15.5) MUTATED   22 80
  DEL PEAK 24(11P15.5) WILD-TYPE 28 84
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(11P15.5) MUTATED     22   80
  DEL PEAK 24(11P15.5) WILD-TYPE   28   84
        clus
vv       DEL PEAK 24(11P15.5) MUTATED DEL PEAK 24(11P15.5) WILD-TYPE
  FEMALE                           22                             28
  MALE                             80                             84
[1] 2 2
[1] FALSE
D56V8, continuous
D56V9, continuous
D56V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(11P15.5) MUTATED      14                         4    74
  DEL PEAK 24(11P15.5) WILD-TYPE     8                         7    96
D56V11, multiclass
                           clus
vv                          DEL PEAK 24(11P15.5) MUTATED
  ASIAN                                               14
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               74
                           clus
vv                          DEL PEAK 24(11P15.5) WILD-TYPE
  ASIAN                                                  8
  BLACK OR AFRICAN AMERICAN                              7
  WHITE                                                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(57) Variable = DEL PEAK 25(11Q23.3) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 25(11Q23.3) MUTATED   57 17
  DEL PEAK 25(11Q23.3) WILD-TYPE 94 40
  DEL PEAK 25(11Q23.3) MUTATED DEL PEAK 25(11Q23.3) WILD-TYPE 
                            74                            134 
  DEL PEAK 25(11Q23.3) MUTATED DEL PEAK 25(11Q23.3) WILD-TYPE 
                            17                             40 
$`DEL PEAK 25(11Q23.3) MUTATED`
TCGA-BL-A0C8 TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B 
       40.08        32.84        14.89         5.59         4.67        15.42 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-CF-A1HS TCGA-CF-A27C 
       28.70         9.99        28.41         8.98         0.43         0.69 
TCGA-CF-A47X TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AB 
        0.10        12.92         5.46         2.14        31.40         8.91 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
      130.88       112.44         7.82         8.22        10.49        50.27 
TCGA-DK-A6AV TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ 
       64.18        30.67        43.59        15.35        26.17         0.49 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        0.59         0.56         0.66         8.94         6.87         4.01 
TCGA-FD-A3SJ TCGA-FD-A43N TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BU TCGA-FD-A5BV 
       24.30        22.98         3.62        12.13         6.87         5.36 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
        6.84         6.87        49.68         2.66         4.83         6.38 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TH TCGA-FT-A61P TCGA-G2-A3IB TCGA-GC-A3BM 
       50.66         9.30         2.20         6.48         7.04         2.89 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GU-A42Q TCGA-GU-A42R 
        1.12         2.66         7.73         2.10         7.66        11.31 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        4.41         6.41         6.67         6.41        19.07        11.54 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-PQ-A6FI 
        6.74        38.60         4.67         2.50         6.48        12.23 
TCGA-XF-A8HE TCGA-XF-A8HG 
       97.45        15.35 

$`DEL PEAK 25(11Q23.3) WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
        7.33         2.66         6.74        12.39         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       19.04        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PJ 
        5.06         8.35         8.25        17.16         3.65        12.82 
TCGA-BT-A3PK TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A47S TCGA-CF-A47T 
        2.07         1.94        23.01         0.46         0.13         0.07 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU 
        0.10         0.07         0.10         4.90         7.20         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AA 
       16.31         1.84         9.34         2.53        18.41        19.00 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IT TCGA-DK-A3IU 
      123.85        87.32         2.20         3.98        21.30        20.02 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
        9.67         8.28        10.55       140.81        48.00        17.98 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E7-A3X6 
       48.53        76.60        67.36        15.68        32.28        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 
        0.10         0.53         1.38         0.82         1.22        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL 
       15.68        12.43        11.93        15.88        45.93        22.45 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       16.47        12.82         5.52        13.18        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BS 
        1.97        14.93        14.96        14.93        13.38        37.15 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A62P TCGA-FD-A6TD TCGA-FD-A6TE 
       11.01         5.69        27.45         6.28         6.71         4.11 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        2.66         4.01        15.19         7.13         3.48         4.08 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        3.25        61.94        30.61         5.69        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       17.26        20.12         0.85         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       15.91        14.07        17.75         3.12        20.98         2.20 
TCGA-GU-A42P TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
        6.41         6.15         5.69         7.63         7.79         4.14 
TCGA-H4-A2HO TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
        1.51         8.75         3.45        10.52         1.74         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN 
        4.27         6.38         6.35         3.45        13.48        16.67 
TCGA-XF-A8HD TCGA-XF-A8HF 
       88.93        56.19 

  DEL PEAK 25(11Q23.3) MUTATED DEL PEAK 25(11Q23.3) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 25(11Q23.3) MUTATED DEL PEAK 25(11Q23.3) WILD-TYPE 
                        130.88                         140.81 
  DEL PEAK 25(11Q23.3) MUTATED DEL PEAK 25(11Q23.3) WILD-TYPE 
                         7.695                         10.095 
[1] "0.1 - 130.9 (7.7)"  "0.1 - 140.8 (10.1)"
[1] "hr=" "1.3"
D57V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 25(11Q23.3) MUTATED          1       1       25        24       22
  DEL PEAK 25(11Q23.3) WILD-TYPE        0       1       43        48       45
D57V3, multiclass
           clus
vv          DEL PEAK 25(11Q23.3) MUTATED DEL PEAK 25(11Q23.3) WILD-TYPE
  STAGE 0A                             1                              0
  STAGE I                              1                              1
  STAGE II                            25                             43
  STAGE III                           24                             48
  STAGE IV                            22                             45
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  DEL PEAK 25(11Q23.3) MUTATED         27 34  9
  DEL PEAK 25(11Q23.3) WILD-TYPE       35 67 23
D57V4, multiclass
          clus
vv         DEL PEAK 25(11Q23.3) MUTATED DEL PEAK 25(11Q23.3) WILD-TYPE
  T0+T1+T2                           27                             35
  T3                                 34                             67
  T4                                  9                             23
[1] 3 2
[1] 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(11Q23.3) MUTATED   45  9 13  0
  DEL PEAK 25(11Q23.3) WILD-TYPE 85 13 25  7
D57V5, multiclass
    clus
vv   DEL PEAK 25(11Q23.3) MUTATED DEL PEAK 25(11Q23.3) WILD-TYPE
  N0                           45                             85
  N1                            9                             13
  N2                           13                             25
  N3                            0                              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"
                                vv
clus                             M0 M1 MX
  DEL PEAK 25(11Q23.3) MUTATED   29  2 45
  DEL PEAK 25(11Q23.3) WILD-TYPE 77  3 57
D57V6, multiclass
    clus
vv   DEL PEAK 25(11Q23.3) MUTATED DEL PEAK 25(11Q23.3) WILD-TYPE
  M0                           29                             77
  M1                            2                              3
  MX                           45                             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"
D57V7, binary
                                cls
clus                               0   1
  DEL PEAK 25(11Q23.3) MUTATED    19  57
  DEL PEAK 25(11Q23.3) WILD-TYPE  31 107
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(11Q23.3) MUTATED     19   57
  DEL PEAK 25(11Q23.3) WILD-TYPE   31  107
        clus
vv       DEL PEAK 25(11Q23.3) MUTATED DEL PEAK 25(11Q23.3) WILD-TYPE
  FEMALE                           19                             31
  MALE                             57                            107
[1] 2 2
[1] FALSE
D57V8, continuous
D57V9, continuous
D57V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(11Q23.3) MUTATED      10                         6    53
  DEL PEAK 25(11Q23.3) WILD-TYPE    12                         5   117
D57V11, multiclass
                           clus
vv                          DEL PEAK 25(11Q23.3) MUTATED
  ASIAN                                               10
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               53
                           clus
vv                          DEL PEAK 25(11Q23.3) WILD-TYPE
  ASIAN                                                 12
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                117
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(58) Variable = DEL PEAK 26(13Q14.2) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 26(13Q14.2) MUTATED   61 26
  DEL PEAK 26(13Q14.2) WILD-TYPE 90 31
  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                            87                            121 
  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                            26                             31 
$`DEL PEAK 26(13Q14.2) MUTATED`
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V 
        2.66         6.74        32.84         5.06        14.89         5.06 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
        8.25        17.16         4.67        12.82         2.07        15.42 
TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CU-A3QU 
       28.70         9.99         8.98         1.94         0.43         5.19 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
        1.84         2.53        18.41       130.88       112.44        16.14 
TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM 
        1.81         7.79       123.85        87.32         2.20         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B6 
        8.22        10.49         9.67        17.98        67.36        30.67 
TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A7DV 
       43.59        24.66         0.49         0.59         0.56         1.22 
TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SJ 
       12.89         8.94         6.87         4.01        11.93        24.30 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A5BU 
       12.82        46.78        19.79         1.97        14.93         6.87 
TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A6TC 
        5.36         6.84        27.45        49.68         2.66         9.30 
TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A2ES 
        4.11         2.20         4.08         6.48        35.24        17.26 
TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OP 
        2.89        15.81         4.50         1.12         2.66         2.10 
TCGA-GD-A6C6 TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QI TCGA-HQ-A2OE TCGA-K4-A4AC 
        2.20         6.41         6.15         4.14        38.60         6.48 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
       10.52         1.74         1.81         6.35         3.45        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD 
       12.23        16.67        88.93 

$`DEL PEAK 26(13Q14.2) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
       40.08         7.33        12.39         6.58        11.93        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB 
       12.16        17.88        19.50        14.96         8.35         5.59 
TCGA-BT-A2LD TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S 
        3.65        28.41        23.01         0.46         0.69         0.13 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN 
        0.07         0.10         0.07         0.10         0.10        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A5 
        4.90         7.20         5.46        16.31         9.34         2.14 
TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
       31.40        19.00         8.91        17.62        15.62        10.59 
TCGA-DK-A3IL TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX 
        3.98        50.27        21.30        20.02         8.28        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 
      140.81        48.00        64.18        48.53        76.60        15.68 
TCGA-DK-A6B5 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KF 
       32.28        15.35        26.17         0.10         0.53         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA 
        1.38         0.82        15.68        12.43        15.88        45.93 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S 
       22.45        16.47         5.52        13.18        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.93         3.62        12.13        13.38        37.15        11.01 
TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
        5.69         6.87         4.83         6.28         6.38        50.66 
TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        6.71         2.66         4.01        15.19         7.13         3.48 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB 
        3.25        61.94        30.61         5.69        26.93         7.04 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
       20.12         0.85         2.24        15.91        14.07        17.75 
TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
        7.73         3.12        20.98         6.41         7.66        11.31 
TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E 
        4.41         5.69         7.63         7.79         6.67         6.41 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A3WU 
       19.07        11.54         1.51         6.74         8.75         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A6MB TCGA-K4-A83P TCGA-XF-A8HE TCGA-XF-A8HF 
        4.67         2.50         4.27         6.38        97.45        56.19 
TCGA-XF-A8HG 
       15.35 

  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                          0.43                           0.07 
  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                        130.88                         140.81 
  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                          7.82                           9.34 
[1] "0.4 - 130.9 (7.8)" "0.1 - 140.8 (9.3)"
[1] "hr=" "1.3"
D58V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 26(13Q14.2) MUTATED          0       0       24        29       32
  DEL PEAK 26(13Q14.2) WILD-TYPE        1       2       44        43       35
D58V3, multiclass
           clus
vv          DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              0                              2
  STAGE II                            24                             44
  STAGE III                           29                             43
  STAGE IV                            32                             35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  DEL PEAK 26(13Q14.2) MUTATED         25 46 11
  DEL PEAK 26(13Q14.2) WILD-TYPE       37 55 21
D58V4, multiclass
          clus
vv         DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE
  T0+T1+T2                           25                             37
  T3                                 46                             55
  T4                                 11                             21
[1] 3 2
[1] 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(13Q14.2) MUTATED   48 10 19  4
  DEL PEAK 26(13Q14.2) WILD-TYPE 82 12 19  3
D58V5, multiclass
    clus
vv   DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE
  N0                           48                             82
  N1                           10                             12
  N2                           19                             19
  N3                            4                              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                             M0 M1 MX
  DEL PEAK 26(13Q14.2) MUTATED   40  1 46
  DEL PEAK 26(13Q14.2) WILD-TYPE 66  4 56
D58V6, multiclass
    clus
vv   DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE
  M0                           40                             66
  M1                            1                              4
  MX                           46                             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"
D58V7, binary
                                cls
clus                              0  1
  DEL PEAK 26(13Q14.2) MUTATED   20 67
  DEL PEAK 26(13Q14.2) WILD-TYPE 30 97
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(13Q14.2) MUTATED     20   67
  DEL PEAK 26(13Q14.2) WILD-TYPE   30   97
        clus
vv       DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE
  FEMALE                           20                             30
  MALE                             67                             97
[1] 2 2
[1] FALSE
D58V8, continuous
D58V9, continuous
D58V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(13Q14.2) MUTATED       4                         6    72
  DEL PEAK 26(13Q14.2) WILD-TYPE    18                         5    98
D58V11, multiclass
                           clus
vv                          DEL PEAK 26(13Q14.2) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               72
                           clus
vv                          DEL PEAK 26(13Q14.2) WILD-TYPE
  ASIAN                                                 18
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                 98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(59) Variable = DEL PEAK 27(14Q12) MUTATION ANALYSIS
D59V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 27(14Q12) MUTATED    42  20
  DEL PEAK 27(14Q12) WILD-TYPE 109  37
  DEL PEAK 27(14Q12) MUTATED DEL PEAK 27(14Q12) WILD-TYPE 
                          62                          146 
  DEL PEAK 27(14Q12) MUTATED DEL PEAK 27(14Q12) WILD-TYPE 
                          20                           37 
$`DEL PEAK 27(14Q12) MUTATED`
TCGA-BT-A20J TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PK 
       19.04        14.89         5.06         5.59         3.65         2.07 
TCGA-BT-A42E TCGA-CF-A1HR TCGA-CF-A47X TCGA-CU-A0YO TCGA-CU-A3QU TCGA-CU-A5W6 
        9.99         0.46         0.10         4.90         5.19         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I6 
        2.53         2.14       130.88       112.44        10.59        87.32 
TCGA-DK-A3IK TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
        2.20        10.49        50.27        48.00        17.98        64.18 
TCGA-DK-A6B5 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A7DV 
       32.28        15.35        26.17         0.49         0.56         1.22 
TCGA-FD-A3B5 TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43U TCGA-FD-A5BX 
        8.94        13.18        46.78        19.79        14.93         5.69 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TG 
        6.87        49.68         6.28        50.66         9.30         2.66 
TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A3IE 
        2.20        15.19         4.08         6.48        61.94        20.12 
TCGA-G2-A3VY TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GU-A42Q TCGA-GV-A3JZ TCGA-GV-A3QF 
        0.85         4.50        14.07         7.66         5.69         7.63 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WU 
        6.67         6.41        11.54         6.74        38.60         3.45 
TCGA-K4-A6MB TCGA-PQ-A6FI 
        4.27        12.23 

$`DEL PEAK 27(14Q12) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       11.93        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A3PJ 
       14.96         8.35         8.25        17.16         4.67        12.82 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
       15.42        28.70        28.41         8.98         1.94        23.01 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.43         0.69         0.13         0.07         0.10         0.07 
TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A72E 
        0.10        12.92         7.20         5.46        16.31         9.34 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF 
       31.40        18.41        19.00         8.91        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IM 
       15.62         1.81         7.79       123.85         3.98         7.82 
TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
        8.22        21.30        20.02         9.67         8.28        10.55 
TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 
      140.81        48.53        76.60        67.36        15.68        30.67 
TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KF 
       43.59        24.66         0.10         0.53         0.59         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 
        1.38         0.82        12.89        15.68         6.87         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.43        11.93        15.88        45.93        24.30        22.45 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       16.47        12.82         5.52         1.97        22.98        14.93 
TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96         3.62        12.13        13.38        37.15        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O 
        6.87         5.36         6.84        27.45         2.66         4.83 
TCGA-FD-A62S TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        6.38         6.71         4.11         4.01         7.13         3.48 
TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
        3.25        30.61         5.69        26.93        35.24        17.26 
TCGA-G2-A3IB TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3WC 
        7.04         2.89         2.24        15.81        15.91        17.75 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        1.12         2.66         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
        2.20         6.41        11.31         4.41         6.41         6.15 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40G TCGA-H4-A2HO TCGA-K4-A3WS TCGA-K4-A3WV 
        7.79         4.14        19.07         1.51         8.75         4.67 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P 
        2.50         6.48        10.52         1.74         1.81         6.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE 
        6.35         3.45        13.48        16.67        88.93        97.45 
TCGA-XF-A8HF TCGA-XF-A8HG 
       56.19        15.35 

  DEL PEAK 27(14Q12) MUTATED DEL PEAK 27(14Q12) WILD-TYPE 
                        0.10                         0.07 
  DEL PEAK 27(14Q12) MUTATED DEL PEAK 27(14Q12) WILD-TYPE 
                      130.88                       140.81 
  DEL PEAK 27(14Q12) MUTATED DEL PEAK 27(14Q12) WILD-TYPE 
                       7.645                        8.830 
[1] "0.1 - 130.9 (7.6)" "0.1 - 140.8 (8.8)"
[1] "hr=" "1.2"
D59V2, continuous
                              vv
clus                           STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 27(14Q12) MUTATED          1       0       17        14       29
  DEL PEAK 27(14Q12) WILD-TYPE        0       2       51        58       38
D59V3, multiclass
           clus
vv          DEL PEAK 27(14Q12) MUTATED DEL PEAK 27(14Q12) WILD-TYPE
  STAGE 0A                           1                            0
  STAGE I                            0                            2
  STAGE II                          17                           51
  STAGE III                         14                           58
  STAGE IV                          29                           38
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1+T2 T3 T4
  DEL PEAK 27(14Q12) MUTATED         18 27 12
  DEL PEAK 27(14Q12) WILD-TYPE       44 74 20
D59V4, multiclass
          clus
vv         DEL PEAK 27(14Q12) MUTATED DEL PEAK 27(14Q12) WILD-TYPE
  T0+T1+T2                         18                           44
  T3                               27                           74
  T4                               12                           20
[1] 3 2
[1] 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(14Q12) MUTATED    29   7  20   2
  DEL PEAK 27(14Q12) WILD-TYPE 101  15  18   5
D59V5, multiclass
    clus
vv   DEL PEAK 27(14Q12) MUTATED DEL PEAK 27(14Q12) WILD-TYPE
  N0                         29                          101
  N1                          7                           15
  N2                         20                           18
  N3                          2                            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                           M0 M1 MX
  DEL PEAK 27(14Q12) MUTATED   32  1 29
  DEL PEAK 27(14Q12) WILD-TYPE 74  4 73
D59V6, multiclass
    clus
vv   DEL PEAK 27(14Q12) MUTATED DEL PEAK 27(14Q12) WILD-TYPE
  M0                         32                           74
  M1                          1                            4
  MX                         29                           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"
D59V7, binary
                              cls
clus                             0   1
  DEL PEAK 27(14Q12) MUTATED    12  51
  DEL PEAK 27(14Q12) WILD-TYPE  38 113
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 27(14Q12) MUTATED     12   51
  DEL PEAK 27(14Q12) WILD-TYPE   38  113
        clus
vv       DEL PEAK 27(14Q12) MUTATED DEL PEAK 27(14Q12) WILD-TYPE
  FEMALE                         12                           38
  MALE                           51                          113
[1] 2 2
[1] FALSE
D59V8, continuous
D59V9, continuous
D59V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(14Q12) MUTATED       7                         3    48
  DEL PEAK 27(14Q12) WILD-TYPE    15                         8   122
D59V11, multiclass
                           clus
vv                          DEL PEAK 27(14Q12) MUTATED
  ASIAN                                              7
  BLACK OR AFRICAN AMERICAN                          3
  WHITE                                             48
                           clus
vv                          DEL PEAK 27(14Q12) WILD-TYPE
  ASIAN                                               15
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                              122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(60) Variable = DEL PEAK 28(14Q24.1) MUTATION ANALYSIS
D60V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 28(14Q24.1) MUTATED    46  18
  DEL PEAK 28(14Q24.1) WILD-TYPE 105  39
  DEL PEAK 28(14Q24.1) MUTATED DEL PEAK 28(14Q24.1) WILD-TYPE 
                            64                            144 
  DEL PEAK 28(14Q24.1) MUTATED DEL PEAK 28(14Q24.1) WILD-TYPE 
                            18                             39 
$`DEL PEAK 28(14Q24.1) MUTATED`
TCGA-BT-A20J TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A3PK 
       19.04        14.89         5.06         8.35         5.59         2.07 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47X TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU 
        0.46         0.43         0.10         4.90         7.20         5.19 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD 
        1.84         2.53         2.14        18.41       130.88       112.44 
TCGA-DK-A2I1 TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B5 
       10.59        10.49        50.27        48.00        64.18        32.28 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SP 
       15.35        26.17         0.49        24.30        12.82        13.18 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5C0 
       46.78        19.79        22.98        14.93        12.13         6.87 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TH 
       49.68         6.28        50.66         9.30         2.66         2.20 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A3IE TCGA-G2-A3VY 
       15.19         4.08         6.48        61.94        20.12         0.85 
TCGA-GC-A3RD TCGA-GD-A2C5 TCGA-GU-A42Q TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI 
       14.07         7.73         7.66         5.69         7.63         4.14 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WU 
        6.41        19.07        11.54         6.74        38.60         3.45 
TCGA-K4-A6MB TCGA-MV-A51V TCGA-PQ-A6FI TCGA-XF-A8HF 
        4.27        13.48        12.23        56.19 

$`DEL PEAK 28(14Q24.1) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       11.93        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
       14.96         8.25        17.16         3.65         4.67        12.82 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
       15.42        28.70         9.99        28.41         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       23.01         0.69         0.13         0.07         0.10         0.07 
TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A6 
        0.10        12.92         5.46        16.31         9.34        31.40 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
       19.00         8.91        16.14        17.62        15.62         1.81 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        7.79       123.85        87.32         2.20         3.98         7.82 
TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
        8.22        21.30        20.02         9.67         8.28        10.55 
TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
      140.81        17.98        48.53        76.60        67.36        15.68 
TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A541 
       30.67        43.59        24.66         0.10         0.53         0.59 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 
        0.56         0.66         1.38         0.82         1.22        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       15.68         8.94         6.87         4.01        12.43        11.93 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SS 
       15.88        45.93        22.45        16.47         5.52         1.97 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.93        14.96         3.62        13.38        37.15        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A62N 
        6.87         5.36         5.69         6.84        27.45         2.66 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TI TCGA-FJ-A3Z9 
        4.83         6.38         6.71         4.11         4.01         7.13 
TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        3.48         3.25        30.61         5.69        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       17.26         7.04         2.89         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ 
       15.91        17.75         1.12         2.66         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW 
       20.98         2.20         6.41        11.31         4.41         6.41 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QK TCGA-H4-A2HO TCGA-K4-A3WS TCGA-K4-A3WV 
        6.15         7.79         6.67         1.51         8.75         4.67 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P 
        2.50         6.48        10.52         1.74         1.81         6.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG 
        6.35         3.45        16.67        88.93        97.45        15.35 

  DEL PEAK 28(14Q24.1) MUTATED DEL PEAK 28(14Q24.1) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 28(14Q24.1) MUTATED DEL PEAK 28(14Q24.1) WILD-TYPE 
                        130.88                         140.81 
  DEL PEAK 28(14Q24.1) MUTATED DEL PEAK 28(14Q24.1) WILD-TYPE 
                        10.540                          8.235 
[1] "0.1 - 130.9 (10.5)" "0.1 - 140.8 (8.2)" 
[1] "hr=" "1.1"
D60V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 28(14Q24.1) MUTATED          1       0       18        17       26
  DEL PEAK 28(14Q24.1) WILD-TYPE        0       2       50        55       41
D60V3, multiclass
           clus
vv          DEL PEAK 28(14Q24.1) MUTATED DEL PEAK 28(14Q24.1) WILD-TYPE
  STAGE 0A                             1                              0
  STAGE I                              0                              2
  STAGE II                            18                             50
  STAGE III                           17                             55
  STAGE IV                            26                             41
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  DEL PEAK 28(14Q24.1) MUTATED         19 29 11
  DEL PEAK 28(14Q24.1) WILD-TYPE       43 72 21
D60V4, multiclass
          clus
vv         DEL PEAK 28(14Q24.1) MUTATED DEL PEAK 28(14Q24.1) WILD-TYPE
  T0+T1+T2                           19                             43
  T3                                 29                             72
  T4                                 11                             21
[1] 3 2
[1] 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(14Q24.1) MUTATED   35  3 21  1
  DEL PEAK 28(14Q24.1) WILD-TYPE 95 19 17  6
D60V5, multiclass
    clus
vv   DEL PEAK 28(14Q24.1) MUTATED DEL PEAK 28(14Q24.1) WILD-TYPE
  N0                           35                             95
  N1                            3                             19
  N2                           21                             17
  N3                            1                              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"
                                vv
clus                             M0 M1 MX
  DEL PEAK 28(14Q24.1) MUTATED   30  1 33
  DEL PEAK 28(14Q24.1) WILD-TYPE 76  4 69
D60V6, multiclass
    clus
vv   DEL PEAK 28(14Q24.1) MUTATED DEL PEAK 28(14Q24.1) WILD-TYPE
  M0                           30                             76
  M1                            1                              4
  MX                           33                             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"
D60V7, binary
                                cls
clus                               0   1
  DEL PEAK 28(14Q24.1) MUTATED    12  53
  DEL PEAK 28(14Q24.1) WILD-TYPE  38 111
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(14Q24.1) MUTATED     12   53
  DEL PEAK 28(14Q24.1) WILD-TYPE   38  111
        clus
vv       DEL PEAK 28(14Q24.1) MUTATED DEL PEAK 28(14Q24.1) WILD-TYPE
  FEMALE                           12                             38
  MALE                             53                            111
[1] 2 2
[1] FALSE
D60V8, continuous
D60V9, continuous
D60V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(14Q24.1) MUTATED       7                         2    51
  DEL PEAK 28(14Q24.1) WILD-TYPE    15                         9   119
D60V11, multiclass
                           clus
vv                          DEL PEAK 28(14Q24.1) MUTATED
  ASIAN                                                7
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               51
                           clus
vv                          DEL PEAK 28(14Q24.1) WILD-TYPE
  ASIAN                                                 15
  BLACK OR AFRICAN AMERICAN                              9
  WHITE                                                119
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(61) Variable = DEL PEAK 29(15Q13.1) MUTATION ANALYSIS
D61V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 29(15Q13.1) MUTATED   64 22
  DEL PEAK 29(15Q13.1) WILD-TYPE 87 35
  DEL PEAK 29(15Q13.1) MUTATED DEL PEAK 29(15Q13.1) WILD-TYPE 
                            86                            122 
  DEL PEAK 29(15Q13.1) MUTATED DEL PEAK 29(15Q13.1) WILD-TYPE 
                            22                             35 
$`DEL PEAK 29(15Q13.1) MUTATED`
TCGA-BL-A0C8 TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A20X 
       40.08         6.58        19.04        32.84         8.35         8.25 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ 
        5.59         3.65        15.42        28.70         9.99         8.98 
TCGA-C4-A0F0 TCGA-CF-A47X TCGA-CU-A0YR TCGA-CU-A3QU TCGA-DK-A1A6 TCGA-DK-A1A7 
        1.94         0.10         7.20         5.19        31.40        18.41 
TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IM TCGA-DK-A3IN 
      112.44         1.81         7.79       123.85         7.82         8.22 
TCGA-DK-A3X2 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E7-A4IJ 
       17.98        15.68        32.28        30.67        43.59         0.49 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3N5 TCGA-FD-A3NA 
        0.59         0.56         1.22        12.89        11.93        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A5BV TCGA-FD-A5BY 
       24.30        12.82        13.18        22.98         5.36         6.84 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
       27.45         6.87        49.68         2.66         4.83         6.38 
TCGA-FD-A6TD TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF 
        6.71         2.20        15.19         4.08         6.48        61.94 
TCGA-G2-A2EL TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD 
       26.93        20.12         0.85        15.81         4.50        14.07 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GV-A3JW 
        1.12         2.66         2.10         2.20         6.41         6.41 
TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        6.15         7.63         7.79         6.41        19.07        11.54 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A5RJ TCGA-K4-A6FZ 
        6.74        38.60         8.75         2.50         1.74         1.81 
TCGA-K4-A6MB TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-XF-A8HD 
        4.27         6.35         3.45        13.48        16.67        88.93 
TCGA-XF-A8HF TCGA-XF-A8HG 
       56.19        15.35 

$`DEL PEAK 29(15Q13.1) WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20O 
        7.33         2.66         6.74        12.39        11.93        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42F TCGA-C4-A0F6 
       17.16         4.67        12.82         2.07        28.41        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69         0.13         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3YL 
        0.07         0.10        12.92         4.90         5.46        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
        1.84         9.34         2.53         2.14        19.00         8.91 
TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I6 
      130.88        16.14        17.62        15.62        10.59        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        2.20         3.98        10.49        50.27        21.30        20.02 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV 
        9.67         8.28        10.55       140.81        48.00        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       48.53        76.60        67.36        15.35        26.17        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A3B4 
        0.10         0.53         0.66         1.38         0.82        15.68 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SL 
        8.94         6.87         4.01        12.43        15.88        22.45 
TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       16.47         5.52        46.78        19.79         1.97        14.93 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       14.96        14.93         3.62        12.13        13.38        37.15 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC 
       11.01         6.87         5.69         6.28        50.66         9.30 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE 
        4.11         2.66         4.01         7.13         3.48         3.25 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-GC-A3BM 
       30.61         5.69        35.24        17.26         7.04         2.89 
TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS 
        2.24        15.91        17.75         7.73         3.12        20.98 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A3QK 
        7.66        11.31         4.41         5.69         4.14         6.67 
TCGA-H4-A2HO TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A83P 
        1.51         3.45         4.67         6.48        10.52         6.38 
TCGA-PQ-A6FI TCGA-XF-A8HE 
       12.23        97.45 

  DEL PEAK 29(15Q13.1) MUTATED DEL PEAK 29(15Q13.1) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 29(15Q13.1) MUTATED DEL PEAK 29(15Q13.1) WILD-TYPE 
                        123.85                         140.81 
  DEL PEAK 29(15Q13.1) MUTATED DEL PEAK 29(15Q13.1) WILD-TYPE 
                          8.02                           9.32 
[1] "0.1 - 123.8 (8.0)" "0.1 - 140.8 (9.3)"
[1] "hr=" "1.2"
D61V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 29(15Q13.1) MUTATED          1       1       23        30       31
  DEL PEAK 29(15Q13.1) WILD-TYPE        0       1       45        42       36
D61V3, multiclass
           clus
vv          DEL PEAK 29(15Q13.1) MUTATED DEL PEAK 29(15Q13.1) WILD-TYPE
  STAGE 0A                             1                              0
  STAGE I                              1                              1
  STAGE II                            23                             45
  STAGE III                           30                             42
  STAGE IV                            31                             36
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  DEL PEAK 29(15Q13.1) MUTATED         22 45  9
  DEL PEAK 29(15Q13.1) WILD-TYPE       40 56 23
D61V4, multiclass
          clus
vv         DEL PEAK 29(15Q13.1) MUTATED DEL PEAK 29(15Q13.1) WILD-TYPE
  T0+T1+T2                           22                             40
  T3                                 45                             56
  T4                                  9                             23
[1] 3 2
[1] 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(15Q13.1) MUTATED   46 11 17  3
  DEL PEAK 29(15Q13.1) WILD-TYPE 84 11 21  4
D61V5, multiclass
    clus
vv   DEL PEAK 29(15Q13.1) MUTATED DEL PEAK 29(15Q13.1) WILD-TYPE
  N0                           46                             84
  N1                           11                             11
  N2                           17                             21
  N3                            3                              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                             M0 M1 MX
  DEL PEAK 29(15Q13.1) MUTATED   33  2 51
  DEL PEAK 29(15Q13.1) WILD-TYPE 73  3 51
D61V6, multiclass
    clus
vv   DEL PEAK 29(15Q13.1) MUTATED DEL PEAK 29(15Q13.1) WILD-TYPE
  M0                           33                             73
  M1                            2                              3
  MX                           51                             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"
D61V7, binary
                                cls
clus                              0  1
  DEL PEAK 29(15Q13.1) MUTATED   20 67
  DEL PEAK 29(15Q13.1) WILD-TYPE 30 97
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(15Q13.1) MUTATED     20   67
  DEL PEAK 29(15Q13.1) WILD-TYPE   30   97
        clus
vv       DEL PEAK 29(15Q13.1) MUTATED DEL PEAK 29(15Q13.1) WILD-TYPE
  FEMALE                           20                             30
  MALE                             67                             97
[1] 2 2
[1] FALSE
D61V8, continuous
D61V9, continuous
D61V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(15Q13.1) MUTATED       5                         3    74
  DEL PEAK 29(15Q13.1) WILD-TYPE    17                         8    96
D61V11, multiclass
                           clus
vv                          DEL PEAK 29(15Q13.1) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               74
                           clus
vv                          DEL PEAK 29(15Q13.1) WILD-TYPE
  ASIAN                                                 17
  BLACK OR AFRICAN AMERICAN                              8
  WHITE                                                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(62) Variable = DEL PEAK 30(16P13.3) MUTATION ANALYSIS
D62V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 30(16P13.3) MUTATED   63 22
  DEL PEAK 30(16P13.3) WILD-TYPE 88 35
  DEL PEAK 30(16P13.3) MUTATED DEL PEAK 30(16P13.3) WILD-TYPE 
                            85                            123 
  DEL PEAK 30(16P13.3) MUTATED DEL PEAK 30(16P13.3) WILD-TYPE 
                            22                             35 
$`DEL PEAK 30(16P13.3) MUTATED`
TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20W TCGA-BT-A2LA 
        2.66         6.58        32.84         5.06         8.35        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0F6 
        5.59         4.67        12.82        28.70         9.99        23.01 
TCGA-CF-A1HS TCGA-CF-A47T TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 
        0.43         0.07        12.92         5.46         5.19         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
        2.53        18.41         1.81       123.85        87.32         2.20 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WX TCGA-DK-A3X2 
        7.82         8.22        21.30         9.67        10.55        17.98 
TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A541 TCGA-E7-A5KE 
       67.36        30.67        15.35        26.17         0.59         0.56 
TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43U 
       12.89         6.87        13.18        19.79        22.98        14.93 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A62N 
       12.13        13.38         5.36         6.84        27.45         2.66 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 
        4.83         6.38         6.71         4.11         2.20        15.19 
TCGA-G2-A2EF TCGA-G2-A2EL TCGA-G2-A3IE TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       61.94        26.93        20.12         4.50        15.91        14.07 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42P 
        1.12         2.66         7.73         2.10         2.20         6.41 
TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A6ZA 
       11.31         6.41         6.15         5.69         7.79        11.54 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ 
        6.74        38.60         8.75         6.48        10.52         1.74 
TCGA-K4-A6FZ TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-XF-A8HF 
        1.81         6.35         3.45        13.48        16.67        56.19 
TCGA-XF-A8HG 
       15.35 

$`DEL PEAK 30(16P13.3) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J 
       40.08         7.33         6.74        12.39        11.93        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       12.16        17.88        19.50        14.89        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0EZ 
        8.25         3.65         2.07        15.42        28.41         8.98 
TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47V TCGA-CF-A47W 
        1.94         0.46         0.69         0.13         0.10         0.07 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A72E 
        0.10         0.10         4.90         7.20        16.31         9.34 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
        2.14        31.40        19.00         8.91       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IL 
       16.14        17.62        15.62        10.59         7.79         3.98 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 
       10.49        50.27        20.02         8.28       140.81        48.00 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC 
       64.18        48.53        76.60        15.68        32.28        43.59 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A677 
       24.66         0.10         0.49         0.53         0.66         1.38 
TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 
        0.82         1.22        15.68         8.94         4.01        12.43 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       11.93        15.88        45.93        24.30        22.45        16.47 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S 
       12.82         5.52        46.78         1.97        14.93        14.96 
TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C0 
        3.62        37.15        11.01         6.87         5.69         6.87 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TI 
       49.68         6.28        50.66         9.30         2.66         4.01 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ 
        7.13         3.48         4.08         3.25         6.48        30.61 
TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-GC-A3BM 
        5.69        35.24        17.26         7.04         0.85         2.89 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3WC TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q 
        2.24        15.81        17.75         3.12        20.98         7.66 
TCGA-GV-A3JV TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
        4.41         7.63         4.14         6.67         6.41        19.07 
TCGA-H4-A2HO TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A6MB TCGA-K4-A83P 
        1.51         3.45         4.67         2.50         4.27         6.38 
TCGA-PQ-A6FI TCGA-XF-A8HD TCGA-XF-A8HE 
       12.23        88.93        97.45 

  DEL PEAK 30(16P13.3) MUTATED DEL PEAK 30(16P13.3) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 30(16P13.3) MUTATED DEL PEAK 30(16P13.3) WILD-TYPE 
                        123.85                         140.81 
  DEL PEAK 30(16P13.3) MUTATED DEL PEAK 30(16P13.3) WILD-TYPE 
                          8.22                           8.94 
[1] "0.1 - 123.8 (8.2)" "0.1 - 140.8 (8.9)"
[1] "hr=" "1"  
D62V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 30(16P13.3) MUTATED          1       0       23        35       24
  DEL PEAK 30(16P13.3) WILD-TYPE        0       2       45        37       43
D62V3, multiclass
           clus
vv          DEL PEAK 30(16P13.3) MUTATED DEL PEAK 30(16P13.3) WILD-TYPE
  STAGE 0A                             1                              0
  STAGE I                              0                              2
  STAGE II                            23                             45
  STAGE III                           35                             37
  STAGE IV                            24                             43
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  DEL PEAK 30(16P13.3) MUTATED         18 45 12
  DEL PEAK 30(16P13.3) WILD-TYPE       44 56 20
D62V4, multiclass
          clus
vv         DEL PEAK 30(16P13.3) MUTATED DEL PEAK 30(16P13.3) WILD-TYPE
  T0+T1+T2                           18                             44
  T3                                 45                             56
  T4                                 12                             20
[1] 3 2
[1] 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(16P13.3) MUTATED   51  6 18  2
  DEL PEAK 30(16P13.3) WILD-TYPE 79 16 20  5
D62V5, multiclass
    clus
vv   DEL PEAK 30(16P13.3) MUTATED DEL PEAK 30(16P13.3) WILD-TYPE
  N0                           51                             79
  N1                            6                             16
  N2                           18                             20
  N3                            2                              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                             M0 M1 MX
  DEL PEAK 30(16P13.3) MUTATED   38  1 46
  DEL PEAK 30(16P13.3) WILD-TYPE 68  4 56
D62V6, multiclass
    clus
vv   DEL PEAK 30(16P13.3) MUTATED DEL PEAK 30(16P13.3) WILD-TYPE
  M0                           38                             68
  M1                            1                              4
  MX                           46                             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"
D62V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(16P13.3) MUTATED    21  64
  DEL PEAK 30(16P13.3) WILD-TYPE  29 100
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16P13.3) MUTATED     21   64
  DEL PEAK 30(16P13.3) WILD-TYPE   29  100
        clus
vv       DEL PEAK 30(16P13.3) MUTATED DEL PEAK 30(16P13.3) WILD-TYPE
  FEMALE                           21                             29
  MALE                             64                            100
[1] 2 2
[1] FALSE
D62V8, continuous
D62V9, continuous
D62V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(16P13.3) MUTATED       4                         2    74
  DEL PEAK 30(16P13.3) WILD-TYPE    18                         9    96
D62V11, multiclass
                           clus
vv                          DEL PEAK 30(16P13.3) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               74
                           clus
vv                          DEL PEAK 30(16P13.3) WILD-TYPE
  ASIAN                                                 18
  BLACK OR AFRICAN AMERICAN                              9
  WHITE                                                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(63) Variable = DEL PEAK 31(16Q23.1) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(16Q23.1) MUTATED    44  17
  DEL PEAK 31(16Q23.1) WILD-TYPE 107  40
  DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE 
                            61                            147 
  DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE 
                            17                             40 
$`DEL PEAK 31(16Q23.1) MUTATED`
TCGA-BL-A0C8 TCGA-CU-A0YN TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1AC 
       40.08        12.92         5.19         1.84         2.53       130.88 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IN 
        1.81        10.59         7.79       123.85        87.32         8.22 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A4TZ 
        9.67         8.28        17.98        67.36        30.67        15.35 
TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A677 TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A3SO 
        0.49         0.59         1.38         8.94        11.93         5.52 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TC 
        1.97        22.98        14.93         2.66         4.83         9.30 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
        6.71         4.11        15.19         6.48        61.94        30.61 
TCGA-G2-A3IE TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42P 
       20.12        15.91        14.07         2.10         2.20         6.41 
TCGA-GU-A42Q TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        7.66         4.41         6.15         5.69         7.63         7.79 
TCGA-GV-A3QI TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A5RJ 
        4.14         6.74        38.60         4.67         6.48         1.74 
TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-XF-A8HE TCGA-XF-A8HF 
        1.81         3.45        13.48        12.23        97.45        56.19 
TCGA-XF-A8HG 
       15.35 

$`DEL PEAK 31(16Q23.1) WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
        7.33         2.66         6.74        12.39         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
       14.89        14.96         5.06         8.35         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
        5.59         3.65         4.67        12.82         2.07        15.42 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
       28.70         9.99        28.41         8.98         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        0.46         0.43         0.69         0.13         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        0.07         0.10         0.10         4.90         7.20         5.46 
TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
       16.31         9.34         2.14        31.40        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IK 
        8.91       112.44        16.14        17.62        15.62         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        3.98         7.82        10.49        50.27        21.30        20.02 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       10.55       140.81        48.00        64.18        48.53        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       15.68        32.28        43.59        26.17        24.66         0.10 
TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 
        0.53         0.56         0.66         0.82         1.22        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA 
       15.68         6.87         4.01        12.43        15.88        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ 
       24.30        22.45        16.47        12.82        13.18        46.78 
TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       19.79        14.93        14.96         3.62        12.13        13.38 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       37.15        11.01         6.87         5.36         5.69         6.84 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       27.45         6.87        49.68         6.28         6.38        50.66 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        2.66         2.20         4.01         7.13         3.48         4.08 
TCGA-FT-A3EE TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
        3.25         5.69        26.93        35.24        17.26         7.04 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC 
        0.85         2.89         2.24        15.81         4.50        17.75 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R 
        1.12         2.66         7.73         3.12        20.98        11.31 
TCGA-GV-A3JW TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
        6.41         6.67         6.41        19.07        11.54         1.51 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A6MB TCGA-K4-A83P 
        8.75         3.45         2.50        10.52         4.27         6.38 
TCGA-LC-A66R TCGA-PQ-A6FN TCGA-XF-A8HD 
        6.35        16.67        88.93 

  DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE 
                          0.49                           0.07 
  DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE 
                        130.88                         140.81 
  DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE 
                          7.79                           8.98 
[1] "0.5 - 130.9 (7.8)" "0.1 - 140.8 (9.0)"
[1] "hr=" "1"  
D63V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 31(16Q23.1) MUTATED          0       1       18        21       20
  DEL PEAK 31(16Q23.1) WILD-TYPE        1       1       50        51       47
D63V3, multiclass
           clus
vv          DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              1                              1
  STAGE II                            18                             50
  STAGE III                           21                             51
  STAGE IV                            20                             47
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  DEL PEAK 31(16Q23.1) MUTATED         16 28  9
  DEL PEAK 31(16Q23.1) WILD-TYPE       46 73 23
D63V4, multiclass
          clus
vv         DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE
  T0+T1+T2                           16                             46
  T3                                 28                             73
  T4                                  9                             23
[1] 3 2
[1] 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(16Q23.1) MUTATED   32  6 12  3
  DEL PEAK 31(16Q23.1) WILD-TYPE 98 16 26  4
D63V5, multiclass
    clus
vv   DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE
  N0                           32                             98
  N1                            6                             16
  N2                           12                             26
  N3                            3                              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                             M0 M1 MX
  DEL PEAK 31(16Q23.1) MUTATED   26  1 34
  DEL PEAK 31(16Q23.1) WILD-TYPE 80  4 68
D63V6, multiclass
    clus
vv   DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE
  M0                           26                             80
  M1                            1                              4
  MX                           34                             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"
D63V7, binary
                                cls
clus                               0   1
  DEL PEAK 31(16Q23.1) MUTATED    10  51
  DEL PEAK 31(16Q23.1) WILD-TYPE  40 113
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(16Q23.1) MUTATED     10   51
  DEL PEAK 31(16Q23.1) WILD-TYPE   40  113
        clus
vv       DEL PEAK 31(16Q23.1) MUTATED DEL PEAK 31(16Q23.1) WILD-TYPE
  FEMALE                           10                             40
  MALE                             51                            113
[1] 2 2
[1] FALSE
D63V8, continuous
D63V9, continuous
D63V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(16Q23.1) MUTATED       3                         3    52
  DEL PEAK 31(16Q23.1) WILD-TYPE    19                         8   118
D63V11, multiclass
                           clus
vv                          DEL PEAK 31(16Q23.1) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               52
                           clus
vv                          DEL PEAK 31(16Q23.1) WILD-TYPE
  ASIAN                                                 19
  BLACK OR AFRICAN AMERICAN                              8
  WHITE                                                118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(64) Variable = DEL PEAK 32(17P12) MUTATION ANALYSIS
D64V1, survival
                              sevent
clus2                           0  1
  DEL PEAK 32(17P12) MUTATED   74 33
  DEL PEAK 32(17P12) WILD-TYPE 77 24
  DEL PEAK 32(17P12) MUTATED DEL PEAK 32(17P12) WILD-TYPE 
                         107                          101 
  DEL PEAK 32(17P12) MUTATED DEL PEAK 32(17P12) WILD-TYPE 
                          33                           24 
$`DEL PEAK 32(17P12) MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P 
       40.08         2.66        12.39        19.04        32.84        17.88 
TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH 
       19.50        14.89         8.25        17.16         5.59         4.67 
TCGA-BT-A3PK TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS 
        2.07         9.99         8.98         1.94         0.46         0.43 
TCGA-CF-A27C TCGA-CF-A47X TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1A6 
        0.69         0.10         5.46         1.84         2.14        31.40 
TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 
       18.41         8.91       130.88       112.44         1.81        10.59 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
       87.32         2.20         3.98         8.22        10.49        50.27 
TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B5 
       21.30         9.67        48.00        17.98        64.18        32.28 
TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A541 
       30.67        43.59        15.35        26.17         0.49         0.59 
TCGA-E7-A5KE TCGA-E7-A677 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3NA TCGA-FD-A3SJ 
        0.56         1.38        15.68         8.94        45.93        24.30 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       12.82         5.52        46.78         1.97        22.98        14.93 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A62O 
       14.93         3.62        13.38         5.36         6.84         4.83 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG 
        6.28         6.38        50.66         9.30         6.71         2.66 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO 
       15.19         3.48        61.94        30.61        26.93        35.24 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3YS 
       20.12         0.85         2.89         4.50        14.07         1.12 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
        7.73         2.10         2.20         6.41         7.66        11.31 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HQ 
        5.69         7.63         7.79         6.41        19.07         6.74 
TCGA-HQ-A2OE TCGA-K4-A4AC TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-LC-A66R TCGA-PQ-A6FI 
       38.60         6.48         1.74         4.27         6.35        12.23 
TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       16.67        88.93        97.45        56.19        15.35 

$`DEL PEAK 32(17P12) WILD-TYPE`
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20R 
        7.33         6.74         6.58        11.93        12.16         5.06 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42B 
       14.96         5.06         8.35         3.65        12.82        15.42 
TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       28.70        28.41        23.01         0.13         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU 
        0.07         0.10        12.92         4.90         7.20         5.19 
TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1AA TCGA-DK-A1AE TCGA-DK-A1AF 
       16.31         9.34         2.53        19.00        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IM TCGA-DK-A3IU TCGA-DK-A3WW 
       15.62         7.79       123.85         7.82        20.02         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       10.55       140.81        48.53        76.60        67.36        15.68 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A7DV 
       24.66         0.10         0.53         0.66         0.82         1.22 
TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       12.89         6.87         4.01        12.43        11.93        15.88 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43S TCGA-FD-A43Y 
       22.45        16.47        13.18        19.79        14.96        12.13 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 
       37.15        11.01         6.87         5.69        27.45         6.87 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z9 
       49.68         2.66         4.11         2.20         4.01         7.13 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2ES TCGA-G2-A3IB 
        4.08         3.25         6.48         5.69        17.26         7.04 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OQ 
        2.24        15.81        15.91        17.75         2.66         3.12 
TCGA-GD-A3OS TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QI TCGA-GV-A3QK 
       20.98         4.41         6.41         6.15         4.14         6.67 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
       11.54         1.51         8.75         3.45         4.67         2.50 
TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-MV-A51V 
       10.52         1.81         6.38         3.45        13.48 

  DEL PEAK 32(17P12) MUTATED DEL PEAK 32(17P12) WILD-TYPE 
                        0.10                         0.07 
  DEL PEAK 32(17P12) MUTATED DEL PEAK 32(17P12) WILD-TYPE 
                      130.88                       140.81 
  DEL PEAK 32(17P12) MUTATED DEL PEAK 32(17P12) WILD-TYPE 
                        9.30                         7.79 
[1] "0.1 - 130.9 (9.3)" "0.1 - 140.8 (7.8)"
[1] "hr=" "1.1"
D64V2, continuous
                              vv
clus                           STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 32(17P12) MUTATED          0       1       35        31       38
  DEL PEAK 32(17P12) WILD-TYPE        1       1       33        41       29
D64V3, multiclass
           clus
vv          DEL PEAK 32(17P12) MUTATED DEL PEAK 32(17P12) WILD-TYPE
  STAGE 0A                           0                            1
  STAGE I                            1                            1
  STAGE II                          35                           33
  STAGE III                         31                           41
  STAGE IV                          38                           29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1+T2 T3 T4
  DEL PEAK 32(17P12) MUTATED         32 49 16
  DEL PEAK 32(17P12) WILD-TYPE       30 52 16
D64V4, multiclass
          clus
vv         DEL PEAK 32(17P12) MUTATED DEL PEAK 32(17P12) WILD-TYPE
  T0+T1+T2                         32                           30
  T3                               49                           52
  T4                               16                           16
[1] 3 2
[1] 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(17P12) MUTATED   61 10 24  3
  DEL PEAK 32(17P12) WILD-TYPE 69 12 14  4
D64V5, multiclass
    clus
vv   DEL PEAK 32(17P12) MUTATED DEL PEAK 32(17P12) WILD-TYPE
  N0                         61                           69
  N1                         10                           12
  N2                         24                           14
  N3                          3                            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                           M0 M1 MX
  DEL PEAK 32(17P12) MUTATED   52  3 53
  DEL PEAK 32(17P12) WILD-TYPE 54  2 49
D64V6, multiclass
    clus
vv   DEL PEAK 32(17P12) MUTATED DEL PEAK 32(17P12) WILD-TYPE
  M0                         52                           54
  M1                          3                            2
  MX                         53                           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"
D64V7, binary
                              cls
clus                            0  1
  DEL PEAK 32(17P12) MUTATED   25 84
  DEL PEAK 32(17P12) WILD-TYPE 25 80
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(17P12) MUTATED     25   84
  DEL PEAK 32(17P12) WILD-TYPE   25   80
        clus
vv       DEL PEAK 32(17P12) MUTATED DEL PEAK 32(17P12) WILD-TYPE
  FEMALE                         25                           25
  MALE                           84                           80
[1] 2 2
[1] FALSE
D64V8, continuous
D64V9, continuous
D64V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(17P12) MUTATED      11                         5    86
  DEL PEAK 32(17P12) WILD-TYPE    11                         6    84
D64V11, multiclass
                           clus
vv                          DEL PEAK 32(17P12) MUTATED
  ASIAN                                             11
  BLACK OR AFRICAN AMERICAN                          5
  WHITE                                             86
                           clus
vv                          DEL PEAK 32(17P12) WILD-TYPE
  ASIAN                                               11
  BLACK OR AFRICAN AMERICAN                            6
  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"

Clustering(65) Variable = DEL PEAK 33(18Q21.2) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 33(18Q21.2) MUTATED   74 19
  DEL PEAK 33(18Q21.2) WILD-TYPE 77 38
  DEL PEAK 33(18Q21.2) MUTATED DEL PEAK 33(18Q21.2) WILD-TYPE 
                            93                            115 
  DEL PEAK 33(18Q21.2) MUTATED DEL PEAK 33(18Q21.2) WILD-TYPE 
                            19                             38 
$`DEL PEAK 33(18Q21.2) MUTATED`
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20W 
       11.93        19.04        32.84         5.06        14.89         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-CF-A1HR 
        8.25        17.16        15.42        28.70         9.99         0.46 
TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A5W6 
        0.43         0.13         0.07        12.92         7.20         1.84 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
        9.34         2.14        18.41         8.91       130.88       112.44 
TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       17.62         1.81        10.59        87.32         2.20         3.98 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X1 
        7.82         8.22        10.49        50.27        21.30        48.00 
TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A4IJ 
       64.18        15.68        32.28        43.59        24.66         0.49 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A7DV TCGA-FD-A3B4 TCGA-FD-A3B7 
        0.59         0.56         1.38         1.22        15.68         4.01 
TCGA-FD-A3NA TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS 
       45.93        12.82         5.52        13.18        46.78         1.97 
TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA 
       22.98        12.13         2.66         4.83         6.38        50.66 
TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-G2-A2EF TCGA-G2-A2EK 
        6.71         2.66         2.20         4.08        61.94         5.69 
TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RC TCGA-GC-A3RD 
       35.24        20.12         0.85         2.89        15.91        14.07 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P 
        1.12         2.66         2.10        20.98         2.20         6.41 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE 
        6.41         6.15        19.07        11.54         6.74        38.60 
TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A5RJ TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI 
        8.75         4.67         1.74         6.35        13.48        12.23 
TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HF 
       16.67        88.93        56.19 

$`DEL PEAK 33(18Q21.2) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A2LB 
       12.16        17.88        19.50        14.96         5.06         5.59 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42F TCGA-C4-A0EZ 
        3.65         4.67        12.82         2.07        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
        1.94        23.01         0.69         0.10         0.07         0.10 
TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 
        0.10         4.90         5.46         5.19        16.31         2.53 
TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AE TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 
       31.40        19.00        16.14        15.62         7.79       123.85 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 
       20.02         9.67         8.28        10.55       140.81        17.98 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 
       48.53        76.60        67.36        30.67        15.35        26.17 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A678 TCGA-FD-A3B3 TCGA-FD-A3B5 
        0.10         0.53         0.66         0.82        12.89         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL 
        6.87        12.43        11.93        15.88        24.30        22.45 
TCGA-FD-A3SM TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       16.47        19.79        14.93        14.96        14.93         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       13.38        37.15        11.01         6.87         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TC 
        6.84        27.45         6.87        49.68         6.28         9.30 
TCGA-FD-A6TE TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE 
        4.11         4.01        15.19         7.13         3.48         3.25 
TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-GC-A3I6 
        6.48        30.61        26.93        17.26         7.04         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GU-A42Q 
       15.81         4.50        17.75         7.73         3.12         7.66 
TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       11.31         4.41         5.69         7.63         7.79         4.14 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HO TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
        6.67         6.41         1.51         3.45         2.50         6.48 
TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-XF-A8HE 
       10.52         1.81         4.27         6.38         3.45        97.45 
TCGA-XF-A8HG 
       15.35 

  DEL PEAK 33(18Q21.2) MUTATED DEL PEAK 33(18Q21.2) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 33(18Q21.2) MUTATED DEL PEAK 33(18Q21.2) WILD-TYPE 
                        130.88                         140.81 
  DEL PEAK 33(18Q21.2) MUTATED DEL PEAK 33(18Q21.2) WILD-TYPE 
                          9.34                           7.79 
[1] "0.1 - 130.9 (9.3)" "0.1 - 140.8 (7.8)"
[1] "hr=" "1.8"
D65V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 33(18Q21.2) MUTATED          1       0       31        31       30
  DEL PEAK 33(18Q21.2) WILD-TYPE        0       2       37        41       37
D65V3, multiclass
           clus
vv          DEL PEAK 33(18Q21.2) MUTATED DEL PEAK 33(18Q21.2) WILD-TYPE
  STAGE 0A                             1                              0
  STAGE I                              0                              2
  STAGE II                            31                             37
  STAGE III                           31                             41
  STAGE IV                            30                             37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  DEL PEAK 33(18Q21.2) MUTATED         30 47 11
  DEL PEAK 33(18Q21.2) WILD-TYPE       32 54 21
D65V4, multiclass
          clus
vv         DEL PEAK 33(18Q21.2) MUTATED DEL PEAK 33(18Q21.2) WILD-TYPE
  T0+T1+T2                           30                             32
  T3                                 47                             54
  T4                                 11                             21
[1] 3 2
[1] 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(18Q21.2) MUTATED   59  9 18  2
  DEL PEAK 33(18Q21.2) WILD-TYPE 71 13 20  5
D65V5, multiclass
    clus
vv   DEL PEAK 33(18Q21.2) MUTATED DEL PEAK 33(18Q21.2) WILD-TYPE
  N0                           59                             71
  N1                            9                             13
  N2                           18                             20
  N3                            2                              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                             M0 M1 MX
  DEL PEAK 33(18Q21.2) MUTATED   53  1 41
  DEL PEAK 33(18Q21.2) WILD-TYPE 53  4 61
D65V6, multiclass
    clus
vv   DEL PEAK 33(18Q21.2) MUTATED DEL PEAK 33(18Q21.2) WILD-TYPE
  M0                           53                             53
  M1                            1                              4
  MX                           41                             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"
D65V7, binary
                                cls
clus                              0  1
  DEL PEAK 33(18Q21.2) MUTATED   23 73
  DEL PEAK 33(18Q21.2) WILD-TYPE 27 91
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(18Q21.2) MUTATED     23   73
  DEL PEAK 33(18Q21.2) WILD-TYPE   27   91
        clus
vv       DEL PEAK 33(18Q21.2) MUTATED DEL PEAK 33(18Q21.2) WILD-TYPE
  FEMALE                           23                             27
  MALE                             73                             91
[1] 2 2
[1] FALSE
D65V8, continuous
D65V9, continuous
D65V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(18Q21.2) MUTATED      13                         4    74
  DEL PEAK 33(18Q21.2) WILD-TYPE     9                         7    96
D65V11, multiclass
                           clus
vv                          DEL PEAK 33(18Q21.2) MUTATED
  ASIAN                                               13
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               74
                           clus
vv                          DEL PEAK 33(18Q21.2) WILD-TYPE
  ASIAN                                                  9
  BLACK OR AFRICAN AMERICAN                              7
  WHITE                                                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(66) Variable = DEL PEAK 34(19P13.3) MUTATION ANALYSIS
D66V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 34(19P13.3) MUTATED   55 24
  DEL PEAK 34(19P13.3) WILD-TYPE 96 33
  DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE 
                            79                            129 
  DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE 
                            24                             33 
$`DEL PEAK 34(19P13.3) MUTATED`
TCGA-BL-A5ZZ TCGA-BT-A20J TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W 
       12.39        19.04         5.06        14.89         5.06         8.35 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E 
        5.59         3.65         4.67         2.07        15.42         9.99 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-DK-A1A5 
       28.41         8.98        23.01         0.46         0.43         2.14 
TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IQ 
       18.41         8.91       112.44        87.32         3.98        10.49 
TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B5 TCGA-E5-A2PC 
       21.30         9.67        48.00        17.98        32.28        43.59 
TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A7DV TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3SJ 
       15.35         0.49         1.22        15.68         6.87        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SS TCGA-FD-A43N 
       22.45        16.47        12.82         5.52         1.97        22.98 
TCGA-FD-A43Y TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
       12.13         5.36         6.84        27.45         6.87        49.68 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A61P 
        9.30         4.11         2.20         3.48         4.08         6.48 
TCGA-G2-A2EF TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3I6 
       61.94        17.26         7.04        20.12         0.85         2.24 
TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
        4.50         1.12         2.66         6.41         7.66        11.31 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ 
        6.41         6.15         5.69        19.07         1.51         6.74 
TCGA-K4-A3WS TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-MV-A51V TCGA-PQ-A6FI 
        8.75        10.52         1.74         4.27        13.48        12.23 
TCGA-PQ-A6FN 
       16.67 

$`DEL PEAK 34(19P13.3) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        11.93 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20X 
       32.84        12.16        17.88        19.50        14.96         8.25 
TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A42C TCGA-C4-A0F0 TCGA-CF-A27C TCGA-CF-A47S 
       17.16        12.82        28.70         1.94         0.69         0.13 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN 
        0.07         0.10         0.07         0.10         0.10        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
        4.90         7.20         5.46         5.19        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AE 
        9.34         2.53        31.40        19.00       130.88        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3WW 
        2.20         7.82         8.22        50.27        20.02         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       10.55       140.81        64.18        48.53        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       15.68        30.67        26.17        24.66         0.10         0.53 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A3B3 
        0.59         0.56         0.66         1.38         0.82        12.89 
TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
        8.94         4.01        12.43        11.93        15.88        45.93 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       13.18        46.78        19.79        14.93        14.96        14.93 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
        3.62        13.38        37.15        11.01         6.87         5.69 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TD 
        2.66         4.83         6.28         6.38        50.66         6.71 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FT-A3EE TCGA-G2-A2EJ 
        2.66         4.01        15.19         7.13         3.25        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RC 
        5.69        26.93        35.24         2.89        15.81        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
       14.07        17.75         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GV-A3JV TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
        2.20         4.41         7.63         7.79         4.14         6.67 
TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        6.41        11.54        38.60         3.45         4.67         2.50 
TCGA-K4-A4AC TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-XF-A8HD 
        6.48         1.81         6.38         6.35         3.45        88.93 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       97.45        56.19        15.35 

  DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE 
                          0.43                           0.07 
  DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE 
                        112.44                         140.81 
  DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE 
                          8.75                           8.28 
[1] "0.4 - 112.4 (8.8)" "0.1 - 140.8 (8.3)"
[1] "hr=" "1.3"
D66V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 34(19P13.3) MUTATED          0       0       20        23       35
  DEL PEAK 34(19P13.3) WILD-TYPE        1       2       48        49       32
D66V3, multiclass
           clus
vv          DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              0                              2
  STAGE II                            20                             48
  STAGE III                           23                             49
  STAGE IV                            35                             32
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  DEL PEAK 34(19P13.3) MUTATED         16 41 14
  DEL PEAK 34(19P13.3) WILD-TYPE       46 60 18
D66V4, multiclass
          clus
vv         DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE
  T0+T1+T2                           16                             46
  T3                                 41                             60
  T4                                 14                             18
[1] 3 2
[1] 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(19P13.3) MUTATED   39 13 15  4
  DEL PEAK 34(19P13.3) WILD-TYPE 91  9 23  3
D66V5, multiclass
    clus
vv   DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE
  N0                           39                             91
  N1                           13                              9
  N2                           15                             23
  N3                            4                              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                             M0 M1 MX
  DEL PEAK 34(19P13.3) MUTATED   32  5 42
  DEL PEAK 34(19P13.3) WILD-TYPE 74  0 60
D66V6, multiclass
    clus
vv   DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE
  M0                           32                             74
  M1                            5                              0
  MX                           42                             60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                                cls
clus                               0   1
  DEL PEAK 34(19P13.3) MUTATED    22  58
  DEL PEAK 34(19P13.3) WILD-TYPE  28 106
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(19P13.3) MUTATED     22   58
  DEL PEAK 34(19P13.3) WILD-TYPE   28  106
        clus
vv       DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE
  FEMALE                           22                             28
  MALE                             58                            106
[1] 2 2
[1] FALSE
D66V8, continuous
D66V9, continuous
D66V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(19P13.3) MUTATED       5                         4    67
  DEL PEAK 34(19P13.3) WILD-TYPE    17                         7   103
D66V11, multiclass
                           clus
vv                          DEL PEAK 34(19P13.3) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               67
                           clus
vv                          DEL PEAK 34(19P13.3) WILD-TYPE
  ASIAN                                                 17
  BLACK OR AFRICAN AMERICAN                              7
  WHITE                                                103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(67) Variable = DEL PEAK 35(22Q13.31) MUTATION ANALYSIS
D67V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 35(22Q13.31) MUTATED   67 26
  DEL PEAK 35(22Q13.31) WILD-TYPE 84 31
  DEL PEAK 35(22Q13.31) MUTATED DEL PEAK 35(22Q13.31) WILD-TYPE 
                             93                             115 
  DEL PEAK 35(22Q13.31) MUTATED DEL PEAK 35(22Q13.31) WILD-TYPE 
                             26                              31 
$`DEL PEAK 35(22Q13.31) MUTATED`
TCGA-BT-A20J TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A3PJ TCGA-BT-A42B 
       19.04         5.06         5.06         8.35        12.82        15.42 
TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A47X 
       28.70         9.99         8.98         1.94        23.01         0.10 
TCGA-CU-A0YN TCGA-CU-A3QU TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I1 
       12.92         5.19        18.41       130.88         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
        7.79       123.85         3.98         7.82         8.22        10.49 
TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       21.30         9.67        17.98        67.36        15.68        32.28 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A7DV 
       43.59        15.35         0.49         0.59         0.56         1.22 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3NA 
       12.89        15.68         8.94         6.87        11.93        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SR TCGA-FD-A3SS 
       24.30        22.45        12.82         5.52        19.79         1.97 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BT TCGA-FD-A5BV 
       22.98        14.93        14.93        12.13        11.01         5.36 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A6TC 
        6.84        27.45         6.87         2.66         6.28         9.30 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF 
        6.71         4.11        15.19         4.08         6.48        61.94 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3RC TCGA-GC-A3YS TCGA-GC-A6I1 
        7.04        20.12         0.85        15.91         1.12         2.66 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JX 
        7.73         2.10         2.20         7.66        11.31         6.15 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A3WU 
        6.41        19.07        11.54         6.74         8.75         3.45 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI 
        1.74         1.81         4.27         6.35         3.45        12.23 
TCGA-PQ-A6FN TCGA-XF-A8HF TCGA-XF-A8HG 
       16.67        56.19        15.35 

$`DEL PEAK 35(22Q13.31) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T 
       11.93        32.84        12.16        17.88        19.50        14.89 
TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
       14.96         8.25        17.16         5.59         3.65         4.67 
TCGA-BT-A3PK TCGA-BT-A42F TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
        2.07        28.41         0.46         0.43         0.69         0.13 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A0YR 
        0.07         0.10         0.07         0.10         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.46        16.31         1.84         9.34         2.53         2.14 
TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       31.40        19.00         8.91       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3WW 
       15.62        87.32         2.20        50.27        20.02         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       10.55       140.81        48.00        64.18        48.53        76.60 
TCGA-DK-A6B6 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KF 
       30.67        26.17        24.66         0.10         0.53         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SM 
        1.38         0.82         4.01        12.43        15.88        16.47 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       13.18        46.78        14.96         3.62        13.38        37.15 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA 
        6.87         5.69        49.68         4.83         6.38        50.66 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE 
        2.66         2.20         4.01         7.13         3.48         3.25 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-GC-A3BM 
       30.61         5.69        26.93        35.24        17.26         2.89 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GD-A3OQ 
        2.24        15.81         4.50        14.07        17.75         3.12 
TCGA-GD-A3OS TCGA-GU-A42P TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF 
       20.98         6.41         4.41         6.41         5.69         7.63 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WV 
        7.79         4.14         6.67         1.51        38.60         4.67 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A83P TCGA-MV-A51V TCGA-XF-A8HD 
        2.50         6.48        10.52         6.38        13.48        88.93 
TCGA-XF-A8HE 
       97.45 

  DEL PEAK 35(22Q13.31) MUTATED DEL PEAK 35(22Q13.31) WILD-TYPE 
                           0.10                            0.07 
  DEL PEAK 35(22Q13.31) MUTATED DEL PEAK 35(22Q13.31) WILD-TYPE 
                         130.88                          140.81 
  DEL PEAK 35(22Q13.31) MUTATED DEL PEAK 35(22Q13.31) WILD-TYPE 
                           8.98                            7.79 
[1] "0.1 - 130.9 (9.0)" "0.1 - 140.8 (7.8)"
[1] "hr=" "1.1"
D67V2, continuous
                                 vv
clus                              STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 35(22Q13.31) MUTATED          1       0       29        30       34
  DEL PEAK 35(22Q13.31) WILD-TYPE        0       2       39        42       33
D67V3, multiclass
           clus
vv          DEL PEAK 35(22Q13.31) MUTATED DEL PEAK 35(22Q13.31) WILD-TYPE
  STAGE 0A                              1                               0
  STAGE I                               0                               2
  STAGE II                             29                              39
  STAGE III                            30                              42
  STAGE IV                             34                              33
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1+T2 T3 T4
  DEL PEAK 35(22Q13.31) MUTATED         25 42 16
  DEL PEAK 35(22Q13.31) WILD-TYPE       37 59 16
D67V4, multiclass
          clus
vv         DEL PEAK 35(22Q13.31) MUTATED DEL PEAK 35(22Q13.31) WILD-TYPE
  T0+T1+T2                            25                              37
  T3                                  42                              59
  T4                                  16                              16
[1] 3 2
[1] 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(22Q13.31) MUTATED   52 11 18  4
  DEL PEAK 35(22Q13.31) WILD-TYPE 78 11 20  3
D67V5, multiclass
    clus
vv   DEL PEAK 35(22Q13.31) MUTATED DEL PEAK 35(22Q13.31) WILD-TYPE
  N0                            52                              78
  N1                            11                              11
  N2                            18                              20
  N3                             4                               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                              M0 M1 MX
  DEL PEAK 35(22Q13.31) MUTATED   35  3 55
  DEL PEAK 35(22Q13.31) WILD-TYPE 71  2 47
D67V6, multiclass
    clus
vv   DEL PEAK 35(22Q13.31) MUTATED DEL PEAK 35(22Q13.31) WILD-TYPE
  M0                            35                              71
  M1                             3                               2
  MX                            55                              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"
D67V7, binary
                                 cls
clus                               0  1
  DEL PEAK 35(22Q13.31) MUTATED   23 71
  DEL PEAK 35(22Q13.31) WILD-TYPE 27 93
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(22Q13.31) MUTATED     23   71
  DEL PEAK 35(22Q13.31) WILD-TYPE   27   93
        clus
vv       DEL PEAK 35(22Q13.31) MUTATED DEL PEAK 35(22Q13.31) WILD-TYPE
  FEMALE                            23                              27
  MALE                              71                              93
[1] 2 2
[1] FALSE
D67V8, continuous
D67V9, continuous
D67V10, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(22Q13.31) MUTATED       6                         7    75
  DEL PEAK 35(22Q13.31) WILD-TYPE    16                         4    95
D67V11, multiclass
                           clus
vv                          DEL PEAK 35(22Q13.31) MUTATED
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                             7
  WHITE                                                75
                           clus
vv                          DEL PEAK 35(22Q13.31) WILD-TYPE
  ASIAN                                                  16
  BLACK OR AFRICAN AMERICAN                               4
  WHITE                                                  95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(68) Variable = DEL PEAK 36(XP11.3) MUTATION ANALYSIS
D68V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 36(XP11.3) MUTATED    36  12
  DEL PEAK 36(XP11.3) WILD-TYPE 115  45
  DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE 
                           48                           160 
  DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE 
                           12                            45 
$`DEL PEAK 36(XP11.3) MUTATED`
TCGA-BL-A13J TCGA-BT-A20P TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A3PH TCGA-BT-A42B 
        2.66        17.88        14.89         5.06         4.67        15.42 
TCGA-BT-A42E TCGA-CF-A27C TCGA-CF-A47X TCGA-CU-A0YN TCGA-CU-A3QU TCGA-DK-A1A5 
        9.99         0.69         0.10        12.92         5.19         2.14 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AG TCGA-DK-A2I6 TCGA-DK-A3IS 
       19.00         8.91       112.44        15.62        87.32        50.27 
TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E7-A3X6 
       21.30         9.67        15.68        32.28        43.59        24.66 
TCGA-E7-A7DV TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A3SS 
        1.22        15.68         6.87        12.82        19.79         1.97 
TCGA-FD-A43Y TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A6TA TCGA-FD-A6TC TCGA-G2-A2EL 
       12.13         6.84         2.66        50.66         9.30        26.93 
TCGA-G2-A3IB TCGA-G2-A3VY TCGA-GD-A3OS TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
        7.04         0.85        20.98         6.15         7.79         4.14 
TCGA-K4-A3WS TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-XF-A8HF 
        8.75         1.74         1.81         3.45        12.23        56.19 

$`DEL PEAK 36(XP11.3) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         6.74        12.39         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       19.04        32.84        12.16        19.50         5.06        14.96 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ 
        8.35         8.25        17.16         5.59         3.65        12.82 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
        2.07        28.70        28.41         8.98         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
        0.46         0.43         0.13         0.07         0.10         0.07 
TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 
        0.10         4.90         7.20         5.46        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AE 
        9.34         2.53        31.40        18.41       130.88        16.14 
TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       17.62         1.81        10.59         7.79       123.85         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3WW 
        3.98         7.82         8.22        10.49        20.02         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       10.55       140.81        48.00        17.98        64.18        48.53 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 
       76.60        67.36        30.67        15.35        26.17         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        0.49         0.53         0.59         0.56         0.66         1.38 
TCGA-E7-A678 TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
        0.82        12.89         8.94         4.01        12.43        11.93 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO 
       15.88        45.93        24.30        22.45        16.47         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       13.18        46.78        22.98        14.93        14.96        14.93 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
        3.62        13.38        37.15        11.01         6.87         5.36 
TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P 
        5.69        27.45         6.87        49.68         4.83         6.28 
TCGA-FD-A62S TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
        6.38         6.71         4.11         2.66         2.20         4.01 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P 
       15.19         7.13         3.48         4.08         3.25         6.48 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE 
       61.94        30.61         5.69        35.24        17.26        20.12 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
        2.89         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       17.75         1.12         2.66         7.73         2.10         3.12 
TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW 
        2.20         6.41         7.66        11.31         4.41         6.41 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        5.69         7.63         6.67         6.41        19.07        11.54 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        1.51         6.74        38.60         3.45         4.67         2.50 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-MV-A51V 
        6.48        10.52         4.27         6.38         6.35        13.48 
TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG 
       16.67        88.93        97.45        15.35 

  DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE 
                       112.44                        140.81 
  DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE 
                         9.83                          8.02 
[1] "0.1 - 112.4 (9.8)" "0.1 - 140.8 (8.0)"
[1] "hr=" "1.2"
D68V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 36(XP11.3) MUTATED          0       0       16        16       17
  DEL PEAK 36(XP11.3) WILD-TYPE        1       2       52        56       50
D68V3, multiclass
           clus
vv          DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE
  STAGE 0A                            0                             1
  STAGE I                             0                             2
  STAGE II                           16                            52
  STAGE III                          16                            56
  STAGE IV                           17                            50
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  DEL PEAK 36(XP11.3) MUTATED         12 21 10
  DEL PEAK 36(XP11.3) WILD-TYPE       50 80 22
D68V4, multiclass
          clus
vv         DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE
  T0+T1+T2                          12                            50
  T3                                21                            80
  T4                                10                            22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 36(XP11.3) MUTATED    27   6   7   2
  DEL PEAK 36(XP11.3) WILD-TYPE 103  16  31   5
D68V5, multiclass
    clus
vv   DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE
  N0                          27                           103
  N1                           6                            16
  N2                           7                            31
  N3                           2                             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                            M0 M1 MX
  DEL PEAK 36(XP11.3) MUTATED   25  0 24
  DEL PEAK 36(XP11.3) WILD-TYPE 81  5 78
D68V6, multiclass
    clus
vv   DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE
  M0                          25                            81
  M1                           0                             5
  MX                          24                            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"
D68V7, binary
                               cls
clus                              0   1
  DEL PEAK 36(XP11.3) MUTATED     9  41
  DEL PEAK 36(XP11.3) WILD-TYPE  41 123
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 36(XP11.3) MUTATED      9   41
  DEL PEAK 36(XP11.3) WILD-TYPE   41  123
        clus
vv       DEL PEAK 36(XP11.3) MUTATED DEL PEAK 36(XP11.3) WILD-TYPE
  FEMALE                           9                            41
  MALE                            41                           123
[1] 2 2
[1] FALSE
D68V8, continuous
D68V9, continuous
D68V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(XP11.3) MUTATED       6                         3    38
  DEL PEAK 36(XP11.3) WILD-TYPE    16                         8   132
D68V11, multiclass
                           clus
vv                          DEL PEAK 36(XP11.3) MUTATED
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              38
                           clus
vv                          DEL PEAK 36(XP11.3) WILD-TYPE
  ASIAN                                                16
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                               132
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(69) Variable = DEL PEAK 37(XQ21.33) MUTATION ANALYSIS
D69V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 37(XQ21.33) MUTATED    33  10
  DEL PEAK 37(XQ21.33) WILD-TYPE 118  47
  DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE 
                            43                            165 
  DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE 
                            10                             47 
$`DEL PEAK 37(XQ21.33) MUTATED`
TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B 
       14.89         5.06         8.25         5.59         4.67        15.42 
TCGA-BT-A42C TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47X TCGA-CU-A3KJ TCGA-CU-A3QU 
       28.70         0.43         0.69         0.10         5.46         5.19 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A6B5 TCGA-E5-A2PC 
        8.91       130.88        50.27        21.30        32.28        43.59 
TCGA-E7-A3X6 TCGA-FD-A3B4 TCGA-FD-A3SN TCGA-FD-A3SS TCGA-FD-A5BY TCGA-FD-A6TA 
       24.66        15.68        12.82         1.97         6.84        50.66 
TCGA-FJ-A3Z7 TCGA-FT-A3EE TCGA-G2-A2EL TCGA-G2-A3IB TCGA-GC-A6I1 TCGA-GD-A6C6 
       15.19         3.25        26.93         7.04         2.66         2.20 
TCGA-GU-A42P TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40G 
        6.41         6.41         6.15         7.79         4.14        19.07 
TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A54R TCGA-K4-A5RJ TCGA-LT-A5Z6 TCGA-MV-A51V 
       38.60         4.67        10.52         1.74         3.45        13.48 
TCGA-PQ-A6FI 
       12.23 

$`DEL PEAK 37(XQ21.33) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       11.93        19.04        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PJ 
        5.06        14.96         8.35        17.16         3.65        12.82 
TCGA-BT-A3PK TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
        2.07         9.99        28.41         8.98         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
        0.46         0.13         0.07         0.10         0.07         0.10 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
       12.92         4.90         7.20        16.31         1.84         9.34 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AD 
        2.53         2.14        31.40        18.41        19.00       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20         3.98         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       10.49        20.02         9.67         8.28        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       48.00        17.98        64.18        48.53        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       15.68        30.67        15.35        26.17         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        0.53         0.59         0.56         0.66         1.38         0.82 
TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
        1.22        12.89         8.94         6.87         4.01        12.43 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       11.93        15.88        45.93        24.30        22.45        16.47 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43P 
        5.52        13.18        46.78        19.79        22.98        14.93 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       14.96        14.93         3.62        12.13        13.38        37.15 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 
       11.01         6.87         5.36         5.69        27.45         6.87 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TC 
       49.68         2.66         4.83         6.28         6.38         9.30 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z9 
        6.71         4.11         2.66         2.20         4.01         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.48         4.08         6.48        61.94        30.61         5.69 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 
       35.24        17.26        20.12         0.85         2.89         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75         1.12 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R 
        7.73         2.10         3.12        20.98         7.66        11.31 
TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA 
        4.41         5.69         7.63         6.67         6.41        11.54 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
        1.51         6.74         8.75         3.45         2.50         6.48 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-PQ-A6FN TCGA-XF-A8HD 
        1.81         4.27         6.38         6.35        16.67        88.93 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       97.45        56.19        15.35 

  DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE 
                        130.88                         140.81 
  DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE 
                          7.79                           8.94 
[1] "0.1 - 130.9 (7.8)" "0.1 - 140.8 (8.9)"
[1] "hr=" "1.2"
D69V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 37(XQ21.33) MUTATED          0       0       15        11       14
  DEL PEAK 37(XQ21.33) WILD-TYPE        1       2       53        61       53
D69V3, multiclass
           clus
vv          DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              0                              2
  STAGE II                            15                             53
  STAGE III                           11                             61
  STAGE IV                            14                             53
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2 T3 T4
  DEL PEAK 37(XQ21.33) MUTATED         13 17  8
  DEL PEAK 37(XQ21.33) WILD-TYPE       49 84 24
D69V4, multiclass
          clus
vv         DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE
  T0+T1+T2                           13                             49
  T3                                 17                             84
  T4                                  8                             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 37(XQ21.33) MUTATED    24   5   7   1
  DEL PEAK 37(XQ21.33) WILD-TYPE 106  17  31   6
D69V5, multiclass
    clus
vv   DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE
  N0                           24                            106
  N1                            5                             17
  N2                            7                             31
  N3                            1                              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"
                                vv
clus                             M0 M1 MX
  DEL PEAK 37(XQ21.33) MUTATED   19  0 24
  DEL PEAK 37(XQ21.33) WILD-TYPE 87  5 78
D69V6, multiclass
    clus
vv   DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE
  M0                           19                             87
  M1                            0                              5
  MX                           24                             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"
D69V7, binary
                                cls
clus                               0   1
  DEL PEAK 37(XQ21.33) MUTATED    10  33
  DEL PEAK 37(XQ21.33) WILD-TYPE  40 131
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(XQ21.33) MUTATED     10   33
  DEL PEAK 37(XQ21.33) WILD-TYPE   40  131
        clus
vv       DEL PEAK 37(XQ21.33) MUTATED DEL PEAK 37(XQ21.33) WILD-TYPE
  FEMALE                           10                             40
  MALE                             33                            131
[1] 2 2
[1] FALSE
D69V8, continuous
D69V9, continuous
D69V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 37(XQ21.33) MUTATED       3                         3    34
  DEL PEAK 37(XQ21.33) WILD-TYPE    19                         8   136
D69V11, multiclass
                           clus
vv                          DEL PEAK 37(XQ21.33) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               34
                           clus
vv                          DEL PEAK 37(XQ21.33) WILD-TYPE
  ASIAN                                                 19
  BLACK OR AFRICAN AMERICAN                              8
  WHITE                                                136
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(70) Variable = DEL PEAK 38(XQ23) MUTATION ANALYSIS
D70V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 38(XQ23) MUTATED    30  10
  DEL PEAK 38(XQ23) WILD-TYPE 121  47
  DEL PEAK 38(XQ23) MUTATED DEL PEAK 38(XQ23) WILD-TYPE 
                         40                         168 
  DEL PEAK 38(XQ23) MUTATED DEL PEAK 38(XQ23) WILD-TYPE 
                         10                          47 
$`DEL PEAK 38(XQ23) MUTATED`
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B 
       19.04        32.84        14.89         5.59         4.67        15.42 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47X TCGA-CU-A3QU TCGA-DK-A1AB TCGA-DK-A1AC 
        0.43         0.69         0.10         5.19         8.91       130.88 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E7-A3X6 
       50.27        21.30         9.67        32.28        43.59        24.66 
TCGA-FD-A3B4 TCGA-FD-A3SN TCGA-FD-A3SS TCGA-FD-A5BY TCGA-FD-A62S TCGA-FJ-A3Z7 
       15.68        12.82         1.97         6.84         6.38        15.19 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EL TCGA-G2-A3IB TCGA-GC-A6I1 TCGA-GD-A6C6 
        4.08         3.25        26.93         7.04         2.66         2.20 
TCGA-GU-A42P TCGA-GV-A3JX TCGA-GV-A3QI TCGA-GV-A40G TCGA-HQ-A2OE TCGA-K4-A3WV 
        6.41         6.15         4.14        19.07        38.60         4.67 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-LT-A5Z6 TCGA-MV-A51V 
       10.52         1.74         3.45        13.48 

$`DEL PEAK 38(XQ23) WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       11.93        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PJ 
        5.06         8.35         8.25        17.16         3.65        12.82 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
        2.07        28.70         9.99        28.41         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       23.01         0.46         0.13         0.07         0.10         0.07 
TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL 
        0.10        12.92         4.90         7.20         5.46        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        1.84         9.34         2.53         2.14        31.40        18.41 
TCGA-DK-A1AA TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
       19.00       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       10.59         7.79       123.85        87.32         2.20         3.98 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX 
        7.82         8.22        10.49        20.02         8.28        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
      140.81        48.00        17.98        64.18        48.53        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 
       67.36        15.68        30.67        15.35        26.17         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        0.49         0.53         0.59         0.56         0.66         1.38 
TCGA-E7-A678 TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        0.82         1.22        12.89         8.94         6.87         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.43        11.93        15.88        45.93        24.30        22.45 
TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N 
       16.47         5.52        13.18        46.78        19.79        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       14.93        14.96        14.93         3.62        12.13        13.38 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ 
       37.15        11.01         6.87         5.36         5.69        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TA 
        6.87        49.68         2.66         4.83         6.28        50.66 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
        9.30         6.71         4.11         2.66         2.20         4.01 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        7.13         3.48         6.48        61.94        30.61         5.69 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 
       35.24        17.26        20.12         0.85         2.89         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75         1.12 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R 
        7.73         2.10         3.12        20.98         7.66        11.31 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK 
        4.41         6.41         5.69         7.63         7.79         6.67 
TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A3WU 
        6.41        11.54         1.51         6.74         8.75         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R 
        2.50         6.48         1.81         4.27         6.38         6.35 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       12.23        16.67        88.93        97.45        56.19        15.35 

  DEL PEAK 38(XQ23) MUTATED DEL PEAK 38(XQ23) WILD-TYPE 
                       0.10                        0.07 
  DEL PEAK 38(XQ23) MUTATED DEL PEAK 38(XQ23) WILD-TYPE 
                     130.88                      140.81 
  DEL PEAK 38(XQ23) MUTATED DEL PEAK 38(XQ23) WILD-TYPE 
                      7.975                       8.550 
[1] "0.1 - 130.9 (8.0)" "0.1 - 140.8 (8.6)"
[1] "hr=" "1.1"
D70V2, continuous
                             vv
clus                          STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 38(XQ23) MUTATED          0       0       13        13       11
  DEL PEAK 38(XQ23) WILD-TYPE        1       2       55        59       56
D70V3, multiclass
           clus
vv          DEL PEAK 38(XQ23) MUTATED DEL PEAK 38(XQ23) WILD-TYPE
  STAGE 0A                          0                           1
  STAGE I                           0                           2
  STAGE II                         13                          55
  STAGE III                        13                          59
  STAGE IV                         11                          56
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1+T2 T3 T4
  DEL PEAK 38(XQ23) MUTATED         12 17  6
  DEL PEAK 38(XQ23) WILD-TYPE       50 84 26
D70V4, multiclass
          clus
vv         DEL PEAK 38(XQ23) MUTATED DEL PEAK 38(XQ23) WILD-TYPE
  T0+T1+T2                        12                          50
  T3                              17                          84
  T4                               6                          26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2  N3
  DEL PEAK 38(XQ23) MUTATED    25   5   4   1
  DEL PEAK 38(XQ23) WILD-TYPE 105  17  34   6
D70V5, multiclass
    clus
vv   DEL PEAK 38(XQ23) MUTATED DEL PEAK 38(XQ23) WILD-TYPE
  N0                        25                         105
  N1                         5                          17
  N2                         4                          34
  N3                         1                           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"
                             vv
clus                          M0 M1 MX
  DEL PEAK 38(XQ23) MUTATED   17  0 23
  DEL PEAK 38(XQ23) WILD-TYPE 89  5 79
D70V6, multiclass
    clus
vv   DEL PEAK 38(XQ23) MUTATED DEL PEAK 38(XQ23) WILD-TYPE
  M0                        17                          89
  M1                         0                           5
  MX                        23                          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"
D70V7, binary
                             cls
clus                            0   1
  DEL PEAK 38(XQ23) MUTATED    10  30
  DEL PEAK 38(XQ23) WILD-TYPE  40 134
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 38(XQ23) MUTATED     10   30
  DEL PEAK 38(XQ23) WILD-TYPE   40  134
        clus
vv       DEL PEAK 38(XQ23) MUTATED DEL PEAK 38(XQ23) WILD-TYPE
  FEMALE                        10                          40
  MALE                          30                         134
[1] 2 2
[1] FALSE
D70V8, continuous
D70V9, continuous
D70V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 38(XQ23) MUTATED       3                         3    31
  DEL PEAK 38(XQ23) WILD-TYPE    19                         8   139
D70V11, multiclass
                           clus
vv                          DEL PEAK 38(XQ23) MUTATED
  ASIAN                                             3
  BLACK OR AFRICAN AMERICAN                         3
  WHITE                                            31
                           clus
vv                          DEL PEAK 38(XQ23) WILD-TYPE
  ASIAN                                              19
  BLACK OR AFRICAN AMERICAN                           8
  WHITE                                             139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
