[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/11541262/BLCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BLCA-TP/11548711/transformed.cor.cli.txt"

nPatients in clinical file=281, in cluster file=408, common to both=278
[1]  70 278
[1] "AMP PEAK  1(1P34.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                           66                           212 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                           66                           212 
[1] "AMP PEAK  2(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          130                           148 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          130                           148 
[1] "AMP PEAK  3(1Q23.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE 
                          140                           138 
  AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE 
                          140                           138 
[1] "AMP PEAK  4(2P25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE 
                           98                           180 
  AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE 
                           98                           180 
[1] "AMP PEAK  5(3P25.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE 
                          124                           154 
  AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE 
                          124                           154 
[1] "AMP PEAK  6(3Q26.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE 
                           141                            137 
  AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE 
                           141                            137 
[1] "AMP PEAK  7(4P16.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                           56                           222 
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                           56                           222 
[1] "AMP PEAK  8(4Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                           42                           236 
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                           42                           236 
[1] "AMP PEAK  9(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                           135                            143 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                           135                            143 
[1] "AMP PEAK 10(6P22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                          102                           176 
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                          102                           176 
[1] "AMP PEAK 11(6Q21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                         21                         257 
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                         21                         257 
[1] "AMP PEAK 12(6Q23.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE 
                           29                           249 
  AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE 
                           29                           249 
[1] "AMP PEAK 13(7P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE 
                          136                           142 
  AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE 
                          136                           142 
[1] "AMP PEAK 14(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE 
                          130                           148 
  AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE 
                          130                           148 
[1] "AMP PEAK 15(8P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE 
                            80                            198 
  AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE 
                            80                            198 
[1] "AMP PEAK 16(8Q22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(8Q22.3) MUTATED AMP PEAK 16(8Q22.3) WILD-TYPE 
                          171                           107 
  AMP PEAK 16(8Q22.3) MUTATED AMP PEAK 16(8Q22.3) WILD-TYPE 
                          171                           107 
[1] "AMP PEAK 17(9P24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(9P24.1) MUTATED AMP PEAK 17(9P24.1) WILD-TYPE 
                           57                           221 
  AMP PEAK 17(9P24.1) MUTATED AMP PEAK 17(9P24.1) WILD-TYPE 
                           57                           221 
[1] "AMP PEAK 18(10P14) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(10P14) MUTATED AMP PEAK 18(10P14) WILD-TYPE 
                         116                          162 
  AMP PEAK 18(10P14) MUTATED AMP PEAK 18(10P14) WILD-TYPE 
                         116                          162 
[1] "AMP PEAK 19(11P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE 
                          34                          244 
  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE 
                          34                          244 
[1] "AMP PEAK 20(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                           103                            175 
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                           103                            175 
[1] "AMP PEAK 21(11Q22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(11Q22.2) MUTATED AMP PEAK 21(11Q22.2) WILD-TYPE 
                            51                            227 
  AMP PEAK 21(11Q22.2) MUTATED AMP PEAK 21(11Q22.2) WILD-TYPE 
                            51                            227 
[1] "AMP PEAK 22(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(12P12.1) MUTATED AMP PEAK 22(12P12.1) WILD-TYPE 
                            85                            193 
  AMP PEAK 22(12P12.1) MUTATED AMP PEAK 22(12P12.1) WILD-TYPE 
                            85                            193 
[1] "AMP PEAK 23(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(12Q15) MUTATED AMP PEAK 23(12Q15) WILD-TYPE 
                          78                          200 
  AMP PEAK 23(12Q15) MUTATED AMP PEAK 23(12Q15) WILD-TYPE 
                          78                          200 
[1] "AMP PEAK 24(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(13Q22.1) MUTATED AMP PEAK 24(13Q22.1) WILD-TYPE 
                            83                            195 
  AMP PEAK 24(13Q22.1) MUTATED AMP PEAK 24(13Q22.1) WILD-TYPE 
                            83                            195 
[1] "AMP PEAK 25(16P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(16P13.2) MUTATED AMP PEAK 25(16P13.2) WILD-TYPE 
                            60                            218 
  AMP PEAK 25(16P13.2) MUTATED AMP PEAK 25(16P13.2) WILD-TYPE 
                            60                            218 
[1] "AMP PEAK 26(16P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(16P11.2) MUTATED AMP PEAK 26(16P11.2) WILD-TYPE 
                            71                            207 
  AMP PEAK 26(16P11.2) MUTATED AMP PEAK 26(16P11.2) WILD-TYPE 
                            71                            207 
[1] "AMP PEAK 27(16Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE 
                            76                            202 
  AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE 
                            76                            202 
[1] "AMP PEAK 28(17P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(17P11.2) MUTATED AMP PEAK 28(17P11.2) WILD-TYPE 
                            61                            217 
  AMP PEAK 28(17P11.2) MUTATED AMP PEAK 28(17P11.2) WILD-TYPE 
                            61                            217 
[1] "AMP PEAK 29(17Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(17Q11.2) MUTATED AMP PEAK 29(17Q11.2) WILD-TYPE 
                           122                            156 
  AMP PEAK 29(17Q11.2) MUTATED AMP PEAK 29(17Q11.2) WILD-TYPE 
                           122                            156 
[1] "AMP PEAK 30(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE 
                         112                          166 
  AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE 
                         112                          166 
[1] "AMP PEAK 31(17Q23.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 31(17Q23.3) MUTATED AMP PEAK 31(17Q23.3) WILD-TYPE 
                           132                            146 
  AMP PEAK 31(17Q23.3) MUTATED AMP PEAK 31(17Q23.3) WILD-TYPE 
                           132                            146 
[1] "AMP PEAK 32(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 32(19Q12) MUTATED AMP PEAK 32(19Q12) WILD-TYPE 
                         108                          170 
  AMP PEAK 32(19Q12) MUTATED AMP PEAK 32(19Q12) WILD-TYPE 
                         108                          170 
[1] "AMP PEAK 33(19Q13.43) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 33(19Q13.43) MUTATED AMP PEAK 33(19Q13.43) WILD-TYPE 
                            101                             177 
  AMP PEAK 33(19Q13.43) MUTATED AMP PEAK 33(19Q13.43) WILD-TYPE 
                            101                             177 
[1] "AMP PEAK 34(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 34(20Q11.21) MUTATED AMP PEAK 34(20Q11.21) WILD-TYPE 
                            173                             105 
  AMP PEAK 34(20Q11.21) MUTATED AMP PEAK 34(20Q11.21) WILD-TYPE 
                            173                             105 
[1] "AMP PEAK 35(22Q12.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 35(22Q12.2) MUTATED AMP PEAK 35(22Q12.2) WILD-TYPE 
                            53                            225 
  AMP PEAK 35(22Q12.2) MUTATED AMP PEAK 35(22Q12.2) WILD-TYPE 
                            53                            225 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            56                            222 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            56                            222 
[1] "DEL PEAK  2(1Q32.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE 
                           50                           228 
  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE 
                           50                           228 
[1] "DEL PEAK  3(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           88                           190 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           88                           190 
[1] "DEL PEAK  4(2Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE 
                        110                         168 
  DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE 
                        110                         168 
[1] "DEL PEAK  5(2Q37.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                          137                           141 
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                          137                           141 
[1] "DEL PEAK  6(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           79                           199 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           79                           199 
[1] "DEL PEAK  7(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                          104                           174 
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                          104                           174 
[1] "DEL PEAK  8(4Q34.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE 
                          118                           160 
  DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE 
                          118                           160 
[1] "DEL PEAK  9(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                          136                           142 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                          136                           142 
[1] "DEL PEAK 10(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                           68                           210 
  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                           68                           210 
[1] "DEL PEAK 11(6Q21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                        130                         148 
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                        130                         148 
[1] "DEL PEAK 12(6Q27) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                        128                         150 
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                        128                         150 
[1] "DEL PEAK 13(7Q36.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                           39                           239 
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                           39                           239 
[1] "DEL PEAK 14(8P23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(8P23.1) MUTATED DEL PEAK 14(8P23.1) WILD-TYPE 
                          156                           122 
  DEL PEAK 14(8P23.1) MUTATED DEL PEAK 14(8P23.1) WILD-TYPE 
                          156                           122 
[1] "DEL PEAK 15(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                        120                         158 
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                        120                         158 
[1] "DEL PEAK 16(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                          159                           119 
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                          159                           119 
[1] "DEL PEAK 17(9Q33.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(9Q33.2) MUTATED DEL PEAK 17(9Q33.2) WILD-TYPE 
                          110                           168 
  DEL PEAK 17(9Q33.2) MUTATED DEL PEAK 17(9Q33.2) WILD-TYPE 
                          110                           168 
[1] "DEL PEAK 18(10P11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(10P11.21) MUTATED DEL PEAK 18(10P11.21) WILD-TYPE 
                             47                             231 
  DEL PEAK 18(10P11.21) MUTATED DEL PEAK 18(10P11.21) WILD-TYPE 
                             47                             231 
[1] "DEL PEAK 19(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                            110                             168 
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                            110                             168 
[1] "DEL PEAK 20(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                           133                            145 
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                           133                            145 
[1] "DEL PEAK 21(11Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                            95                            183 
  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                            95                            183 
[1] "DEL PEAK 22(11Q25) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(11Q25) MUTATED DEL PEAK 22(11Q25) WILD-TYPE 
                          88                          190 
  DEL PEAK 22(11Q25) MUTATED DEL PEAK 22(11Q25) WILD-TYPE 
                          88                          190 
[1] "DEL PEAK 23(12P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(12P13.1) MUTATED DEL PEAK 23(12P13.1) WILD-TYPE 
                            43                            235 
  DEL PEAK 23(12P13.1) MUTATED DEL PEAK 23(12P13.1) WILD-TYPE 
                            43                            235 
[1] "DEL PEAK 24(12Q24.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(12Q24.33) MUTATED DEL PEAK 24(12Q24.33) WILD-TYPE 
                             58                             220 
  DEL PEAK 24(12Q24.33) MUTATED DEL PEAK 24(12Q24.33) WILD-TYPE 
                             58                             220 
[1] "DEL PEAK 25(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(13Q14.2) MUTATED DEL PEAK 25(13Q14.2) WILD-TYPE 
                           103                            175 
  DEL PEAK 25(13Q14.2) MUTATED DEL PEAK 25(13Q14.2) WILD-TYPE 
                           103                            175 
[1] "DEL PEAK 26(14Q24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(14Q24.1) MUTATED DEL PEAK 26(14Q24.1) WILD-TYPE 
                            87                            191 
  DEL PEAK 26(14Q24.1) MUTATED DEL PEAK 26(14Q24.1) WILD-TYPE 
                            87                            191 
[1] "DEL PEAK 27(15Q13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(15Q13.1) MUTATED DEL PEAK 27(15Q13.1) WILD-TYPE 
                           109                            169 
  DEL PEAK 27(15Q13.1) MUTATED DEL PEAK 27(15Q13.1) WILD-TYPE 
                           109                            169 
[1] "DEL PEAK 28(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                           113                            165 
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                           113                            165 
[1] "DEL PEAK 29(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE 
                            77                            201 
  DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE 
                            77                            201 
[1] "DEL PEAK 30(17P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(17P12) MUTATED DEL PEAK 30(17P12) WILD-TYPE 
                         138                          140 
  DEL PEAK 30(17P12) MUTATED DEL PEAK 30(17P12) WILD-TYPE 
                         138                          140 
[1] "DEL PEAK 31(18Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(18Q23) MUTATED DEL PEAK 31(18Q23) WILD-TYPE 
                         114                          164 
  DEL PEAK 31(18Q23) MUTATED DEL PEAK 31(18Q23) WILD-TYPE 
                         114                          164 
[1] "DEL PEAK 32(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                            98                            180 
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                            98                            180 
[1] "DEL PEAK 33(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE 
                            121                             157 
  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE 
                            121                             157 
[1] "DEL PEAK 34(XP11.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE 
                           63                           215 
  DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE 
                           63                           215 
[1] "DEL PEAK 35(XQ21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE 
                            55                            223 
  DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE 
                            55                            223 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "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 278 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
         678           NA         2555         3148         2991          147 
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-CF-A5U8 TCGA-CF-A5UA TCGA-CU-A0YN TCGA-CU-A0YO 
           3            3           NA           NA           NA           NA 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
         219          166          158          496           NA          284 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
          77           NA         2020          560          578          271 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
        3981         3420          491          536          475           55 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
         322           NA         3767         2656           67          121 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
         238           NA          319         1529          648          609 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
          NA          252           NA         4283         1460           NA 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
        1952         1264         2330         2049          477         1249 
TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
         933         1326           NA          796          750            3 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
          15           16           NA           18           17           20 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN 
          42           25          395          436           37           14 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
         392          477           NA          209           NA          378 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
         363          483         1397           NA          683          186 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
         390           NA          401           NA           NA           60 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
         699          454          455          454          110          369 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
         407         1130           NA          209           NA           NA 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
         208           NA          209         1511           81          147 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
          NA          194         1541          572          283          204 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
         125           63           81           67          122          330 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P 
         462          217          106          124           NA          197 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
        1884          931          173           NA         1072          525 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
         214           NA           26         1602           NA          592 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
          88           68          481          137          484          428 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
         540           34           81          235           64           95 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
         638           67          224          195          231          344 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV 
          62          824          171           NA           NA          134 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QG TCGA-GV-A3QH 
         195          187          173          232           NA          237 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
         126          203          195          580          351           46 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
         205         1174           93           NA          250          266 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ 
         105          142           76          197          320           53 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
          55          130          194          193          105          359 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
         410          372          507          433           NA          114 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
        1370           NA         2705         2964         1709           NA 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX 
          NA           NA           NA         2423           NA           NA 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
         640           NA          799           NA           68           NA 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML 
        2027           64           NA           NA           NA           NA 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 
        2790           NA           NA           NA           NA           NA 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
          NA         2293           NA          315          147           NA 
TCGA-YF-AA3L TCGA-YF-AA3M 
         242          275 
Variable 1:'AGE':	nDistinctValues=50,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=82,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=175,	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=3,	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=60,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=19,	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=FALSE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=26,	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"                       
[11] "ETHNICITY"                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 278 columns, 1 survival variables, and 11 non-survival variables.
AGE, nv=50, 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  80 136  39 
[1] "table(vv)"
vv
T0+T1+T2       T3       T4 
      82      136       39 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1   1  80 136  39 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T0+T1+T2       T3       T4 
      82      136       39 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
166  28  55   7 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
166  28  55   7 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
166  28  55   7 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
166  28  55   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=60, binary=FALSE, numeric=TRUE
NUMBER.OF.LYMPH.NODES, nv=19, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1P34.2) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  1(1P34.2) MUTATED    45  21
  AMP PEAK  1(1P34.2) WILD-TYPE 137  67
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                           66                           204 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                           21                            67 
$`AMP PEAK  1(1P34.2) MUTATED`
TCGA-2F-A9KP TCGA-BT-A20J TCGA-BT-A20R TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PJ 
       11.97        19.04         5.06        17.16         3.65        12.82 
TCGA-BT-A3PK TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CU-A0YN 
        2.07         9.99         8.98         1.94         0.43        12.92 
TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A2I1 TCGA-DK-A2I4 
        5.19         2.53        18.41         8.91        10.59       123.85 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3X2 TCGA-DK-A6AV 
        3.98         7.82         8.22        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-GD-A76B 
       15.81        14.07         1.12         7.73        20.98         7.36 
TCGA-GU-A42P TCGA-GU-A767 TCGA-GV-A3JW TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A2OE 
        6.41         4.73         6.41        19.07        11.54        38.60 
TCGA-K4-A3WV TCGA-K4-A6MB TCGA-MV-A51V TCGA-XF-A8HD TCGA-XF-AAML TCGA-YF-AA3M 
        4.67         4.27        13.48        88.93         7.63         9.04 

$`AMP PEAK  1(1P34.2) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 
       22.29        84.00       103.50        98.33         4.83        40.08 
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-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-A20W TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B 
        5.06         8.35         8.25         5.59         4.67        15.42 
TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S 
       28.70        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-A0YO 
        0.07         0.10         0.07         0.10         0.10         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 
        7.20         5.46        16.31         1.84         9.34         2.14 
TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       66.41        19.00       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IQ 
       15.62         1.81         7.79        87.32         2.20        10.49 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       50.27        21.30         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        41.56        76.60        67.36        15.68        41.06 
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-A6ME TCGA-E7-A6MF TCGA-E7-A7DV 
        0.66         1.38         0.82        12.99        14.33         1.22 
TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 
        0.46        12.89        15.68         6.87        12.43        11.93 
TCGA-FD-A3N6 TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       15.88         6.12        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-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A62N 
       11.01         5.36         5.69         6.84        27.45         2.66 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD 
        4.83         6.28         6.38        50.66        18.81         6.71 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        4.11         2.07         2.20        10.85         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-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
       17.26         7.04         0.85        52.67         6.94        19.46 
TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OP 
        2.24         4.50        15.91        17.75         2.66         2.10 
TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        3.12         2.20         7.59        11.31         2.04        27.09 
TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        5.62        10.65         4.41         6.15         5.69         7.63 
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-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
        3.06         9.01         8.22         8.75         3.45         2.50 
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-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
        3.45        11.80        12.23        16.67        14.24         0.85 
TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
        3.75        45.04         6.58        97.45        56.19        15.35 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX 
        1.87        17.88        64.80        79.66        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMR 
       66.64         2.10        92.98        10.82        54.90        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 
        2.96         8.32         6.77        56.48        30.94        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39         3.88        10.36         4.83         0.66         7.96 

  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 
                        9.170                         9.175 
[1] "0.4 - 123.8 (9.2)" "0.1 - 140.8 (9.2)"
[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       22        16       25
  AMP PEAK  1(1P34.2) WILD-TYPE        0       2       64        77       67
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                           22                            64
  STAGE III                          16                            77
  STAGE IV                           25                            67
[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         24  28  10
  AMP PEAK  1(1P34.2) WILD-TYPE       58 108  29
D1V4, multiclass
          clus
vv         AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  T0+T1+T2                          24                            58
  T3                                28                           108
  T4                                10                            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  1(1P34.2) MUTATED    35   9  15   2
  AMP PEAK  1(1P34.2) WILD-TYPE 131  19  40   5
D1V5, multiclass
    clus
vv   AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  N0                          35                           131
  N1                           9                            19
  N2                          15                            40
  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    29   2  35
  AMP PEAK  1(1P34.2) WILD-TYPE 100   5 106
D1V6, multiclass
    clus
vv   AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  M0                          29                           100
  M1                           2                             5
  MX                          35                           106
[1] 3 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    18  48
  AMP PEAK  1(1P34.2) WILD-TYPE  59 153
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.2) MUTATED     18   48
  AMP PEAK  1(1P34.2) WILD-TYPE   59  153
        clus
vv       AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  FEMALE                          18                            59
  MALE                            48                           153
[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    53
  AMP PEAK  1(1P34.2) WILD-TYPE    28                        10   162
D1V11, multiclass
                           clus
vv                          AMP PEAK  1(1P34.2) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              53
                           clus
vv                          AMP PEAK  1(1P34.2) WILD-TYPE
  ASIAN                                                28
  BLACK OR AFRICAN AMERICAN                            10
  WHITE                                               162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P34.2) MUTATED     1  61
  AMP PEAK  1(1P34.2) WILD-TYPE   4 197
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.2) MUTATED      1   61
  AMP PEAK  1(1P34.2) WILD-TYPE    4  197
                        clus
vv                       AMP PEAK  1(1P34.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          61
                        clus
vv                       AMP PEAK  1(1P34.2) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           197
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(1Q21.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  2(1Q21.3) MUTATED   83 46
  AMP PEAK  2(1Q21.3) WILD-TYPE 99 42
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          129                           141 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           46                            42 
$`AMP PEAK  2(1Q21.3) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KW TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20N 
       22.29         4.83         2.66         6.74        19.04        32.84 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB 
        5.06        14.89         5.06         8.35        17.16         5.59 
TCGA-BT-A2LD TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A47V 
        3.65        28.70         8.98         1.94         0.43         0.10 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 
        5.46         5.19         1.84         2.53         2.14        18.41 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
      130.88       112.44         1.81        10.59         7.79       123.85 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IU 
        2.20         3.98         7.82         8.22        21.30        20.02 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-E5-A2PC TCGA-E5-A4TZ 
       48.00        17.98        67.36        15.68        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A5KF 
       26.17        24.66         0.10         0.49         0.56         0.66 
TCGA-E7-A6ME TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.99         1.22         4.01        45.93        24.30        22.45 
TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
        6.12         5.52        19.79         1.97        22.98        14.93 
TCGA-FD-A43Y TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62P 
       12.13        11.01         6.87        27.45         6.87         6.28 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 
        9.30         4.11         2.07         2.20         4.01        15.19 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3IE 
        3.48         4.08         3.25         6.48        17.26        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB 
        0.85        52.67        19.46         2.89        15.81         4.50 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A76B 
       17.75         1.12         7.73         2.10        20.98         7.36 
TCGA-GU-A42P TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
        6.41        10.65         4.41         6.41         6.15         5.69 
TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
        7.63         4.14         6.41        19.07        11.54         1.51 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A4AC TCGA-K4-A5RJ 
       38.60         3.06         9.01         8.75         6.48         1.74 
TCGA-K4-A6MB TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-S5-AA26 
        4.27         6.35         3.45        13.48        12.23         3.75 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SI TCGA-XF-A9SW 
        6.58        88.93        15.35        17.88        79.66        11.90 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN0 
       66.64         2.10         7.63         2.96         6.77        56.48 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        0.66         7.96         9.04 

$`AMP PEAK  2(1Q21.3) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-BL-A0C8 TCGA-BL-A13I 
       11.97        84.00       103.50        98.33        40.08         7.33 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       12.39         6.58        11.93        12.16        17.88        19.50 
TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
       14.96         8.25         4.67        12.82         2.07        15.42 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S 
        9.99        28.41        23.01         0.46         0.69         0.13 
TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO 
        0.07         0.07         0.10         0.10        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB 
        7.20        16.31         9.34        66.41        19.00         8.91 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I6 TCGA-DK-A3IQ TCGA-DK-A3IS 
       16.14        17.62        15.62        87.32        10.49        50.27 
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        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A677 
       76.60        41.06        30.67         0.53         0.59         1.38 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
        0.82        14.33         0.46        12.89        15.68         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SN TCGA-FD-A3SP 
        6.87        12.43        11.93        15.88        12.82        13.18 
TCGA-FD-A3SQ TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       46.78        14.96        14.93         3.62        13.38        37.15 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        5.36         5.69         6.84        49.68         2.66         4.83 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TK 
        6.38        50.66        18.81         6.71         2.66        10.85 
TCGA-FJ-A3Z9 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        7.13        61.94        30.61         5.69        26.93        35.24 
TCGA-G2-A3IB TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 
        7.04         6.94         2.24        15.91        14.07         2.66 
TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        3.12         2.20         7.59        11.31         2.04        27.09 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3QH TCGA-GV-A3QK TCGA-H4-A2HQ TCGA-HQ-A5NE 
        5.62         4.73         7.79         6.67         6.74         8.22 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A83P 
        3.45         4.67         2.50        10.52         1.81         6.38 
TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-XF-A8HB TCGA-XF-A8HE 
       11.80        16.67        14.24         0.85        45.04        97.45 
TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A9SH TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       56.19         1.87        64.80        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMF 
       26.27        18.90         2.24        16.27        92.98        10.82 
TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
       54.90        91.73         8.32        30.94        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
        3.88        10.36         4.83 

  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 
                         7.63                         11.93 
[1] "0.1 - 130.9 (7.6)"  "0.1 - 140.8 (11.9)"
[1] "hr=" "1.5"
D2V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  2(1Q21.3) MUTATED          1       0       40        33       54
  AMP PEAK  2(1Q21.3) WILD-TYPE        0       2       46        60       38
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                           40                            46
  STAGE III                          33                            60
  STAGE IV                           54                            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  2(1Q21.3) MUTATED         38 62 20
  AMP PEAK  2(1Q21.3) WILD-TYPE       44 74 19
D2V4, multiclass
          clus
vv         AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  T0+T1+T2                          38                            44
  T3                                62                            74
  T4                                20                            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
  AMP PEAK  2(1Q21.3) MUTATED    65  18  31   5
  AMP PEAK  2(1Q21.3) WILD-TYPE 101  10  24   2
D2V5, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  N0                          65                           101
  N1                          18                            10
  N2                          31                            24
  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   56  6 67
  AMP PEAK  2(1Q21.3) WILD-TYPE 73  1 74
D2V6, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  M0                          56                            73
  M1                           6                             1
  MX                          67                            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"
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED    34  96
  AMP PEAK  2(1Q21.3) WILD-TYPE  43 105
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     34   96
  AMP PEAK  2(1Q21.3) WILD-TYPE   43  105
        clus
vv       AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  FEMALE                          34                            43
  MALE                            96                           105
[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      10                         6   103
  AMP PEAK  2(1Q21.3) WILD-TYPE    21                         7   112
D2V11, multiclass
                           clus
vv                          AMP PEAK  2(1Q21.3) MUTATED
  ASIAN                                              10
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                             103
                           clus
vv                          AMP PEAK  2(1Q21.3) WILD-TYPE
  ASIAN                                                21
  BLACK OR AFRICAN AMERICAN                             7
  WHITE                                               112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED     2 119
  AMP PEAK  2(1Q21.3) WILD-TYPE   3 139
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED      2  119
  AMP PEAK  2(1Q21.3) WILD-TYPE    3  139
                        clus
vv                       AMP PEAK  2(1Q21.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         119
                        clus
vv                       AMP PEAK  2(1Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           139
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(1Q23.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  3(1Q23.3) MUTATED   92 46
  AMP PEAK  3(1Q23.3) WILD-TYPE 90 42
  AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE 
                          138                           132 
  AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE 
                           46                            42 
$`AMP PEAK  3(1Q23.3) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 TCGA-BL-A13J 
       22.29        11.97        98.33         4.83        40.08         2.66 
TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W 
        6.74        19.04        32.84        14.89         5.06         8.35 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
       17.16         5.59         3.65         4.67        12.82         2.07 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A47V TCGA-CU-A0YR 
       28.70         8.98         1.94         0.43         0.10         7.20 
TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AC 
        5.46         1.84         2.53         2.14        18.41       130.88 
TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
      112.44        10.59         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        3.98         7.82         8.22        50.27        21.30        20.02 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-E5-A2PC TCGA-E5-A4U1 
       48.00        17.98        67.36        15.68        43.59        26.17 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
       24.66         0.10         0.49         0.59         0.56         0.66 
TCGA-E7-A6ME TCGA-E7-A7DV TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ 
       12.99         1.22        15.68         4.01        45.93        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A3SS 
       22.45         6.12         5.52        13.18        19.79         1.97 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BT TCGA-FD-A5BU 
       22.98        14.93         3.62        12.13        11.01         6.87 
TCGA-FD-A5BZ TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       27.45         6.28         9.30         4.11         2.66         2.20 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EF 
        4.01        15.19         3.48         4.08         3.25        61.94 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3WC 
        0.85        52.67        19.46         2.89        15.81        17.75 
TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P 
        1.12         7.73         2.10        20.98         7.36         6.41 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
        4.73        10.65         4.41         6.41         6.15         5.69 
TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
        7.63         4.14        19.07        11.54         1.51         6.74 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC 
       38.60         3.06         9.01         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-S5-AA26 TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SI 
        3.75         6.58        88.93        15.35        17.88        79.66 
TCGA-XF-A9SW TCGA-XF-A9SZ TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAML TCGA-XF-AAMT 
       11.90        28.24        66.64         2.10         7.63         2.96 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        6.77        56.48        27.06         0.66         7.96         9.04 

$`AMP PEAK  3(1Q23.3) WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       84.00       103.50         7.33        12.39         6.58        11.93 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X 
       12.16        17.88        19.50         5.06        14.96         8.25 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C 
       15.42         9.99        28.41        23.01         0.46         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN 
        0.13         0.07         0.07         0.10         0.10        12.92 
TCGA-CU-A0YO TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1AA 
        4.90         5.19        16.31         9.34        66.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A3IQ 
        8.91        16.14        17.62        15.62         1.81        10.49 
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        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E7-A4XJ TCGA-E7-A677 
       76.60        41.06        30.67        15.35         0.53         1.38 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 
        0.82        14.33         0.46        12.89         8.94         6.87 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A43S 
       12.43        11.93        15.88        12.82        46.78        14.96 
TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       14.93        13.38        37.15         5.36         5.69         6.84 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA 
        6.87        49.68         2.66         4.83         6.38        50.66 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FT-A61P 
       18.81         6.71         2.07        10.85         7.13         6.48 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       30.61         5.69        26.93        35.24        17.26         7.04 
TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       20.12         6.94         2.24         4.50        15.91        14.07 
TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.66         3.12         2.20         7.59        11.31         2.04 
TCGA-GU-A763 TCGA-GU-A766 TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E TCGA-HQ-A5NE 
       27.09         5.62         7.79         6.67         6.41         8.22 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LT-A8JT 
        4.67         2.50        10.52         1.81         6.38        11.80 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-XF-A8HB TCGA-XF-A8HE TCGA-XF-A8HF 
       16.67        14.24         0.85        45.04        97.45        56.19 
TCGA-XF-A8HH TCGA-XF-A9SH TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
        1.87        64.80        23.64        21.04        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMR 
        2.24        16.27        92.98        10.82        54.90        91.73 
TCGA-XF-AAMW TCGA-XF-AAN1 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
        8.32        30.94        75.39         3.88        10.36         4.83 

  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 
                        7.805                        10.835 
[1] "0.1 - 130.9 (7.8)"  "0.1 - 140.8 (10.8)"
[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       43        37       56
  AMP PEAK  3(1Q23.3) WILD-TYPE        0       1       43        56       36
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                           43                            43
  STAGE III                          37                            56
  STAGE IV                           56                            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
  AMP PEAK  3(1Q23.3) MUTATED         45 64 21
  AMP PEAK  3(1Q23.3) WILD-TYPE       37 72 18
D3V4, multiclass
          clus
vv         AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE
  T0+T1+T2                          45                            37
  T3                                64                            72
  T4                                21                            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  3(1Q23.3) MUTATED   73 17 32  7
  AMP PEAK  3(1Q23.3) WILD-TYPE 93 11 23  0
D3V5, multiclass
    clus
vv   AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE
  N0                          73                            93
  N1                          17                            11
  N2                          32                            23
  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   58  6 75
  AMP PEAK  3(1Q23.3) WILD-TYPE 71  1 66
D3V6, multiclass
    clus
vv   AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE
  M0                          58                            71
  M1                           6                             1
  MX                          75                            66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q23.3) MUTATED    34 106
  AMP PEAK  3(1Q23.3) WILD-TYPE  43  95
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q23.3) MUTATED     34  106
  AMP PEAK  3(1Q23.3) WILD-TYPE   43   95
        clus
vv       AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE
  FEMALE                          34                            43
  MALE                           106                            95
[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      10                         8   110
  AMP PEAK  3(1Q23.3) WILD-TYPE    21                         5   105
D3V11, multiclass
                           clus
vv                          AMP PEAK  3(1Q23.3) MUTATED
  ASIAN                                              10
  BLACK OR AFRICAN AMERICAN                           8
  WHITE                                             110
                           clus
vv                          AMP PEAK  3(1Q23.3) WILD-TYPE
  ASIAN                                                21
  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"
D3V12, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q23.3) MUTATED     2 128
  AMP PEAK  3(1Q23.3) WILD-TYPE   3 130
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q23.3) MUTATED      2  128
  AMP PEAK  3(1Q23.3) WILD-TYPE    3  130
                        clus
vv                       AMP PEAK  3(1Q23.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         128
                        clus
vv                       AMP PEAK  3(1Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           130
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(2P25.1) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(2P25.1) MUTATED    63  33
  AMP PEAK  4(2P25.1) WILD-TYPE 119  55
  AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE 
                           96                           174 
  AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE 
                           33                            55 
$`AMP PEAK  4(2P25.1) MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
       40.08         2.66        12.39        11.93        19.04        32.84 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06        14.89         5.06         8.35         5.59         3.65 
TCGA-BT-A3PJ TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HS 
       12.82        28.70        28.41         8.98        23.01         0.43 
TCGA-CF-A27C TCGA-CF-A47X TCGA-CU-A0YR TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
        0.69         0.10         7.20         2.53         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 
       18.41       130.88       112.44        10.59         7.79        87.32 
TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
        2.20         7.82         8.22        48.00        17.98        64.18 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E7-A541 TCGA-E7-A6ME 
       67.36        15.68        30.67        43.59         0.59        12.99 
TCGA-FD-A3B5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
        8.94        45.93        24.30        46.78        19.79         1.97 
TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TC 
       14.93        14.93        27.45         4.83         6.28         9.30 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3ZF 
        4.11         2.07         2.66         2.20        10.85         4.08 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3RB 
        3.25         6.48         0.85        52.67        19.46         4.50 
TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GU-AATO 
       14.07         2.66         7.73         2.10        20.98        10.65 
TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A6ZA 
        6.41         7.63         7.79         4.14         6.67        11.54 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A6FZ 
        6.74        38.60         8.22         8.75         4.67         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-MV-A51V TCGA-XF-A8HD TCGA-XF-A8HG TCGA-XF-A8HH 
        4.27         6.38        13.48        88.93        15.35         1.87 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T5 TCGA-XF-AAML TCGA-XF-AAMX TCGA-XF-AAN8 
       28.24        26.27        66.64         7.63         6.77         3.88 

$`AMP PEAK  4(2P25.1) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        7.33         6.74         6.58        12.16        17.88        19.50 
TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B 
       14.96         8.25        17.16         4.67         2.07        15.42 
TCGA-BT-A42E TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        9.99         1.94         0.46         0.13         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU 
        0.07         0.10        12.92         4.90         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE 
       16.31         1.84         9.34        19.00         8.91        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IQ 
       17.62        15.62         1.81       123.85         3.98        10.49 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        20.02         9.67         8.28        10.55 
TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-E5-A4TZ TCGA-E5-A4U1 
      140.81        41.56        76.60        41.06        15.35        26.17 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF 
       24.66         0.10         0.49         0.53         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 
        1.38         0.82        14.33         1.22         0.46        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-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N 
       22.45         6.12        12.82         5.52        13.18        22.98 
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-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
        6.87         5.36         5.69         6.84         6.87        49.68 
TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TI 
        2.66         6.38        50.66        18.81         6.71         4.01 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       15.19         7.13         3.48        61.94        30.61         5.69 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C 
       26.93        35.24        17.26         7.04        20.12         6.94 
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-A3OQ TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
        3.12         2.20         7.36         6.41         7.59        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JX 
        2.04        27.09         5.62         4.73         4.41         6.15 
TCGA-GV-A3JZ TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-HQ-A5ND 
        5.69         6.41        19.07         1.51         3.06         9.01 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-LC-A66R 
        3.45         2.50         6.48        10.52         1.74         6.35 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
        3.45        11.80        12.23        16.67        14.24         0.85 
TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HI 
        3.75        45.04         6.58        97.45        56.19        17.88 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T2 
       64.80        79.66        11.90        23.64        21.04        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ 
        2.24        16.27         2.10        92.98        10.82        54.90 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 
       91.73         2.96         8.32        56.48        30.94        27.06 
TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
       75.39        10.36         4.83         0.66         7.96         9.04 

  AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE 
                         0.10                          0.07 
  AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE 
                       130.88                        140.81 
  AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE 
                        8.845                         9.830 
[1] "0.1 - 130.9 (8.8)" "0.1 - 140.8 (9.8)"
[1] "hr=" "1"  
D4V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  4(2P25.1) MUTATED          1       1       23        27       43
  AMP PEAK  4(2P25.1) WILD-TYPE        0       1       63        66       49
D4V3, multiclass
           clus
vv          AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             1                             1
  STAGE II                           23                            63
  STAGE III                          27                            66
  STAGE IV                           43                            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  4(2P25.1) MUTATED         27 50 14
  AMP PEAK  4(2P25.1) WILD-TYPE       55 86 25
D4V4, multiclass
          clus
vv         AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE
  T0+T1+T2                          27                            55
  T3                                50                            86
  T4                                14                            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  4(2P25.1) MUTATED    45  15  26   4
  AMP PEAK  4(2P25.1) WILD-TYPE 121  13  29   3
D4V5, multiclass
    clus
vv   AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE
  N0                          45                           121
  N1                          15                            13
  N2                          26                            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  4(2P25.1) MUTATED   44  3 50
  AMP PEAK  4(2P25.1) WILD-TYPE 85  4 91
D4V6, multiclass
    clus
vv   AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE
  M0                          44                            85
  M1                           3                             4
  MX                          50                            91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P25.1) MUTATED    33  65
  AMP PEAK  4(2P25.1) WILD-TYPE  44 136
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P25.1) MUTATED     33   65
  AMP PEAK  4(2P25.1) WILD-TYPE   44  136
        clus
vv       AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE
  FEMALE                          33                            44
  MALE                            65                           136
[1] 2 2
[1] FALSE
D4V8, continuous
D4V9, continuous
D4V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(2P25.1) MUTATED       7                         5    78
  AMP PEAK  4(2P25.1) WILD-TYPE    24                         8   137
D4V11, multiclass
                           clus
vv                          AMP PEAK  4(2P25.1) MUTATED
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              78
                           clus
vv                          AMP PEAK  4(2P25.1) WILD-TYPE
  ASIAN                                                24
  BLACK OR AFRICAN AMERICAN                             8
  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"
D4V12, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P25.1) MUTATED     0  88
  AMP PEAK  4(2P25.1) WILD-TYPE   5 170
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P25.1) MUTATED      0   88
  AMP PEAK  4(2P25.1) WILD-TYPE    5  170
                        clus
vv                       AMP PEAK  4(2P25.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          88
                        clus
vv                       AMP PEAK  4(2P25.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           170
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(3P25.2) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  5(3P25.2) MUTATED   84 36
  AMP PEAK  5(3P25.2) WILD-TYPE 98 52
  AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE 
                          120                           150 
  AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE 
                           36                            52 
$`AMP PEAK  5(3P25.2) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 TCGA-BL-A13I 
       22.29        11.97        98.33         4.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB 
        2.66        12.39        32.84         8.35        17.16         5.59 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42C TCGA-CF-A1HR TCGA-CU-A0YO 
        3.65         4.67         2.07        28.70         0.46         4.90 
TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 
        7.20         5.19        16.31         1.84         2.53         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 
       66.41        18.41       130.88       112.44         1.81        10.59 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU 
      123.85        87.32         7.82         8.22        50.27        20.02 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       48.00        17.98        64.18        15.68        41.06        30.67 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE 
       15.35        26.17         0.10         0.49         0.59         0.56 
TCGA-E7-A6ME TCGA-E7-A7DV TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.99         1.22         8.94         6.87        24.30        22.45 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A5C0 TCGA-FD-A62O 
       22.98        14.93        14.93         5.36         6.87         4.83 
TCGA-FD-A62P TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        6.28         6.71         4.11         2.07         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-G2-AA3B 
       61.94        35.24        17.26        20.12         0.85        52.67 
TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GD-A3OP TCGA-GD-A3OS 
       19.46        15.81         4.50        14.07         2.10        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV 
        2.20         7.36         6.41         4.73        10.65         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-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-A6MB TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
        4.67         4.27         6.35         3.45        13.48        12.23 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
       14.24         0.85         6.58        88.93        56.19        15.35 
TCGA-XF-A8HH TCGA-XF-A9SI TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAML TCGA-XF-AAMX 
        1.87        79.66         2.10        10.82         7.63         6.77 

$`AMP PEAK  5(3P25.2) WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
       84.00       103.50         6.74         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-A3PJ TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
        5.06         8.25        12.82        15.42         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-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-A3KJ TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF 
        5.46         9.34        19.00         8.91        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IT 
       15.62         7.79         2.20         3.98        10.49        21.30 
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        41.56        76.60 
TCGA-DK-A6B1 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A677 
       67.36        43.59        24.66         0.53         0.66         1.38 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B7 
        0.82        14.33         0.46        12.89        15.68         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SN 
       12.43        11.93        15.88        45.93         6.12        12.82 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43S 
        5.52        13.18        46.78        19.79         1.97        14.96 
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-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62S 
        5.69         6.84        27.45        49.68         2.66         6.38 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-G2-A2EJ 
       50.66        18.81         9.30        10.85         7.13        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 
        5.69        26.93         7.04         6.94         2.89         2.24 
TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ 
       15.91        17.75         1.12         2.66         7.73         3.12 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GV-A3JX 
        7.59        11.31         2.04        27.09         5.62         6.15 
TCGA-GV-A40E TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A4AB 
        6.41         6.74         3.06         9.01         8.22         2.50 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LT-A8JT 
        6.48        10.52         1.74         1.81         6.38        11.80 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HE TCGA-XF-A8HI TCGA-XF-A9SH 
       16.67         3.75        45.04        97.45        17.88        64.80 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       11.90        23.64        21.04        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-AAME TCGA-XF-AAMJ TCGA-XF-AAMR 
        2.24        16.27        66.64        92.98        54.90        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
        2.96         8.32        56.48        30.94        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        3.88        10.36         4.83         0.66         7.96         9.04 

  AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE 
                         0.10                          0.07 
  AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE 
                       130.88                        140.81 
  AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE 
                        7.710                        10.505 
[1] "0.1 - 130.9 (7.7)"  "0.1 - 140.8 (10.5)"
[1] "hr=" "1.1"
D5V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  5(3P25.2) MUTATED          1       1       37        35       48
  AMP PEAK  5(3P25.2) WILD-TYPE        0       1       49        58       44
D5V3, multiclass
           clus
vv          AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             1                             1
  STAGE II                           37                            49
  STAGE III                          35                            58
  STAGE IV                           48                            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  5(3P25.2) MUTATED         36 55 22
  AMP PEAK  5(3P25.2) WILD-TYPE       46 81 17
D5V4, multiclass
          clus
vv         AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE
  T0+T1+T2                          36                            46
  T3                                55                            81
  T4                                22                            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  5(3P25.2) MUTATED    64  12  34   4
  AMP PEAK  5(3P25.2) WILD-TYPE 102  16  21   3
D5V5, multiclass
    clus
vv   AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE
  N0                          64                           102
  N1                          12                            16
  N2                          34                            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  5(3P25.2) MUTATED   57  3 63
  AMP PEAK  5(3P25.2) WILD-TYPE 72  4 78
D5V6, multiclass
    clus
vv   AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE
  M0                          57                            72
  M1                           3                             4
  MX                          63                            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"
D5V7, binary
                               cls
clus                              0   1
  AMP PEAK  5(3P25.2) MUTATED    25  99
  AMP PEAK  5(3P25.2) WILD-TYPE  52 102
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(3P25.2) MUTATED     25   99
  AMP PEAK  5(3P25.2) WILD-TYPE   52  102
        clus
vv       AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE
  FEMALE                          25                            52
  MALE                            99                           102
[1] 2 2
[1] FALSE
D5V8, continuous
D5V9, continuous
D5V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(3P25.2) MUTATED      11                         3   104
  AMP PEAK  5(3P25.2) WILD-TYPE    20                        10   111
D5V11, multiclass
                           clus
vv                          AMP PEAK  5(3P25.2) MUTATED
  ASIAN                                              11
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                             104
                           clus
vv                          AMP PEAK  5(3P25.2) WILD-TYPE
  ASIAN                                                20
  BLACK OR AFRICAN AMERICAN                            10
  WHITE                                               111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V12, binary
                               cls
clus                              0   1
  AMP PEAK  5(3P25.2) MUTATED     0 116
  AMP PEAK  5(3P25.2) WILD-TYPE   5 142
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(3P25.2) MUTATED      0  116
  AMP PEAK  5(3P25.2) WILD-TYPE    5  142
                        clus
vv                       AMP PEAK  5(3P25.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                         116
                        clus
vv                       AMP PEAK  5(3P25.2) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           142
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(3Q26.33) MUTATION ANALYSIS
D6V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  6(3Q26.33) MUTATED   95 42
  AMP PEAK  6(3Q26.33) WILD-TYPE 87 46
  AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE 
                           137                            133 
  AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE 
                            42                             46 
$`AMP PEAK  6(3Q26.33) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KW TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       22.29       103.50         4.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20R 
        6.74        12.39        11.93        19.04        32.84         5.06 
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-A42E TCGA-CF-A1HR TCGA-CF-A1HS 
       12.82         2.07        28.70         9.99         0.46         0.43 
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-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
        2.53        66.41        18.41       130.88       112.44        16.14 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3IU 
        1.81        10.59         2.20         7.82        50.27        20.02 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       48.00        17.98        64.18        15.68        41.06        30.67 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE 
       43.59        15.35         0.10         0.49         0.59         0.56 
TCGA-E7-A6ME TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3N5 
       12.99         1.22        12.89        15.68         6.87        11.93 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43Y 
       45.93        24.30        22.45        14.93        14.93        12.13 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62O TCGA-FD-A62P 
        6.87         5.36         6.84         6.87         4.83         6.28 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
        9.30         4.11         2.07         2.66         2.20         4.01 
TCGA-FJ-A3ZE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A2ES 
        3.48         6.48        61.94        30.61        35.24        17.26 
TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
        7.04         0.85        52.67         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OS 
       15.91        14.07        17.75         1.12         2.66        20.98 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A767 TCGA-GU-AATO 
        7.36         6.41         7.59         2.04         4.73        10.65 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
        6.41         6.15         7.63         7.79         4.14         6.67 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE 
       19.07        11.54         6.74        38.60         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A6MB TCGA-PQ-A6FI TCGA-R3-A69X 
        8.75         3.45         4.67         4.27        12.23        14.24 
TCGA-S5-A6DX TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
        0.85        45.04         6.58        88.93        56.19        15.35 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SI TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T5 
        1.87        17.88        79.66        28.24        26.27        66.64 
TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN4 TCGA-YF-AA3M 
        7.63         2.96         6.77        27.06         9.04 

$`AMP PEAK  6(3Q26.33) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-BT-A0S7 TCGA-BT-A20O TCGA-BT-A20P 
       11.97        84.00        98.33         6.58        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A2LD TCGA-BT-A42B TCGA-BT-A42F 
       19.50        14.89        14.96         3.65        15.42        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        8.98         1.94        23.01         0.69         0.13         0.07 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A3QU TCGA-CU-A72E 
        0.10         0.07         0.10         0.10         5.19         9.34 
TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 
        2.14        19.00         8.91        17.62        15.62         7.79 
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-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 
        9.67         8.28        10.55       140.81        41.56        76.60 
TCGA-DK-A6B1 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A677 
       67.36        26.17        24.66         0.53         0.66         1.38 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 
        0.82        14.33         0.46         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         6.12        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-A6TB TCGA-FD-A6TD TCGA-FD-A6TK TCGA-FJ-A3Z7 
        6.38        50.66        18.81         6.71        10.85        15.19 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IE 
        7.13         4.08         3.25         5.69        26.93        20.12 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
        6.94        19.46         2.89         7.73         2.10         3.12 
TCGA-GD-A6C6 TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A766 TCGA-GV-A3JV TCGA-GV-A3JZ 
        2.20        11.31        27.09         5.62         4.41         5.69 
TCGA-GV-A40E TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        6.41         1.51         3.06         2.50         6.48        10.52 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
        1.74         1.81         6.38         6.35         3.45        11.80 
TCGA-MV-A51V TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-XF-A8HE TCGA-XF-A9SH TCGA-XF-A9SW 
       13.48        16.67         3.75        97.45        64.80        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 
       23.64        21.04        18.90         2.24        16.27         2.10 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAN0 
       92.98        10.82        54.90        91.73         8.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       30.94        75.39         3.88        10.36         4.83         0.66 
TCGA-YF-AA3L 
        7.96 

  AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE 
                        130.88                         140.81 
  AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE 
                          8.75                          10.36 
[1] "0.1 - 130.9 (8.8)"  "0.1 - 140.8 (10.4)"
[1] "hr=" "1.1"
D6V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  6(3Q26.33) MUTATED          1       1       42        45       49
  AMP PEAK  6(3Q26.33) WILD-TYPE        0       1       44        48       43
D6V3, multiclass
           clus
vv          AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE
  STAGE 0A                             1                              0
  STAGE I                              1                              1
  STAGE II                            42                             44
  STAGE III                           45                             48
  STAGE IV                            49                             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
  AMP PEAK  6(3Q26.33) MUTATED         40 70 20
  AMP PEAK  6(3Q26.33) WILD-TYPE       42 66 19
D6V4, multiclass
          clus
vv         AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE
  T0+T1+T2                           40                             42
  T3                                 70                             66
  T4                                 20                             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
  AMP PEAK  6(3Q26.33) MUTATED   79 11 36  4
  AMP PEAK  6(3Q26.33) WILD-TYPE 87 17 19  3
D6V5, multiclass
    clus
vv   AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE
  N0                           79                             87
  N1                           11                             17
  N2                           36                             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
  AMP PEAK  6(3Q26.33) MUTATED   65  4 71
  AMP PEAK  6(3Q26.33) WILD-TYPE 64  3 70
D6V6, multiclass
    clus
vv   AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE
  M0                           65                             64
  M1                            4                              3
  MX                           71                             70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                                cls
clus                               0   1
  AMP PEAK  6(3Q26.33) MUTATED    41 100
  AMP PEAK  6(3Q26.33) WILD-TYPE  36 101
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.33) MUTATED     41  100
  AMP PEAK  6(3Q26.33) WILD-TYPE   36  101
        clus
vv       AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE
  FEMALE                           41                             36
  MALE                            100                            101
[1] 2 2
[1] FALSE
D6V8, continuous
D6V9, continuous
D6V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(3Q26.33) MUTATED      12                         8   110
  AMP PEAK  6(3Q26.33) WILD-TYPE    19                         5   105
D6V11, multiclass
                           clus
vv                          AMP PEAK  6(3Q26.33) MUTATED
  ASIAN                                               12
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                              110
                           clus
vv                          AMP PEAK  6(3Q26.33) WILD-TYPE
  ASIAN                                                 19
  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"
D6V12, binary
                                cls
clus                               0   1
  AMP PEAK  6(3Q26.33) MUTATED     2 128
  AMP PEAK  6(3Q26.33) WILD-TYPE   3 130
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.33) MUTATED      2  128
  AMP PEAK  6(3Q26.33) WILD-TYPE    3  130
                        clus
vv                       AMP PEAK  6(3Q26.33) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          128
                        clus
vv                       AMP PEAK  6(3Q26.33) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            130
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(4P16.3) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  7(4P16.3) MUTATED    41  11
  AMP PEAK  7(4P16.3) WILD-TYPE 141  77
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                           52                           218 
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                           11                            77 
$`AMP PEAK  7(4P16.3) MUTATED`
TCGA-2F-A9KP TCGA-2F-A9KT TCGA-BL-A0C8 TCGA-BT-A20P TCGA-BT-A20T TCGA-BT-A3PJ 
       11.97        98.33        40.08        17.88        14.89        12.82 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47V TCGA-CF-A47X TCGA-CU-A3KJ 
        1.94        23.01         0.69         0.10         0.10         5.46 
TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AC TCGA-DK-A2I2 TCGA-DK-A2I6 
        1.84         2.14        66.41       130.88         7.79        87.32 
TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-E5-A4U1 TCGA-E7-A541 
        7.82        50.27        64.18        67.36        26.17         0.59 
TCGA-E7-A5KE TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A5C1 
        0.56        45.93        22.45         5.36        27.45        49.68 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3B 
        9.30         4.11        35.24        17.26         0.85        52.67 
TCGA-GC-A3BM TCGA-GC-A3RC TCGA-GD-A76B TCGA-GU-A42R TCGA-GV-A6ZA TCGA-H4-A2HO 
        2.89        15.91         7.36        11.31        11.54         1.51 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A4AC TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-MV-A51V 
        9.01         8.75         6.48         1.81         4.27        13.48 
TCGA-XF-A9SZ TCGA-XF-A9T3 TCGA-YF-AA3L TCGA-YF-AA3M 
       28.24         2.24         7.96         9.04 

$`AMP PEAK  7(4P16.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-BL-A13I TCGA-BL-A13J 
       22.29        84.00       103.50         4.83         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        11.93        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       12.16        19.50         5.06        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK 
        8.25        17.16         5.59         3.65         4.67         2.07 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-CF-A1HR 
       15.42        28.70         9.99        28.41         8.98         0.46 
TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN 
        0.43         0.13         0.07         0.07         0.10        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 
        4.90         7.20         5.19        16.31         9.34         2.53 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       18.41        19.00         8.91       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-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
        8.22        10.49        21.30        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        41.56        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 
       15.68        41.06        30.67        43.59        15.35        24.66 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        0.10         0.49         0.53         0.66         1.38         0.82 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 
       12.99        14.33         1.22         0.46        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-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       24.30         6.12        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-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
        5.69         6.84         6.87         2.66         4.83         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG 
        6.38        50.66        18.81         6.71         2.07         2.66 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        2.20         4.01        10.85        15.19         7.13         3.48 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        4.08         3.25         6.48        61.94        30.61         5.69 
TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 
       26.93         7.04        20.12         6.94        19.46         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-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
        7.59         2.04        27.09         5.62         4.73        10.65 
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-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE 
        4.14         6.67         6.41        19.07         6.74        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R 
        3.06         8.22         3.45         4.67         2.50        10.52 
TCGA-K4-A5RJ TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI 
        1.74         6.38         6.35         3.45        11.80        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC 
       16.67        14.24         0.85         3.75        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI 
       88.93        97.45        56.19        15.35         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 
       64.80        79.66        11.90        23.64        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF 
       18.90        16.27        66.64         2.10        92.98        10.82 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       54.90         7.63        91.73         2.96         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
       56.48        30.94        27.06        75.39         3.88        10.36 
TCGA-YC-A8S6 TCGA-YC-A9TC 
        4.83         0.66 

  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                         0.10                          0.07 
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                       130.88                        140.81 
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                       10.305                         8.960 
[1] "0.1 - 130.9 (10.3)" "0.1 - 140.8 (9.0)" 
[1] "hr=" "1.9"
D7V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  7(4P16.3) MUTATED          1       1       25        16       12
  AMP PEAK  7(4P16.3) WILD-TYPE        0       1       61        77       80
D7V3, multiclass
           clus
vv          AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             1                             1
  STAGE II                           25                            61
  STAGE III                          16                            77
  STAGE IV                           12                            80
[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(4P16.3) MUTATED         26  24   4
  AMP PEAK  7(4P16.3) WILD-TYPE       56 112  35
D7V4, multiclass
          clus
vv         AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE
  T0+T1+T2                          26                            56
  T3                                24                           112
  T4                                 4                            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"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK  7(4P16.3) MUTATED    39   6   5   2
  AMP PEAK  7(4P16.3) WILD-TYPE 127  22  50   5
D7V5, multiclass
    clus
vv   AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE
  N0                          39                           127
  N1                           6                            22
  N2                           5                            50
  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  7(4P16.3) MUTATED    34   1  20
  AMP PEAK  7(4P16.3) WILD-TYPE  95   6 121
D7V6, multiclass
    clus
vv   AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE
  M0                          34                            95
  M1                           1                             6
  MX                          20                           121
[1] 3 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(4P16.3) MUTATED    14  42
  AMP PEAK  7(4P16.3) WILD-TYPE  63 159
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4P16.3) MUTATED     14   42
  AMP PEAK  7(4P16.3) WILD-TYPE   63  159
        clus
vv       AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE
  FEMALE                          14                            63
  MALE                            42                           159
[1] 2 2
[1] FALSE
D7V8, continuous
D7V9, continuous
D7V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(4P16.3) MUTATED      10                         0    38
  AMP PEAK  7(4P16.3) WILD-TYPE    21                        13   177
D7V11, multiclass
                           clus
vv                          AMP PEAK  7(4P16.3) MUTATED
  ASIAN                                              10
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              38
                           clus
vv                          AMP PEAK  7(4P16.3) WILD-TYPE
  ASIAN                                                21
  BLACK OR AFRICAN AMERICAN                            13
  WHITE                                               177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V12, binary
                               cls
clus                              0   1
  AMP PEAK  7(4P16.3) MUTATED     2  48
  AMP PEAK  7(4P16.3) WILD-TYPE   3 210
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4P16.3) MUTATED      2   48
  AMP PEAK  7(4P16.3) WILD-TYPE    3  210
                        clus
vv                       AMP PEAK  7(4P16.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          48
                        clus
vv                       AMP PEAK  7(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           210
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(4Q13.3) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  8(4Q13.3) MUTATED    30  12
  AMP PEAK  8(4Q13.3) WILD-TYPE 152  76
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                           42                           228 
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                           12                            76 
$`AMP PEAK  8(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-G2-AA3B 
        6.38         9.30         4.11        30.61         0.85        52.67 
TCGA-GC-A3WC TCGA-GD-A2C5 TCGA-GD-A76B TCGA-GU-A42P TCGA-GV-A3JW TCGA-GV-A6ZA 
       17.75         7.73         7.36         6.41         6.41        11.54 
TCGA-HQ-A5ND TCGA-K4-A3WV TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-XF-A9T4 TCGA-YF-AA3L 
        9.01         4.67         3.45        13.48        16.27         7.96 

$`AMP PEAK  8(4Q13.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
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        66.41 
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-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        41.56        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 
       15.68        41.06        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-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 
        0.82        12.99        14.33         1.22         0.46        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-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       15.88        24.30        22.45         6.12        12.82         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       13.18        46.78         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-A5BX TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
        5.69         6.84        49.68         2.66         4.83         6.28 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
       50.66        18.81         6.71         2.07         2.66         2.20 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        4.01        10.85        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-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM 
       17.26         7.04        20.12         6.94        19.46         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-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q 
        2.66         2.10         3.12        20.98         2.20         7.59 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
       11.31         2.04        27.09         5.62         4.73        10.65 
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-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        6.67         6.41        19.07         1.51         6.74        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
        3.06         8.22         8.75         3.45         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-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       11.80        12.23        16.67        14.24         0.85         3.75 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       45.04         6.58        88.93        97.45        56.19        15.35 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX 
        1.87        17.88        64.80        79.66        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 
       21.04        28.24        26.27        18.90         2.24        66.64 
TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR 
        2.10        92.98        10.82        54.90         7.63        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 
        2.96         8.32         6.77        56.48        30.94        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3M 
       75.39         3.88        10.36         4.83         0.66         9.04 

  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                         0.10                          0.07 
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                        87.32                        140.81 
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                        9.645                         9.010 
[1] "0.1 - 87.3 (9.6)"  "0.1 - 140.8 (9.0)"
[1] "hr=" "1.3"
D8V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  8(4Q13.3) MUTATED          1       0       17        11       13
  AMP PEAK  8(4Q13.3) WILD-TYPE        0       2       69        82       79
D8V3, multiclass
           clus
vv          AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             0                             2
  STAGE II                           17                            69
  STAGE III                          11                            82
  STAGE IV                           13                            79
[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(4Q13.3) MUTATED         16  19   3
  AMP PEAK  8(4Q13.3) WILD-TYPE       66 117  36
D8V4, multiclass
          clus
vv         AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE
  T0+T1+T2                          16                            66
  T3                                19                           117
  T4                                 3                            36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK  8(4Q13.3) MUTATED    26   6   6   1
  AMP PEAK  8(4Q13.3) WILD-TYPE 140  22  49   6
D8V5, multiclass
    clus
vv   AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE
  N0                          26                           140
  N1                           6                            22
  N2                           6                            49
  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(4Q13.3) MUTATED    20   0  21
  AMP PEAK  8(4Q13.3) WILD-TYPE 109   7 120
D8V6, multiclass
    clus
vv   AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE
  M0                          20                           109
  M1                           0                             7
  MX                          21                           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"
D8V7, binary
                               cls
clus                              0   1
  AMP PEAK  8(4Q13.3) MUTATED    17  25
  AMP PEAK  8(4Q13.3) WILD-TYPE  60 176
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(4Q13.3) MUTATED     17   25
  AMP PEAK  8(4Q13.3) WILD-TYPE   60  176
        clus
vv       AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE
  FEMALE                          17                            60
  MALE                            25                           176
[1] 2 2
[1] FALSE
D8V8, continuous
D8V9, continuous
D8V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(4Q13.3) MUTATED       3                         1    31
  AMP PEAK  8(4Q13.3) WILD-TYPE    28                        12   184
D8V11, multiclass
                           clus
vv                          AMP PEAK  8(4Q13.3) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              31
                           clus
vv                          AMP PEAK  8(4Q13.3) WILD-TYPE
  ASIAN                                                28
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                               184
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, binary
                               cls
clus                              0   1
  AMP PEAK  8(4Q13.3) MUTATED     1  37
  AMP PEAK  8(4Q13.3) WILD-TYPE   4 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(4Q13.3) MUTATED      1   37
  AMP PEAK  8(4Q13.3) WILD-TYPE    4  221
                        clus
vv                       AMP PEAK  8(4Q13.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          37
                        clus
vv                       AMP PEAK  8(4Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           221
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(5P15.33) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  9(5P15.33) MUTATED   90 41
  AMP PEAK  9(5P15.33) WILD-TYPE 92 47
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                           131                            139 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                            41                             47 
$`AMP PEAK  9(5P15.33) MUTATED`
TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A20P 
       98.33         4.83        40.08         6.74        12.39        17.88 
TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A3PK 
       14.89         5.06         8.35        17.16        12.82         2.07 
TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A47S 
       28.70         9.99         8.98        23.01         0.43         0.13 
TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1AD 
       12.92         7.20         5.19         1.84         2.53       112.44 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV 
      123.85        87.32         7.82         8.22        20.02         9.67 
TCGA-DK-A3WX TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4TZ 
       10.55        64.18        67.36        41.06        30.67        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A6ME TCGA-E7-A7DV 
       26.17        24.66         0.49         0.59        12.99         1.22 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ 
       12.89        15.68         8.94        11.93        45.93        24.30 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43Y TCGA-FD-A5BR 
       12.82         5.52        13.18        19.79        12.13        13.38 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        6.87         5.36         6.84        49.68         2.66         4.83 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28         6.38        18.81         9.30         6.71         4.11 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P 
        2.66         2.20        10.85         4.08         3.25         6.48 
TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       61.94        35.24         7.04        20.12         0.85        52.67 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       19.46         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3YS TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A762 
        1.12         2.10        20.98         7.36         6.41         2.04 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ 
        5.62         4.73        10.65         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-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A4AB TCGA-K4-A4AC 
       38.60         3.06         9.01         8.22         2.50         6.48 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X 
        1.81         4.27         6.35        13.48        16.67        14.24 
TCGA-S5-A6DX TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A9SI TCGA-XF-A9SX TCGA-XF-A9SZ 
        0.85         6.58        56.19        79.66        23.64        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF 
       26.27         2.24        66.64         2.10        92.98        10.82 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMX TCGA-YF-AA3M 
       54.90         7.63         2.96         6.77         9.04 

$`AMP PEAK  9(5P15.33) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-BL-A13I TCGA-BL-A13J 
       22.29        11.97        84.00       103.50         7.33         2.66 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20Q 
        6.58        11.93        19.04        32.84        12.16        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        5.06        14.96         8.25         5.59         3.65         4.67 
TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47T 
       15.42        28.41         1.94         0.46         0.69         0.07 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A3KJ 
        0.10         0.07         0.10         0.10         4.90         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        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
        8.91       130.88        16.14        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS 
       10.59         7.79         2.20         3.98        10.49        50.27 
TCGA-DK-A3IT TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW 
       21.30         8.28       140.81        48.00        17.98        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-E5-A2PC TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KE 
       76.60        15.68        43.59         0.10         0.53         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B6 
        0.66         1.38         0.82        14.33         0.46         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         6.12        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-A6TF TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-G2-A2EJ 
        2.07         4.01        15.19         7.13         3.48        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3WC 
        5.69        26.93        17.26         6.94         2.89        17.75 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        2.66         7.73         3.12         2.20         7.59        11.31 
TCGA-GU-A763 TCGA-GV-A3JW TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-K4-A3WS 
       27.09         6.41         6.67        11.54         1.51         8.75 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A83P TCGA-LT-A5Z6 
        3.45         4.67        10.52         1.74         6.38         3.45 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE 
       11.80        12.23         3.75        45.04        88.93        97.45 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SW TCGA-XF-A9SY 
       15.35         1.87        17.88        64.80        11.90        21.04 
TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 
       18.90        16.27        91.73         8.32        56.48        30.94 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39         3.88        10.36         4.83         0.66 
TCGA-YF-AA3L 
        7.96 

  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 
                          8.98                          10.49 
[1] "0.1 - 123.8 (9.0)"  "0.1 - 140.8 (10.5)"
[1] "hr=" "1.1"
D9V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  9(5P15.33) MUTATED          0       1       41        49       42
  AMP PEAK  9(5P15.33) WILD-TYPE        1       1       45        44       50
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                            41                             45
  STAGE III                           49                             44
  STAGE IV                            42                             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
  AMP PEAK  9(5P15.33) MUTATED         38 65 20
  AMP PEAK  9(5P15.33) WILD-TYPE       44 71 19
D9V4, multiclass
          clus
vv         AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  T0+T1+T2                           38                             44
  T3                                 65                             71
  T4                                 20                             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
  AMP PEAK  9(5P15.33) MUTATED   78 13 27  3
  AMP PEAK  9(5P15.33) WILD-TYPE 88 15 28  4
D9V5, multiclass
    clus
vv   AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  N0                           78                             88
  N1                           13                             15
  N2                           27                             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  9(5P15.33) MUTATED   56  2 76
  AMP PEAK  9(5P15.33) WILD-TYPE 73  5 65
D9V6, multiclass
    clus
vv   AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  M0                           56                             73
  M1                            2                              5
  MX                           76                             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"
D9V7, binary
                                cls
clus                               0   1
  AMP PEAK  9(5P15.33) MUTATED    35 100
  AMP PEAK  9(5P15.33) WILD-TYPE  42 101
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED     35  100
  AMP PEAK  9(5P15.33) WILD-TYPE   42  101
        clus
vv       AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  FEMALE                           35                             42
  MALE                            100                            101
[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      14                         9   103
  AMP PEAK  9(5P15.33) WILD-TYPE    17                         4   112
D9V11, multiclass
                           clus
vv                          AMP PEAK  9(5P15.33) MUTATED
  ASIAN                                               14
  BLACK OR AFRICAN AMERICAN                            9
  WHITE                                              103
                           clus
vv                          AMP PEAK  9(5P15.33) WILD-TYPE
  ASIAN                                                 17
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V12, binary
                                cls
clus                               0   1
  AMP PEAK  9(5P15.33) MUTATED     2 126
  AMP PEAK  9(5P15.33) WILD-TYPE   3 132
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED      2  126
  AMP PEAK  9(5P15.33) WILD-TYPE    3  132
                        clus
vv                       AMP PEAK  9(5P15.33) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          126
                        clus
vv                       AMP PEAK  9(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            132
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(6P22.3) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(6P22.3) MUTATED    74  27
  AMP PEAK 10(6P22.3) WILD-TYPE 108  61
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                          101                           169 
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                           27                            61 
$`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        66.41        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-A3WX TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 
        7.82        50.27        10.55        64.18        67.36        15.68 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6ME 
       43.59        15.35         0.49         0.59         0.56        12.99 
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-A6TA TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FJ-A3Z7 
       50.66         9.30         4.11         2.07         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-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       52.67        19.46         2.89         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GU-A42P TCGA-GU-A42R 
       15.91        14.07         1.12         7.73         6.41        11.31 
TCGA-GU-A762 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QH 
        2.04         4.73        10.65         6.41         5.69         7.79 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WV 
        6.41        19.07        11.54        38.60         8.22         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-A8HC TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A9T0 
       12.23        16.67         6.58        88.93        56.19        26.27 
TCGA-XF-A9T3 TCGA-XF-AAMF TCGA-XF-AAML TCGA-YF-AA3L TCGA-YF-AA3M 
        2.24        10.82         7.63         7.96         9.04 

$`AMP PEAK 10(6P22.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
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-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
        8.22        10.49        21.30        20.02         9.67         8.28 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 
      140.81        48.00        17.98        41.56        76.60        41.06 
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-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B4 TCGA-FD-A3B5 
        1.38         0.82        14.33         0.46        15.68         8.94 
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         6.12        12.82 
TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
        5.52        46.78         1.97        14.96        14.93         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX 
       12.13        13.38        37.15        11.01         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
        6.84        27.45         6.87         2.66         4.83         6.28 
TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
        6.38        18.81         6.71         2.20         4.01        10.85 
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-G2-AA3C TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OP 
        7.04        20.12         6.94        17.75         2.66         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A763 
        3.12        20.98         2.20         7.36         7.59        27.09 
TCGA-GU-A766 TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK 
        5.62         4.41         6.15         7.63         4.14         6.67 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
        1.51         6.74         3.06         9.01         8.75         3.45 
TCGA-K4-A4AB TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-LT-A8JT TCGA-MV-A51V TCGA-R3-A69X 
        2.50         1.74         1.81        11.80        13.48        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HH 
        0.85         3.75        45.04        97.45        15.35         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
       17.88        64.80        79.66        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME 
       28.24        18.90        16.27        66.64         2.10        92.98 
TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       54.90        91.73         2.96         8.32         6.77        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       30.94        27.06        75.39         3.88        10.36         4.83 
TCGA-YC-A9TC 
        0.66 

  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 
                         8.35                          9.99 
[1] "0.1 - 130.9 (8.3)"  "0.1 - 140.8 (10.0)"
[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       37        24       38
  AMP PEAK 10(6P22.3) WILD-TYPE        0       2       49        69       54
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                           37                            49
  STAGE III                          24                            69
  STAGE IV                           38                            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
  AMP PEAK 10(6P22.3) MUTATED         37 42 14
  AMP PEAK 10(6P22.3) WILD-TYPE       45 94 25
D10V4, multiclass
          clus
vv         AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE
  T0+T1+T2                          37                            45
  T3                                42                            94
  T4                                14                            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 10(6P22.3) MUTATED    53  13  22   5
  AMP PEAK 10(6P22.3) WILD-TYPE 113  15  33   2
D10V5, multiclass
    clus
vv   AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE
  N0                          53                           113
  N1                          13                            15
  N2                          22                            33
  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   45  3 53
  AMP PEAK 10(6P22.3) WILD-TYPE 84  4 88
D10V6, multiclass
    clus
vv   AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE
  M0                          45                            84
  M1                           3                             4
  MX                          53                            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"
D10V7, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P22.3) MUTATED    25  77
  AMP PEAK 10(6P22.3) WILD-TYPE  52 124
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P22.3) MUTATED     25   77
  AMP PEAK 10(6P22.3) WILD-TYPE   52  124
        clus
vv       AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE
  FEMALE                          25                            52
  MALE                            77                           124
[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      10                         4    80
  AMP PEAK 10(6P22.3) WILD-TYPE    21                         9   135
D10V11, multiclass
                           clus
vv                          AMP PEAK 10(6P22.3) MUTATED
  ASIAN                                              10
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              80
                           clus
vv                          AMP PEAK 10(6P22.3) WILD-TYPE
  ASIAN                                                21
  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"
D10V12, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P22.3) MUTATED     2  93
  AMP PEAK 10(6P22.3) WILD-TYPE   3 165
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P22.3) MUTATED      2   93
  AMP PEAK 10(6P22.3) WILD-TYPE    3  165
                        clus
vv                       AMP PEAK 10(6P22.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          93
                        clus
vv                       AMP PEAK 10(6P22.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           165
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(6Q21) MUTATION ANALYSIS
D11V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 11(6Q21) MUTATED    17   4
  AMP PEAK 11(6Q21) WILD-TYPE 165  84
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                         21                         249 
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                          4                          84 
$`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-E7-A6ME TCGA-FD-A43P 
       18.41       130.88        10.55        41.06        12.99        14.93 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3YS 
       15.19         3.48         4.08         2.89        15.81         1.12 
TCGA-GD-A2C5 TCGA-GU-AATO TCGA-XF-A9T5 
        7.73        10.65        66.64 

$`AMP PEAK 11(6Q21) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
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        66.41        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        41.56        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-A6MF TCGA-E7-A7DV TCGA-E7-A7XN 
        0.66         1.38         0.82        14.33         1.22         0.46 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       12.89        15.68         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         6.12 
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-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-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-A62N TCGA-FD-A62O TCGA-FD-A62P 
       27.45         6.87        49.68         2.66         4.83         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.38        50.66        18.81         9.30         6.71         4.11 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 
        2.07         2.66         2.20         4.01        10.85         7.13 
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-G2-AA3B 
       35.24        17.26         7.04        20.12         0.85        52.67 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
        6.94        19.46         2.24         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       17.75         2.66         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        7.36         6.41         7.59        11.31         2.04        27.09 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
        5.62         4.73         4.41         6.41         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-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       11.54         1.51         6.74        38.60         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        8.22         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-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
        3.45        11.80        13.48        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
        0.85         3.75        45.04         6.58        88.93        97.45 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI 
       56.19        15.35         1.87        17.88        64.80        79.66 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       11.90        23.64        21.04        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ 
        2.24        16.27         2.10        92.98        10.82        54.90 
TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
        7.63        91.73         2.96         8.32         6.77        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       30.94        27.06        75.39         3.88        10.36         4.83 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        0.66         7.96         9.04 

  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 
                      10.65                        9.01 
[1] "0.1 - 130.9 (10.7)" "0.1 - 140.8 (9.0)" 
[1] "hr=" "1.8"
D11V2, continuous
                             vv
clus                          STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 11(6Q21) MUTATED          0       0        6         5       10
  AMP PEAK 11(6Q21) WILD-TYPE        1       2       80        88       82
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                          6                          80
  STAGE III                         5                          88
  STAGE IV                         10                          82
[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          7   8   4
  AMP PEAK 11(6Q21) WILD-TYPE       75 128  35
D11V4, multiclass
          clus
vv         AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  T0+T1+T2                         7                          75
  T3                               8                         128
  T4                               4                          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"
                             vv
clus                           N0  N1  N2  N3
  AMP PEAK 11(6Q21) MUTATED    10   2   7   1
  AMP PEAK 11(6Q21) WILD-TYPE 156  26  48   6
D11V5, multiclass
    clus
vv   AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  N0                        10                         156
  N1                         2                          26
  N2                         7                          48
  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    12   1   8
  AMP PEAK 11(6Q21) WILD-TYPE 117   6 133
D11V6, multiclass
    clus
vv   AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  M0                        12                         117
  M1                         1                           6
  MX                         8                         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"
D11V7, binary
                             cls
clus                            0   1
  AMP PEAK 11(6Q21) MUTATED     4  17
  AMP PEAK 11(6Q21) WILD-TYPE  73 184
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(6Q21) MUTATED      4   17
  AMP PEAK 11(6Q21) WILD-TYPE   73  184
        clus
vv       AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  FEMALE                         4                          73
  MALE                          17                         184
[1] 2 2
[1] FALSE
D11V8, continuous
D11V9, continuous
D11V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(6Q21) MUTATED       2                         1    18
  AMP PEAK 11(6Q21) WILD-TYPE    29                        12   197
D11V11, multiclass
                           clus
vv                          AMP PEAK 11(6Q21) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         1
  WHITE                                            18
                           clus
vv                          AMP PEAK 11(6Q21) WILD-TYPE
  ASIAN                                              29
  BLACK OR AFRICAN AMERICAN                          12
  WHITE                                             197
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V12, binary
                             cls
clus                            0   1
  AMP PEAK 11(6Q21) MUTATED     0  20
  AMP PEAK 11(6Q21) WILD-TYPE   5 238
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(6Q21) MUTATED      0   20
  AMP PEAK 11(6Q21) WILD-TYPE    5  238
                        clus
vv                       AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  HISPANIC OR LATINO                             0                           5
  NOT HISPANIC OR LATINO                        20                         238
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(6Q23.3) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 12(6Q23.3) MUTATED    21   8
  AMP PEAK 12(6Q23.3) WILD-TYPE 161  80
  AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE 
                           29                           241 
  AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE 
                            8                            80 
$`AMP PEAK 12(6Q23.3) MUTATED`
TCGA-BT-A0S7 TCGA-BT-A20T TCGA-BT-A2LA TCGA-CF-A1HS TCGA-CF-A47V TCGA-CU-A0YR 
        6.58        14.89        17.16         0.43         0.10         7.20 
TCGA-CU-A3KJ TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A3IM TCGA-DK-A3WX TCGA-DK-A6B6 
        5.46        18.41       130.88         7.82        10.55        30.67 
TCGA-E7-A541 TCGA-FD-A3SS TCGA-FD-A6TD TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-G2-AA3F 
        0.59         1.97         6.71         3.48         4.08        19.46 
TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GU-AATO TCGA-GV-A3JV 
        2.89        15.81         4.50         1.12        10.65         4.41 
TCGA-GV-A40G TCGA-HQ-A2OE TCGA-XF-A9SZ TCGA-XF-A9T5 TCGA-XF-AAN8 
       19.07        38.60        28.24        66.64         3.88 

$`AMP PEAK 12(6Q23.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
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-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-A27C 
       28.41         8.98         1.94        23.01         0.46         0.69 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YN 
        0.13         0.07         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-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE 
        2.14        66.41        19.00         8.91       112.44        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-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-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 
       21.30        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        41.56        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       41.06        43.59        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-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 
       12.99        14.33         1.22         0.46        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         6.12        12.82         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       13.18        46.78        19.79        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-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-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
       18.81         9.30         4.11         2.07         2.66         2.20 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FT-A3EE TCGA-FT-A61P 
        4.01        10.85        15.19         7.13         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-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 
        7.04        20.12         0.85        52.67         6.94         2.24 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP 
       15.91        14.07        17.75         2.66         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36         6.41         7.59 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JW 
       11.31         2.04        27.09         5.62         4.73         6.41 
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-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND 
        6.41        11.54         1.51         6.74         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        8.22         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-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
        3.45        11.80        13.48        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
        0.85         3.75        45.04         6.58        88.93        97.45 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI 
       56.19        15.35         1.87        17.88        64.80        79.66 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       11.90        23.64        21.04        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML 
       16.27         2.10        92.98        10.82        54.90         7.63 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 
       91.73         2.96         8.32         6.77        56.48        30.94 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       27.06        75.39        10.36         4.83         0.66         7.96 
TCGA-YF-AA3M 
        9.04 

  AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE 
                         0.10                          0.07 
  AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE 
                       130.88                        140.81 
  AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE 
                         7.20                          9.34 
[1] "0.1 - 130.9 (7.2)" "0.1 - 140.8 (9.3)"
[1] "hr=" "1.1"
D12V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 12(6Q23.3) MUTATED          0       0        6        10       11
  AMP PEAK 12(6Q23.3) WILD-TYPE        1       2       80        83       81
D12V3, multiclass
           clus
vv          AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE
  STAGE 0A                            0                             1
  STAGE I                             0                             2
  STAGE II                            6                            80
  STAGE III                          10                            83
  STAGE IV                           11                            81
[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(6Q23.3) MUTATED          7  16   3
  AMP PEAK 12(6Q23.3) WILD-TYPE       75 120  36
D12V4, multiclass
          clus
vv         AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE
  T0+T1+T2                           7                            75
  T3                                16                           120
  T4                                 3                            36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK 12(6Q23.3) MUTATED    16   5   5   2
  AMP PEAK 12(6Q23.3) WILD-TYPE 150  23  50   5
D12V5, multiclass
    clus
vv   AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE
  N0                          16                           150
  N1                           5                            23
  N2                           5                            50
  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 12(6Q23.3) MUTATED    15   1  13
  AMP PEAK 12(6Q23.3) WILD-TYPE 114   6 128
D12V6, multiclass
    clus
vv   AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE
  M0                          15                           114
  M1                           1                             6
  MX                          13                           128
[1] 3 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(6Q23.3) MUTATED     5  24
  AMP PEAK 12(6Q23.3) WILD-TYPE  72 177
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(6Q23.3) MUTATED      5   24
  AMP PEAK 12(6Q23.3) WILD-TYPE   72  177
        clus
vv       AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE
  FEMALE                           5                            72
  MALE                            24                           177
[1] 2 2
[1] FALSE
D12V8, continuous
D12V9, continuous
D12V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(6Q23.3) MUTATED       2                         0    26
  AMP PEAK 12(6Q23.3) WILD-TYPE    29                        13   189
D12V11, multiclass
                           clus
vv                          AMP PEAK 12(6Q23.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              26
                           clus
vv                          AMP PEAK 12(6Q23.3) WILD-TYPE
  ASIAN                                                29
  BLACK OR AFRICAN AMERICAN                            13
  WHITE                                               189
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V12, binary
                               cls
clus                              0   1
  AMP PEAK 12(6Q23.3) MUTATED     0  27
  AMP PEAK 12(6Q23.3) WILD-TYPE   5 231
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(6Q23.3) MUTATED      0   27
  AMP PEAK 12(6Q23.3) WILD-TYPE    5  231
                        clus
vv                       AMP PEAK 12(6Q23.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          27
                        clus
vv                       AMP PEAK 12(6Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           231
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(7P21.1) MUTATION ANALYSIS
D13V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 13(7P21.1) MUTATED   89 44
  AMP PEAK 13(7P21.1) WILD-TYPE 93 44
  AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE 
                          133                           137 
  AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE 
                           44                            44 
$`AMP PEAK 13(7P21.1) MUTATED`
TCGA-2F-A9KP TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A5ZZ 
       11.97        98.33         4.83        40.08         2.66        12.39 
TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
        6.58        32.84        12.16         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       17.16         5.59         3.65        12.82         2.07        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CU-A0YN TCGA-CU-A0YO 
        9.99        28.41        23.01         0.46        12.92         4.90 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 
        5.46         5.19         9.34         2.53         2.14        18.41 
TCGA-DK-A1AC TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
      130.88        10.59         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV 
        3.98         7.82         8.22        50.27        20.02         9.67 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 
       48.00        17.98        64.18        67.36        15.68        30.67 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A6ME TCGA-E7-A7DV 
       43.59        15.35         0.49         0.59        12.99         1.22 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 
       12.89        15.68         8.94         6.87         4.01        11.93 
TCGA-FD-A3SJ TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       24.30        46.78        19.79         1.97        22.98        14.93 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BZ 
       14.93         3.62        13.38        11.01         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-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZE 
        4.11         2.07         2.66         4.01        15.19         3.48 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B 
        4.08         3.25         6.48        35.24         0.85        52.67 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       19.46         2.89         2.24         4.50        15.91        14.07 
TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q 
        1.12         7.73        20.98         2.20         6.41         7.59 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A3QK 
        5.62         4.73         6.41         5.69         4.14         6.67 
TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A6FZ 
        6.41        11.54         6.74         9.01         8.22         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-MV-A51V TCGA-S5-A6DX TCGA-XF-A8HD 
        4.27         6.38         6.35        13.48         0.85        88.93 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SI TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T3 
       56.19        15.35        79.66        21.04        26.27         2.24 
TCGA-XF-A9T5 TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN5 
       66.64         7.63         2.96         6.77        56.48        75.39 
TCGA-YF-AA3M 
        9.04 

$`AMP PEAK 13(7P21.1) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0YX 
       22.29        84.00       103.50         7.33         6.74        11.93 
TCGA-BT-A20J TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       19.04        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A27C 
        4.67        15.42         8.98         1.94         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-A0YR TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB 
        7.20        16.31         1.84        66.41        19.00         8.91 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A3IQ 
      112.44        16.14        17.62        15.62         1.81        10.49 
TCGA-DK-A3IT TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 
       21.30         8.28        10.55       140.81        41.56        76.60 
TCGA-DK-A6B5 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KE 
       41.06        26.17        24.66         0.10         0.53         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B8 
        0.66         1.38         0.82        14.33         0.46        12.43 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       15.88        45.93        22.45         6.12        12.82         5.52 
TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BX 
       13.18        14.96        12.13        37.15         6.87         5.69 
TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TH 
        6.84         2.66        50.66        18.81         9.30         2.20 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
       10.85         7.13        61.94        30.61         5.69        26.93 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3OO TCGA-GC-A3WC 
       17.26         7.04        20.12         6.94        15.81        17.75 
TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A76B TCGA-GU-A42R TCGA-GU-A762 
        2.66         2.10         3.12         7.36        11.31         2.04 
TCGA-GU-A763 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH 
       27.09        10.65         4.41         6.15         7.63         7.79 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A3WU 
       19.07         1.51        38.60         3.06         8.75         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-LT-A5Z6 
        4.67         2.50         6.48        10.52         1.74         3.45 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 TCGA-XF-A8HB 
       11.80        12.23        16.67        14.24         3.75        45.04 
TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SW 
        6.58        97.45         1.87        17.88        64.80        11.90 
TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME 
       23.64        28.24        18.90        16.27         2.10        92.98 
TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAN1 TCGA-XF-AAN4 
       10.82        54.90        91.73         8.32        30.94        27.06 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
        3.88        10.36         4.83         0.66         7.96 

  AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE 
                         0.46                          0.07 
  AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE 
                       130.88                        140.81 
  AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE 
                         8.25                         10.55 
[1] "0.5 - 130.9 (8.2)"  "0.1 - 140.8 (10.6)"
[1] "hr=" "1.1"
D13V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 13(7P21.1) MUTATED          1       1       35        45       53
  AMP PEAK 13(7P21.1) WILD-TYPE        0       1       51        48       39
D13V3, multiclass
           clus
vv          AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             1                             1
  STAGE II                           35                            51
  STAGE III                          45                            48
  STAGE IV                           53                            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 13(7P21.1) MUTATED         36 69 22
  AMP PEAK 13(7P21.1) WILD-TYPE       46 67 17
D13V4, multiclass
          clus
vv         AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE
  T0+T1+T2                          36                            46
  T3                                69                            67
  T4                                22                            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 13(7P21.1) MUTATED   71 16 32  6
  AMP PEAK 13(7P21.1) WILD-TYPE 95 12 23  1
D13V5, multiclass
    clus
vv   AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE
  N0                          71                            95
  N1                          16                            12
  N2                          32                            23
  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(7P21.1) MUTATED   60  3 72
  AMP PEAK 13(7P21.1) WILD-TYPE 69  4 69
D13V6, multiclass
    clus
vv   AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE
  M0                          60                            69
  M1                           3                             4
  MX                          72                            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"
D13V7, binary
                               cls
clus                              0   1
  AMP PEAK 13(7P21.1) MUTATED    35 101
  AMP PEAK 13(7P21.1) WILD-TYPE  42 100
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7P21.1) MUTATED     35  101
  AMP PEAK 13(7P21.1) WILD-TYPE   42  100
        clus
vv       AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE
  FEMALE                          35                            42
  MALE                           101                           100
[1] 2 2
[1] FALSE
D13V8, continuous
D13V9, continuous
D13V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(7P21.1) MUTATED       9                         9   113
  AMP PEAK 13(7P21.1) WILD-TYPE    22                         4   102
D13V11, multiclass
                           clus
vv                          AMP PEAK 13(7P21.1) MUTATED
  ASIAN                                               9
  BLACK OR AFRICAN AMERICAN                           9
  WHITE                                             113
                           clus
vv                          AMP PEAK 13(7P21.1) WILD-TYPE
  ASIAN                                                22
  BLACK OR AFRICAN AMERICAN                             4
  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"
D13V12, binary
                               cls
clus                              0   1
  AMP PEAK 13(7P21.1) MUTATED     1 130
  AMP PEAK 13(7P21.1) WILD-TYPE   4 128
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7P21.1) MUTATED      1  130
  AMP PEAK 13(7P21.1) WILD-TYPE    4  128
                        clus
vv                       AMP PEAK 13(7P21.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         130
                        clus
vv                       AMP PEAK 13(7P21.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           128
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(7P11.2) MUTATION ANALYSIS
D14V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 14(7P11.2) MUTATED   84 43
  AMP PEAK 14(7P11.2) WILD-TYPE 98 45
  AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE 
                          127                           143 
  AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE 
                           43                            45 
$`AMP PEAK 14(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-A6ME TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 
        0.59        12.99         1.22        12.89         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-A5BV 
       22.98        14.93        14.93         3.62        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-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3ZE 
        6.71         4.11         2.07         2.66         4.01         3.48 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B 
        4.08         3.25         6.48        35.24         0.85        52.67 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       19.46         2.89         2.24         4.50        15.91        14.07 
TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A766 
        7.73        20.98         2.20         6.41         7.59         5.62 
TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E 
        6.41         5.69         7.63         7.79         6.67         6.41 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE 
       19.07        11.54         6.74        38.60         9.01         8.22 
TCGA-K4-A3WV TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-MV-A51V TCGA-S5-A6DX 
        4.67         1.81         6.38         6.35        13.48         0.85 
TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SI TCGA-XF-A9SY TCGA-XF-A9T3 
       88.93        56.19        15.35        79.66        21.04         2.24 
TCGA-XF-A9T5 TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN5 
       66.64         7.63         2.96         6.77        56.48        75.39 
TCGA-YF-AA3M 
        9.04 

$`AMP PEAK 14(7P11.2) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
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        66.41        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 
       41.56        76.60        15.68        41.06        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-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA 
       14.33         0.46        15.68        12.43        15.88        45.93 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S 
       22.45         6.12        12.82         5.52        13.18        14.96 
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-A62N TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TH TCGA-FD-A6TK 
        2.66        50.66        18.81         9.30         2.20        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
       15.19         7.13        61.94        30.61         5.69        26.93 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3OO TCGA-GC-A3WC 
       17.26         7.04        20.12         6.94        15.81        17.75 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A76B TCGA-GU-A42R 
        1.12         2.66         2.10         3.12         7.36        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JX 
        2.04        27.09         4.73        10.65         4.41         6.15 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
        4.14         1.51         3.06         8.75         3.45         2.50 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-LT-A5Z6 TCGA-LT-A8JT 
        6.48        10.52         1.74         4.27         3.45        11.80 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC 
       12.23        16.67        14.24         3.75        45.04         6.58 
TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SW TCGA-XF-A9SX 
       97.45         1.87        17.88        64.80        11.90        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME 
       28.24        26.27        18.90        16.27         2.10        92.98 
TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAN1 TCGA-XF-AAN4 
       10.82        54.90        91.73         8.32        30.94        27.06 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
        3.88        10.36         4.83         0.66         7.96 

  AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE 
                         0.43                          0.07 
  AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE 
                       130.88                        140.81 
  AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE 
                         8.25                         10.55 
[1] "0.4 - 130.9 (8.2)"  "0.1 - 140.8 (10.6)"
[1] "hr=" "1"  
D14V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 14(7P11.2) MUTATED          1       1       37        40       49
  AMP PEAK 14(7P11.2) WILD-TYPE        0       1       49        53       43
D14V3, multiclass
           clus
vv          AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             1                             1
  STAGE II                           37                            49
  STAGE III                          40                            53
  STAGE IV                           49                            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
  AMP PEAK 14(7P11.2) MUTATED         37 63 20
  AMP PEAK 14(7P11.2) WILD-TYPE       45 73 19
D14V4, multiclass
          clus
vv         AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE
  T0+T1+T2                          37                            45
  T3                                63                            73
  T4                                20                            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
  AMP PEAK 14(7P11.2) MUTATED   67 12 33  6
  AMP PEAK 14(7P11.2) WILD-TYPE 99 16 22  1
D14V5, multiclass
    clus
vv   AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE
  N0                          67                            99
  N1                          12                            16
  N2                          33                            22
  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 14(7P11.2) MUTATED   59  3 67
  AMP PEAK 14(7P11.2) WILD-TYPE 70  4 74
D14V6, multiclass
    clus
vv   AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE
  M0                          59                            70
  M1                           3                             4
  MX                          67                            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"
D14V7, binary
                               cls
clus                              0   1
  AMP PEAK 14(7P11.2) MUTATED    36  94
  AMP PEAK 14(7P11.2) WILD-TYPE  41 107
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7P11.2) MUTATED     36   94
  AMP PEAK 14(7P11.2) WILD-TYPE   41  107
        clus
vv       AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE
  FEMALE                          36                            41
  MALE                            94                           107
[1] 2 2
[1] FALSE
D14V8, continuous
D14V9, continuous
D14V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(7P11.2) MUTATED       9                         8   106
  AMP PEAK 14(7P11.2) WILD-TYPE    22                         5   109
D14V11, multiclass
                           clus
vv                          AMP PEAK 14(7P11.2) MUTATED
  ASIAN                                               9
  BLACK OR AFRICAN AMERICAN                           8
  WHITE                                             106
                           clus
vv                          AMP PEAK 14(7P11.2) WILD-TYPE
  ASIAN                                                22
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                               109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V12, binary
                               cls
clus                              0   1
  AMP PEAK 14(7P11.2) MUTATED     1 121
  AMP PEAK 14(7P11.2) WILD-TYPE   4 137
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7P11.2) MUTATED      1  121
  AMP PEAK 14(7P11.2) WILD-TYPE    4  137
                        clus
vv                       AMP PEAK 14(7P11.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         121
                        clus
vv                       AMP PEAK 14(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           137
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(8P11.23) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(8P11.23) MUTATED    56  23
  AMP PEAK 15(8P11.23) WILD-TYPE 126  65
  AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE 
                            79                            191 
  AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE 
                            23                             65 
$`AMP PEAK 15(8P11.23) MUTATED`
TCGA-2F-A9KO TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20V 
       22.29         2.66         6.74        12.39        32.84         5.06 
TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CU-A3QU 
       17.16         3.65         9.99        23.01         0.69         5.19 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IK 
        9.34         2.14       112.44        10.59        87.32         2.20 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-DK-A6B6 
       10.49        50.27        20.02        10.55        17.98        30.67 
TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A677 TCGA-E7-A6ME TCGA-FD-A3B7 
       43.59        24.66         0.49         1.38        12.99         4.01 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       45.93        24.30         6.12        46.78        19.79         1.97 
TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A5BS TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A6TD 
       14.93        14.93        37.15        49.68         4.83         6.71 
TCGA-FD-A6TI TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3IE 
        4.01         3.48         3.25         6.48        17.26        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GD-A2C5 
        0.85        52.67         2.89         2.24        14.07         7.73 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QI 
        2.20         7.36         4.41         6.41         6.15         4.14 
TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU 
        6.41        11.54        38.60         9.01         8.22         3.45 
TCGA-K4-A3WV TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-LT-A8JT TCGA-PQ-A6FI 
        4.67        10.52         1.81         4.27        11.80        12.23 
TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SH TCGA-XF-A9T5 
       45.04        88.93        56.19        15.35        64.80        66.64 
TCGA-YF-AA3M 
        9.04 

$`AMP PEAK 15(8P11.23) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 
       11.97        84.00       103.50        98.33         4.83        40.08 
TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        7.33         6.58        11.93        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X 
       19.50         5.06        14.89        14.96         8.35         8.25 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
        5.59         4.67        12.82         2.07        15.42        28.70 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S 
       28.41         8.98         1.94         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-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 
        4.90         7.20         5.46        16.31         1.84         2.53 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE 
       66.41        18.41        19.00         8.91       130.88        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL 
       17.62        15.62         1.81         7.79       123.85         3.98 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY 
        7.82         8.22        21.30         9.67         8.28       140.81 
TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       48.00        64.18        41.56        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A541 
       41.06        15.35        26.17         0.10         0.53         0.59 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN 
        0.56         0.66         0.82        14.33         1.22         0.46 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 
       12.89        15.68         8.94         6.87        12.43        11.93 
TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N 
       15.88        22.45        12.82         5.52        13.18        22.98 
TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BU 
       14.96         3.62        12.13        13.38        11.01         6.87 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N 
        5.36         5.69         6.84        27.45         6.87         2.66 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE 
        6.28         6.38        50.66        18.81         9.30         4.11 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        2.07         2.66         2.20        10.85        15.19         7.13 
TCGA-FJ-A3ZF TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        4.08        61.94        30.61         5.69        26.93        35.24 
TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
        7.04         6.94        19.46        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-GU-A762 TCGA-GU-A763 TCGA-GU-A766 
        6.41         7.59        11.31         2.04        27.09         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK 
        4.73        10.65         5.69         7.63         7.79         6.67 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A4AB 
       19.07         1.51         6.74         3.06         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-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HC TCGA-XF-A8HE 
       16.67        14.24         0.85         3.75         6.58        97.45 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        1.87        17.88        79.66        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 
       28.24        26.27        18.90         2.24        16.27         2.10 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT 
       92.98        10.82        54.90         7.63        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
        8.32         6.77        56.48        30.94        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
        3.88        10.36         4.83         0.66         7.96 

  AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE 
                          0.49                           0.07 
  AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE 
                        112.44                         140.81 
  AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE 
                         10.49                           8.91 
[1] "0.5 - 112.4 (10.5)" "0.1 - 140.8 (8.9)" 
[1] "hr=" "1.2"
D15V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 15(8P11.23) MUTATED          1       0       27        25       25
  AMP PEAK 15(8P11.23) WILD-TYPE        0       2       59        68       67
D15V3, multiclass
           clus
vv          AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE
  STAGE 0A                             1                              0
  STAGE I                              0                              2
  STAGE II                            27                             59
  STAGE III                           25                             68
  STAGE IV                            25                             67
[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(8P11.23) MUTATED         28 38  9
  AMP PEAK 15(8P11.23) WILD-TYPE       54 98 30
D15V4, multiclass
          clus
vv         AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE
  T0+T1+T2                           28                             54
  T3                                 38                             98
  T4                                  9                             30
[1] 3 2
[1] 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(8P11.23) MUTATED    44  10  15   2
  AMP PEAK 15(8P11.23) WILD-TYPE 122  18  40   5
D15V5, multiclass
    clus
vv   AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE
  N0                           44                            122
  N1                           10                             18
  N2                           15                             40
  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 15(8P11.23) MUTATED    36   2  41
  AMP PEAK 15(8P11.23) WILD-TYPE  93   5 100
D15V6, multiclass
    clus
vv   AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE
  M0                           36                             93
  M1                            2                              5
  MX                           41                            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"
D15V7, binary
                                cls
clus                               0   1
  AMP PEAK 15(8P11.23) MUTATED    19  61
  AMP PEAK 15(8P11.23) WILD-TYPE  58 140
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8P11.23) MUTATED     19   61
  AMP PEAK 15(8P11.23) WILD-TYPE   58  140
        clus
vv       AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE
  FEMALE                           19                             58
  MALE                             61                            140
[1] 2 2
[1] FALSE
D15V8, continuous
D15V9, continuous
D15V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(8P11.23) MUTATED       7                         3    61
  AMP PEAK 15(8P11.23) WILD-TYPE    24                        10   154
D15V11, multiclass
                           clus
vv                          AMP PEAK 15(8P11.23) MUTATED
  ASIAN                                                7
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               61
                           clus
vv                          AMP PEAK 15(8P11.23) WILD-TYPE
  ASIAN                                                 24
  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"
D15V12, binary
                                cls
clus                               0   1
  AMP PEAK 15(8P11.23) MUTATED     2  70
  AMP PEAK 15(8P11.23) WILD-TYPE   3 188
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8P11.23) MUTATED      2   70
  AMP PEAK 15(8P11.23) WILD-TYPE    3  188
                        clus
vv                       AMP PEAK 15(8P11.23) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           70
                        clus
vv                       AMP PEAK 15(8P11.23) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            188
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(8Q22.3) MUTATION ANALYSIS
D16V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 16(8Q22.3) MUTATED   119  49
  AMP PEAK 16(8Q22.3) WILD-TYPE  63  39
  AMP PEAK 16(8Q22.3) MUTATED AMP PEAK 16(8Q22.3) WILD-TYPE 
                          168                           102 
  AMP PEAK 16(8Q22.3) MUTATED AMP PEAK 16(8Q22.3) WILD-TYPE 
                           49                            39 
$`AMP PEAK 16(8Q22.3) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KW TCGA-BL-A0C8 TCGA-BL-A13J 
       22.29        11.97       103.50         4.83        40.08         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V 
        6.74        12.39        19.04        32.84        14.89         5.06 
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-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-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47X TCGA-CU-A0YN 
       23.01         0.43         0.69         0.13         0.10        12.92 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        7.20         5.46         5.19         1.84         9.34         2.53 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
        2.14        66.41        18.41       130.88       112.44        16.14 
TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN 
       10.59       123.85        87.32         2.20         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A3X2 
       10.49        50.27        20.02        10.55        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       64.18        15.68        30.67        43.59        15.35        26.17 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A6ME 
        0.49         0.53         0.59         0.56         1.38        12.99 
TCGA-E7-A7DV TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N6 TCGA-FD-A3NA 
        1.22         8.94         6.87         4.01        15.88        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A5BR 
       24.30        13.18        46.78        22.98        14.93        13.38 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 
       37.15        11.01         5.36         5.69        27.45         6.87 
TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TD TCGA-FD-A6TE 
       49.68         4.83         6.28         6.38         6.71         4.11 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        2.66         2.20         4.01        10.85        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-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB 
        0.85        52.67        19.46         2.89         2.24         4.50 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
       14.07        17.75         2.66         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A766 TCGA-GU-A767 
        2.20         7.36         6.41        11.31         5.62         4.73 
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-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        4.14         6.41        11.54         1.51         6.74        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
        3.06         9.01         8.22         8.75         3.45         2.50 
TCGA-K4-A4AC TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 
        6.48         1.81         4.27         6.38         6.35         3.45 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       11.80        13.48        12.23        16.67        14.24         0.85 
TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SH 
       45.04        88.93        56.19        15.35         1.87        64.80 
TCGA-XF-A9SI TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMJ 
       79.66        26.27         2.24         2.10        92.98        54.90 
TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YF-AA3M 
        7.63         2.96         8.32        75.39        10.36         9.04 

$`AMP PEAK 16(8Q22.3) WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O 
       84.00        98.33         7.33         6.58        11.93        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A3PH TCGA-BT-A3PK 
       17.88        19.50         5.06        14.96         4.67         2.07 
TCGA-CF-A1HR TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YO 
        0.46         0.07         0.10         0.07         0.10         4.90 
TCGA-CU-A3YL TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
       16.31        19.00         8.91        17.62        15.62         1.81 
TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY 
        7.79         3.98        21.30         9.67         8.28       140.81 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       41.56        76.60        67.36        41.06        24.66         0.10 
TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 
        0.66         0.82        14.33         0.46        12.89        15.68 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       12.43        11.93        22.45         6.12        12.82         5.52 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y 
       19.79         1.97        14.93        14.96         3.62        12.13 
TCGA-FD-A5BU TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        6.87         6.84         2.66        50.66        18.81         9.30 
TCGA-FD-A6TF TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL 
        2.07         4.08         6.48        61.94        30.61        26.93 
TCGA-G2-A3IB TCGA-G2-AA3C TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3YS TCGA-GD-A2C5 
        7.04         6.94        15.81        15.91         1.12         7.73 
TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-AATO TCGA-GV-A3QK TCGA-GV-A40G 
        7.59         2.04        27.09        10.65         6.67        19.07 
TCGA-K4-A3WV TCGA-K4-A54R TCGA-K4-A5RJ TCGA-S5-AA26 TCGA-XF-A8HC TCGA-XF-A8HE 
        4.67        10.52         1.74         3.75         6.58        97.45 
TCGA-XF-A8HI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 
       17.88        11.90        23.64        21.04        28.24        18.90 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-AAMF TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAN0 
       16.27        66.64        10.82        91.73         6.77        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       30.94        27.06         3.88         4.83         0.66         7.96 

  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 
                         8.55                         11.36 
[1] "0.1 - 130.9 (8.6)"  "0.1 - 140.8 (11.4)"
[1] "hr=" "1.2"
D16V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 16(8Q22.3) MUTATED          1       2       52        58       55
  AMP PEAK 16(8Q22.3) WILD-TYPE        0       0       34        35       37
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                           52                            34
  STAGE III                          58                            35
  STAGE IV                           55                            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 16(8Q22.3) MUTATED         52 84 22
  AMP PEAK 16(8Q22.3) WILD-TYPE       30 52 17
D16V4, multiclass
          clus
vv         AMP PEAK 16(8Q22.3) MUTATED AMP PEAK 16(8Q22.3) WILD-TYPE
  T0+T1+T2                          52                            30
  T3                                84                            52
  T4                                22                            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 16(8Q22.3) MUTATED   100  22  30   4
  AMP PEAK 16(8Q22.3) WILD-TYPE  66   6  25   3
D16V5, multiclass
    clus
vv   AMP PEAK 16(8Q22.3) MUTATED AMP PEAK 16(8Q22.3) WILD-TYPE
  N0                         100                            66
  N1                          22                             6
  N2                          30                            25
  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   78  3 89
  AMP PEAK 16(8Q22.3) WILD-TYPE 51  4 52
D16V6, multiclass
    clus
vv   AMP PEAK 16(8Q22.3) MUTATED AMP PEAK 16(8Q22.3) WILD-TYPE
  M0                          78                            51
  M1                           3                             4
  MX                          89                            52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                               cls
clus                              0   1
  AMP PEAK 16(8Q22.3) MUTATED    45 126
  AMP PEAK 16(8Q22.3) WILD-TYPE  32  75
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(8Q22.3) MUTATED     45  126
  AMP PEAK 16(8Q22.3) WILD-TYPE   32   75
        clus
vv       AMP PEAK 16(8Q22.3) MUTATED AMP PEAK 16(8Q22.3) WILD-TYPE
  FEMALE                          45                            32
  MALE                           126                            75
[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      17                         6   134
  AMP PEAK 16(8Q22.3) WILD-TYPE    14                         7    81
D16V11, multiclass
                           clus
vv                          AMP PEAK 16(8Q22.3) MUTATED
  ASIAN                                              17
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                             134
                           clus
vv                          AMP PEAK 16(8Q22.3) WILD-TYPE
  ASIAN                                                14
  BLACK OR AFRICAN AMERICAN                             7
  WHITE                                                81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V12, binary
                               cls
clus                              0   1
  AMP PEAK 16(8Q22.3) MUTATED     2 155
  AMP PEAK 16(8Q22.3) WILD-TYPE   3 103
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(8Q22.3) MUTATED      2  155
  AMP PEAK 16(8Q22.3) WILD-TYPE    3  103
                        clus
vv                       AMP PEAK 16(8Q22.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         155
                        clus
vv                       AMP PEAK 16(8Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           103
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(9P24.1) MUTATION ANALYSIS
D17V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 17(9P24.1) MUTATED    39  18
  AMP PEAK 17(9P24.1) WILD-TYPE 143  70
  AMP PEAK 17(9P24.1) MUTATED AMP PEAK 17(9P24.1) WILD-TYPE 
                           57                           213 
  AMP PEAK 17(9P24.1) MUTATED AMP PEAK 17(9P24.1) WILD-TYPE 
                           18                            70 
$`AMP PEAK 17(9P24.1) MUTATED`
TCGA-2F-A9KO TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20V TCGA-BT-A3PJ TCGA-CU-A0YR 
       22.29         6.74         6.58         5.06        12.82         7.20 
TCGA-CU-A3QU TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I4 TCGA-DK-A2I6 
        5.19         2.14       130.88       112.44       123.85        87.32 
TCGA-DK-A3IM TCGA-DK-A6B6 TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 
        7.82        30.67        12.89         6.87         4.01        11.93 
TCGA-FD-A3SL TCGA-FD-A43P TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A62N 
       22.45        14.93        11.01         6.87         5.69         2.66 
TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-G2-A2EF TCGA-G2-A2EJ 
        6.71         2.07         2.20        15.19        61.94        30.61 
TCGA-G2-A3IE TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GD-A2C5 TCGA-GD-A3OP 
       20.12         2.89         2.24        15.91         7.73         2.10 
TCGA-GU-A763 TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G 
       27.09         5.69         7.63         4.14         6.41        19.07 
TCGA-HQ-A5NE TCGA-K4-A6FZ TCGA-LC-A66R TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG 
        8.22         1.81         6.35         6.58        56.19        15.35 
TCGA-XF-A9SI TCGA-XF-A9SY TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-AAML TCGA-XF-AAMT 
       79.66        21.04        16.27        66.64         7.63         2.96 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YF-AA3M 
       27.06        75.39         9.04 

$`AMP PEAK 17(9P24.1) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 
       11.97        84.00       103.50        98.33         4.83        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        7.33         2.66        12.39        11.93        19.04        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-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        8.35         8.25        17.16         5.59         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-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-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-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        4.90         5.46        16.31         1.84         9.34         2.53 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF 
       66.41        18.41        19.00         8.91        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-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        10.49        50.27        21.30        20.02         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
        8.28        10.55       140.81        48.00        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC 
       41.56        76.60        67.36        15.68        41.06        43.59 
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-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
        0.59         0.56         0.66         1.38         0.82        12.99 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 
       14.33         1.22         0.46        15.68         8.94        12.43 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       15.88        45.93        24.30         6.12        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-A5BV 
       14.93         3.62        12.13        13.38        37.15         5.36 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P 
        6.84        27.45         6.87        49.68         4.83         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG 
        6.38        50.66        18.81         9.30         4.11         2.66 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
        4.01        10.85         7.13         3.48         4.08         3.25 
TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
        6.48         5.69        26.93        35.24        17.26         7.04 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB 
        0.85        52.67         6.94        19.46        15.81         4.50 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A3OS 
       14.07        17.75         1.12         2.66         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36         6.41         7.59        11.31         2.04 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
        5.62         4.73        10.65         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-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        3.06         9.01         8.75         3.45         4.67         2.50 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A5Z6 
        6.48        10.52         1.74         4.27         6.38         3.45 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       11.80        13.48        12.23        16.67        14.24         0.85 
TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI 
        3.75        45.04        88.93        97.45         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       64.80        11.90        23.64        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMR 
        2.24         2.10        92.98        10.82        54.90        91.73 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN8 TCGA-YC-A89H 
        8.32         6.77        56.48        30.94         3.88        10.36 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
        4.83         0.66         7.96 

  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 
                         8.22                          9.34 
[1] "1.8 - 130.9 (8.2)" "0.1 - 140.8 (9.3)"
[1] "hr=" "1.2"
D17V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 17(9P24.1) MUTATED          0       0       16        20       21
  AMP PEAK 17(9P24.1) WILD-TYPE        1       2       70        73       71
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                           16                            70
  STAGE III                          20                            73
  STAGE IV                           21                            71
[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         15  29   8
  AMP PEAK 17(9P24.1) WILD-TYPE       67 107  31
D17V4, multiclass
          clus
vv         AMP PEAK 17(9P24.1) MUTATED AMP PEAK 17(9P24.1) WILD-TYPE
  T0+T1+T2                          15                            67
  T3                                29                           107
  T4                                 8                            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 17(9P24.1) MUTATED    31   6  14   2
  AMP PEAK 17(9P24.1) WILD-TYPE 135  22  41   5
D17V5, multiclass
    clus
vv   AMP PEAK 17(9P24.1) MUTATED AMP PEAK 17(9P24.1) WILD-TYPE
  N0                          31                           135
  N1                           6                            22
  N2                          14                            41
  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    20   2  35
  AMP PEAK 17(9P24.1) WILD-TYPE 109   5 106
D17V6, multiclass
    clus
vv   AMP PEAK 17(9P24.1) MUTATED AMP PEAK 17(9P24.1) WILD-TYPE
  M0                          20                           109
  M1                           2                             5
  MX                          35                           106
[1] 3 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    14  43
  AMP PEAK 17(9P24.1) WILD-TYPE  63 158
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9P24.1) MUTATED     14   43
  AMP PEAK 17(9P24.1) WILD-TYPE   63  158
        clus
vv       AMP PEAK 17(9P24.1) MUTATED AMP PEAK 17(9P24.1) WILD-TYPE
  FEMALE                          14                            63
  MALE                            43                           158
[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       3                         5    47
  AMP PEAK 17(9P24.1) WILD-TYPE    28                         8   168
D17V11, multiclass
                           clus
vv                          AMP PEAK 17(9P24.1) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              47
                           clus
vv                          AMP PEAK 17(9P24.1) WILD-TYPE
  ASIAN                                                28
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                               168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V12, binary
                               cls
clus                              0   1
  AMP PEAK 17(9P24.1) MUTATED     1  53
  AMP PEAK 17(9P24.1) WILD-TYPE   4 205
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(9P24.1) MUTATED      1   53
  AMP PEAK 17(9P24.1) WILD-TYPE    4  205
                        clus
vv                       AMP PEAK 17(9P24.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          53
                        clus
vv                       AMP PEAK 17(9P24.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           205
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(10P14) MUTATION ANALYSIS
D18V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 18(10P14) MUTATED    69  43
  AMP PEAK 18(10P14) WILD-TYPE 113  45
  AMP PEAK 18(10P14) MUTATED AMP PEAK 18(10P14) WILD-TYPE 
                         112                          158 
  AMP PEAK 18(10P14) MUTATED AMP PEAK 18(10P14) WILD-TYPE 
                          43                           45 
$`AMP PEAK 18(10P14) MUTATED`
TCGA-2F-A9KO TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20Q 
       22.29        40.08         2.66         6.58        32.84        19.50 
TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ 
        5.06         5.06         8.35         5.59         3.65        12.82 
TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A3KJ 
        9.99         8.98        23.01         0.43        12.92         5.46 
TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AC 
        5.19         1.84         2.53         2.14        66.41       130.88 
TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IN 
      112.44         1.81        10.59        87.32         3.98         8.22 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 
        9.67        48.00        64.18        67.36        15.68        30.67 
TCGA-E5-A4U1 TCGA-E7-A6ME TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 
       26.17        12.99         1.22        12.89         8.94         6.87 
TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
       11.93        45.93        24.30        19.79         1.97        22.98 
TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BZ TCGA-FD-A5C0 
       14.93        12.13        13.38        37.15        27.45         6.87 
TCGA-FD-A5C1 TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 
       49.68         4.11         2.07         2.66         4.01        15.19 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
        3.25         6.48        17.26        20.12         0.85        52.67 
TCGA-G2-AA3F TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OS 
       19.46         4.50        14.07         2.66         7.73        20.98 
TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JW 
        2.20         6.41         5.62         4.73        10.65         6.41 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HQ 
        5.69         7.63         7.79         6.41        11.54         6.74 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A4AC 
       38.60         3.06         9.01         8.22         8.75         6.48 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 
       10.52         1.74         1.81         6.38         6.35         3.45 
TCGA-MV-A51V TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SH TCGA-XF-A9SI 
       13.48        88.93        56.19        15.35        64.80        79.66 
TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML 
       23.64        28.24         2.10        10.82        54.90         7.63 
TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN4 TCGA-YF-AA3M 
        2.96         6.77        27.06         9.04 

$`AMP PEAK 18(10P14) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A13I 
       11.97        84.00       103.50        98.33         4.83         7.33 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        6.74        12.39        11.93        19.04        12.16        17.88 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A3PK 
       14.89        14.96         8.25        17.16         4.67         2.07 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A27C 
       15.42        28.70        28.41         1.94         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-A3YL TCGA-CU-A72E TCGA-DK-A1A7 TCGA-DK-A1AA 
        4.90         7.20        16.31         9.34        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 
        8.91        16.14        17.62        15.62         7.79       123.85 
TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        2.20         7.82        10.49        50.27        21.30        20.02 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 
        8.28        10.55       140.81        17.98        41.56        76.60 
TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       41.06        43.59        15.35        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-A6MF TCGA-E7-A7XN TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 
       14.33         0.46        15.68         4.01        12.43        15.88 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       22.45         6.12        12.82         5.52        13.18        46.78 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
       14.96        14.93         3.62        11.01         6.87         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
        5.69         6.84         2.66         4.83         6.28         6.38 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TH TCGA-FD-A6TK 
       50.66        18.81         9.30         6.71         2.20        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        7.13         3.48         4.08        61.94        30.61         5.69 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 
       26.93        35.24         7.04         6.94         2.89         2.24 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A3OP TCGA-GD-A3OQ 
       15.81        15.91        17.75         1.12         2.10         3.12 
TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GV-A3JV 
        7.36         7.59        11.31         2.04        27.09         4.41 
TCGA-GV-A3JX TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G TCGA-H4-A2HO TCGA-K4-A3WU 
        6.15         4.14         6.67        19.07         1.51         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A6MB TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN 
        4.67         2.50         4.27        11.80        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE 
       14.24         0.85         3.75        45.04         6.58        97.45 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
        1.87        17.88        11.90        21.04        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-AAME TCGA-XF-AAMR TCGA-XF-AAMW 
        2.24        16.27        66.64        92.98        91.73         8.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       56.48        30.94        75.39         3.88        10.36         4.83 
TCGA-YC-A9TC TCGA-YF-AA3L 
        0.66         7.96 

  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 
                       9.025                        9.320 
[1] "0.4 - 130.9 (9.0)" "0.1 - 140.8 (9.3)"
[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       35        34       43
  AMP PEAK 18(10P14) WILD-TYPE        0       1       51        59       49
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                          35                           51
  STAGE III                         34                           59
  STAGE IV                          43                           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 18(10P14) MUTATED         34 56 17
  AMP PEAK 18(10P14) WILD-TYPE       48 80 22
D18V4, multiclass
          clus
vv         AMP PEAK 18(10P14) MUTATED AMP PEAK 18(10P14) WILD-TYPE
  T0+T1+T2                         34                           48
  T3                               56                           80
  T4                               17                           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 18(10P14) MUTATED    59  15  25   4
  AMP PEAK 18(10P14) WILD-TYPE 107  13  30   3
D18V5, multiclass
    clus
vv   AMP PEAK 18(10P14) MUTATED AMP PEAK 18(10P14) WILD-TYPE
  N0                         59                          107
  N1                         15                           13
  N2                         25                           30
  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   51  3 61
  AMP PEAK 18(10P14) WILD-TYPE 78  4 80
D18V6, multiclass
    clus
vv   AMP PEAK 18(10P14) MUTATED AMP PEAK 18(10P14) WILD-TYPE
  M0                         51                           78
  M1                          3                            4
  MX                         61                           80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                              cls
clus                             0   1
  AMP PEAK 18(10P14) MUTATED    32  84
  AMP PEAK 18(10P14) WILD-TYPE  45 117
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(10P14) MUTATED     32   84
  AMP PEAK 18(10P14) WILD-TYPE   45  117
        clus
vv       AMP PEAK 18(10P14) MUTATED AMP PEAK 18(10P14) WILD-TYPE
  FEMALE                         32                           45
  MALE                           84                          117
[1] 2 2
[1] FALSE
D18V8, continuous
D18V9, continuous
D18V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(10P14) MUTATED      11                         6    89
  AMP PEAK 18(10P14) WILD-TYPE    20                         7   126
D18V11, multiclass
                           clus
vv                          AMP PEAK 18(10P14) MUTATED
  ASIAN                                             11
  BLACK OR AFRICAN AMERICAN                          6
  WHITE                                             89
                           clus
vv                          AMP PEAK 18(10P14) WILD-TYPE
  ASIAN                                               20
  BLACK OR AFRICAN AMERICAN                            7
  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"
D18V12, binary
                              cls
clus                             0   1
  AMP PEAK 18(10P14) MUTATED     1 104
  AMP PEAK 18(10P14) WILD-TYPE   4 154
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(10P14) MUTATED      1  104
  AMP PEAK 18(10P14) WILD-TYPE    4  154
                        clus
vv                       AMP PEAK 18(10P14) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                        104
                        clus
vv                       AMP PEAK 18(10P14) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          154
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(11P13) MUTATION ANALYSIS
D19V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 19(11P13) MUTATED    21  13
  AMP PEAK 19(11P13) WILD-TYPE 161  75
  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE 
                          34                          236 
  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE 
                          13                           75 
$`AMP PEAK 19(11P13) MUTATED`
TCGA-BL-A3JM TCGA-BT-A20R TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-CU-A0YN TCGA-CU-A0YO 
        6.74         5.06        17.16        12.82        12.92         4.90 
TCGA-DK-A2I2 TCGA-DK-A3IV TCGA-DK-A3WX TCGA-E5-A2PC TCGA-E7-A5KE TCGA-E7-A6ME 
        7.79         9.67        10.55        43.59         0.56        12.99 
TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A5BT TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A6TI 
        1.22         6.87        11.01         2.66         6.28         4.01 
TCGA-FJ-A3Z7 TCGA-GC-A3RC TCGA-GU-A762 TCGA-GU-A766 TCGA-GV-A3JZ TCGA-GV-A3QI 
       15.19        15.91         2.04         5.62         5.69         4.14 
TCGA-GV-A40E TCGA-K4-A3WS TCGA-K4-A4AC TCGA-LC-A66R TCGA-PQ-A6FI TCGA-XF-A9SX 
        6.41         8.75         6.48         6.35        12.23        23.64 
TCGA-XF-A9SY TCGA-XF-A9T3 TCGA-XF-AAMT TCGA-YF-AA3M 
       21.04         2.24         2.96         9.04 

$`AMP PEAK 19(11P13) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
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-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T 
       19.04        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-A2LD 
       14.96         5.06         8.35         8.25         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-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        7.20         5.46         5.19        16.31         1.84         9.34 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
        2.53         2.14        66.41        18.41        19.00         8.91 
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-A3IM 
       10.59       123.85        87.32         2.20         3.98         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW 
        8.22        10.49        50.27        21.30        20.02         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        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 
       67.36        15.68        41.06        30.67        15.35        26.17 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KF 
       24.66         0.10         0.49         0.53         0.59         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 
        1.38         0.82        14.33         0.46        12.89        15.68 
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-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        22.45         6.12        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-A5BU 
       14.93         3.62        12.13        13.38        37.15         6.87 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        5.36         5.69         6.84        27.45         6.87        49.68 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        4.83         6.38        50.66        18.81         9.30         6.71 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z9 
        4.11         2.07         2.66         2.20        10.85         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
        3.48         4.08         3.25         6.48        61.94        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-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
        0.85        52.67         6.94        19.46         2.89         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-GD-A76B 
        7.73         2.10         3.12        20.98         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A767 TCGA-GU-AATO 
        6.41         7.59        11.31        27.09         4.73        10.65 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK 
        4.41         6.41         6.15         7.63         7.79         6.67 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.07        11.54         1.51         6.74        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R 
        9.01         8.22         3.45         4.67         2.50        10.52 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-LT-A8JT 
        1.74         1.81         4.27         6.38         3.45        11.80 
TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB 
       13.48        16.67        14.24         0.85         3.75        45.04 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH 
        6.58        88.93        97.45        56.19        15.35         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SZ TCGA-XF-A9T0 
       17.88        64.80        79.66        11.90        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF 
       18.90        16.27        66.64         2.10        92.98        10.82 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       54.90         7.63        91.73         8.32         6.77        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       30.94        27.06        75.39         3.88        10.36         4.83 
TCGA-YC-A9TC TCGA-YF-AA3L 
        0.66         7.96 

  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE 
                        0.56                         0.07 
  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE 
                       43.59                       140.81 
  AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE 
                       6.805                       10.425 
[1] "0.6 - 43.6 (6.8)"   "0.1 - 140.8 (10.4)"
[1] "hr=" "1.8"
D19V2, continuous
                              vv
clus                           STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 19(11P13) MUTATED          0       0       11         9       14
  AMP PEAK 19(11P13) WILD-TYPE        1       2       75        84       78
D19V3, multiclass
           clus
vv          AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE
  STAGE 0A                           0                            1
  STAGE I                            0                            2
  STAGE II                          11                           75
  STAGE III                          9                           84
  STAGE IV                          14                           78
[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(11P13) MUTATED         10  16   6
  AMP PEAK 19(11P13) WILD-TYPE       72 120  33
D19V4, multiclass
          clus
vv         AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE
  T0+T1+T2                         10                           72
  T3                               16                          120
  T4                                6                           33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2  N3
  AMP PEAK 19(11P13) MUTATED    15   3   8   4
  AMP PEAK 19(11P13) WILD-TYPE 151  25  47   3
D19V5, multiclass
    clus
vv   AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE
  N0                         15                          151
  N1                          3                           25
  N2                          8                           47
  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(11P13) MUTATED    11   0  23
  AMP PEAK 19(11P13) WILD-TYPE 118   7 118
D19V6, multiclass
    clus
vv   AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE
  M0                         11                          118
  M1                          0                            7
  MX                         23                          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"
D19V7, binary
                              cls
clus                             0   1
  AMP PEAK 19(11P13) MUTATED     9  25
  AMP PEAK 19(11P13) WILD-TYPE  68 176
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(11P13) MUTATED      9   25
  AMP PEAK 19(11P13) WILD-TYPE   68  176
        clus
vv       AMP PEAK 19(11P13) MUTATED AMP PEAK 19(11P13) WILD-TYPE
  FEMALE                          9                           68
  MALE                           25                          176
[1] 2 2
[1] FALSE
D19V8, continuous
D19V9, continuous
D19V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(11P13) MUTATED       3                         0    29
  AMP PEAK 19(11P13) WILD-TYPE    28                        13   186
D19V11, multiclass
                           clus
vv                          AMP PEAK 19(11P13) MUTATED
  ASIAN                                              3
  BLACK OR AFRICAN AMERICAN                          0
  WHITE                                             29
                           clus
vv                          AMP PEAK 19(11P13) WILD-TYPE
  ASIAN                                               28
  BLACK OR AFRICAN AMERICAN                           13
  WHITE                                              186
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V12, binary
                              cls
clus                             0   1
  AMP PEAK 19(11P13) MUTATED     1  32
  AMP PEAK 19(11P13) WILD-TYPE   4 226
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(11P13) MUTATED      1   32
  AMP PEAK 19(11P13) WILD-TYPE    4  226
                        clus
vv                       AMP PEAK 19(11P13) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         32
                        clus
vv                       AMP PEAK 19(11P13) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          226
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(11Q13.3) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 20(11Q13.3) MUTATED    68  34
  AMP PEAK 20(11Q13.3) WILD-TYPE 114  54
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                           102                            168 
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                            34                             54 
$`AMP PEAK 20(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        66.41        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-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3BM 
       17.26         7.04        20.12        52.67        19.46         2.89 
TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OS 
        2.24        15.91        14.07         2.66         7.73        20.98 
TCGA-GD-A6C6 TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW 
        2.20         2.04         5.62         4.73         4.41         6.41 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
        5.69         7.63         7.79         4.14         6.67         6.41 
TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-K4-A3WV TCGA-K4-A4AB 
       19.07         6.74        38.60         9.01         4.67         2.50 
TCGA-K4-A4AC TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX 
        6.48         6.35        11.80        12.23        14.24         0.85 
TCGA-S5-AA26 TCGA-XF-A8HF TCGA-XF-A9SY TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAML 
        3.75        56.19        21.04        16.27         2.10         7.63 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YF-AA3M 
        2.96         8.32         6.77        27.06         3.88         9.04 

$`AMP PEAK 20(11Q13.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
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 
       41.56        76.60        67.36        15.68        41.06        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-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 
        0.82        12.99        14.33         0.46        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         6.12        12.82 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43S 
        5.52        13.18        46.78        19.79         1.97        14.96 
TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
        3.62        37.15         6.87         5.69         6.84        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB 
        6.87        49.68         4.83         6.28        50.66        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TK 
        9.30         6.71         4.11         2.07         2.20        10.85 
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-G2-AA3C 
       30.61         5.69        26.93        35.24         0.85         6.94 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A3OP TCGA-GD-A3OQ 
       15.81         4.50        17.75         1.12         2.10         3.12 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-AATO 
        7.36         6.41         7.59        11.31        27.09        10.65 
TCGA-GV-A3JX TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WS 
        6.15        11.54         1.51         3.06         8.22         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-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
        3.45        13.48        16.67        45.04         6.58        88.93 
TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI 
       97.45        15.35         1.87        17.88        64.80        79.66 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       11.90        23.64        28.24        26.27        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAN0 
       66.64        92.98        10.82        54.90        91.73        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       30.94        75.39        10.36         4.83         0.66         7.96 

  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                         87.32                         140.81 
  AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE 
                         7.805                         10.585 
[1] "0.1 - 87.3 (7.8)"   "0.1 - 140.8 (10.6)"
[1] "hr=" "1.2"
D20V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 20(11Q13.3) MUTATED          0       0       33        31       37
  AMP PEAK 20(11Q13.3) WILD-TYPE        1       2       53        62       55
D20V3, multiclass
           clus
vv          AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              0                              2
  STAGE II                            33                             53
  STAGE III                           31                             62
  STAGE IV                            37                             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 20(11Q13.3) MUTATED         34 47 14
  AMP PEAK 20(11Q13.3) WILD-TYPE       48 89 25
D20V4, multiclass
          clus
vv         AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE
  T0+T1+T2                           34                             48
  T3                                 47                             89
  T4                                 14                             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 20(11Q13.3) MUTATED    57  11  22   4
  AMP PEAK 20(11Q13.3) WILD-TYPE 109  17  33   3
D20V5, multiclass
    clus
vv   AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE
  N0                           57                            109
  N1                           11                             17
  N2                           22                             33
  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 20(11Q13.3) MUTATED   42  1 60
  AMP PEAK 20(11Q13.3) WILD-TYPE 87  6 81
D20V6, multiclass
    clus
vv   AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE
  M0                           42                             87
  M1                            1                              6
  MX                           60                             81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                                cls
clus                               0   1
  AMP PEAK 20(11Q13.3) MUTATED    29  74
  AMP PEAK 20(11Q13.3) WILD-TYPE  48 127
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(11Q13.3) MUTATED     29   74
  AMP PEAK 20(11Q13.3) WILD-TYPE   48  127
        clus
vv       AMP PEAK 20(11Q13.3) MUTATED AMP PEAK 20(11Q13.3) WILD-TYPE
  FEMALE                           29                             48
  MALE                             74                            127
[1] 2 2
[1] FALSE
D20V8, continuous
D20V9, continuous
D20V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(11Q13.3) MUTATED       7                         8    81
  AMP PEAK 20(11Q13.3) WILD-TYPE    24                         5   134
D20V11, multiclass
                           clus
vv                          AMP PEAK 20(11Q13.3) MUTATED
  ASIAN                                                7
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                               81
                           clus
vv                          AMP PEAK 20(11Q13.3) WILD-TYPE
  ASIAN                                                 24
  BLACK OR AFRICAN AMERICAN                              5
  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"
D20V12, binary
                                cls
clus                               0   1
  AMP PEAK 20(11Q13.3) MUTATED     1  96
  AMP PEAK 20(11Q13.3) WILD-TYPE   4 162
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(11Q13.3) MUTATED      1   96
  AMP PEAK 20(11Q13.3) WILD-TYPE    4  162
                        clus
vv                       AMP PEAK 20(11Q13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           96
                        clus
vv                       AMP PEAK 20(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            162
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(11Q22.2) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 21(11Q22.2) MUTATED    39  12
  AMP PEAK 21(11Q22.2) WILD-TYPE 143  76
  AMP PEAK 21(11Q22.2) MUTATED AMP PEAK 21(11Q22.2) WILD-TYPE 
                            51                            219 
  AMP PEAK 21(11Q22.2) MUTATED AMP PEAK 21(11Q22.2) WILD-TYPE 
                            12                             76 
$`AMP PEAK 21(11Q22.2) MUTATED`
TCGA-2F-A9KO TCGA-BT-A20W TCGA-BT-A3PJ TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F6 
       22.29         8.35        12.82         9.99         1.94        23.01 
TCGA-CU-A0YR TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IL 
        7.20         1.84         2.53        10.59        87.32         3.98 
TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-E5-A2PC TCGA-E7-A5KF TCGA-E7-A7DV 
       10.55        48.00        17.98        43.59         0.66         1.22 
TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A43P TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BZ 
        6.87        45.93        14.93        13.38        11.01        27.45 
TCGA-FD-A5C1 TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-G2-AA3B TCGA-G2-AA3F 
       49.68         2.66         4.01        15.19        52.67        19.46 
TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3YS TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A762 
        2.24        15.91         1.12        20.98         2.20         2.04 
TCGA-GU-A766 TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A40E TCGA-K4-A4AB TCGA-K4-A4AC 
        5.62         7.63         4.14         6.41         2.50         6.48 
TCGA-K4-A6MB TCGA-LC-A66R TCGA-PQ-A6FI TCGA-S5-A6DX TCGA-XF-A8HF TCGA-XF-A9SY 
        4.27         6.35        12.23         0.85        56.19        21.04 
TCGA-XF-A9T6 TCGA-XF-AAMX TCGA-YF-AA3M 
        2.10         6.77         9.04 

$`AMP PEAK 21(11Q22.2) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 
       11.97        84.00       103.50        98.33         4.83        40.08 
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-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.89        14.96         5.06         8.25        17.16         5.59 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F 
        3.65         4.67         2.07        15.42        28.70        28.41 
TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        8.98         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-A1A5 TCGA-DK-A1A6 
        5.46         5.19        16.31         9.34         2.14        66.41 
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-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       17.62        15.62         1.81         7.79       123.85         2.20 
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-A3WY TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
        9.67         8.28       140.81        64.18        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 
       67.36        15.68        41.06        30.67        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-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B3 
        1.38         0.82        12.99        14.33         0.46        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       15.68         8.94         4.01        12.43        11.93        15.88 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        22.45         6.12        12.82         5.52        13.18 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       46.78        19.79         1.97        22.98        14.96        14.93 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
        3.62        12.13        37.15         6.87         5.36         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-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       50.66        18.81         9.30         6.71         4.11         2.07 
TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
        2.20        10.85         7.13         3.48         4.08         3.25 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        6.48        61.94        30.61         5.69        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C TCGA-GC-A3BM 
       17.26         7.04        20.12         0.85         6.94         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-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12         7.36         6.41         7.59        11.31 
TCGA-GU-A763 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       27.09         4.73        10.65         4.41         6.41         6.15 
TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
        5.69         7.79         6.67        19.07        11.54         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
        6.74        38.60         3.06         9.01         8.22         8.75 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P 
        3.45         4.67        10.52         1.74         1.81         6.38 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 
        3.45        11.80        13.48        16.67        14.24         3.75 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HH 
       45.04         6.58        88.93        97.45        15.35         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ 
       17.88        64.80        79.66        11.90        23.64        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-AAME 
       26.27        18.90         2.24        16.27        66.64        92.98 
TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       10.82        54.90         7.63        91.73         2.96         8.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
       56.48        30.94        27.06        75.39         3.88        10.36 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
        4.83         0.66         7.96 

  AMP PEAK 21(11Q22.2) MUTATED AMP PEAK 21(11Q22.2) WILD-TYPE 
                          0.66                           0.07 
  AMP PEAK 21(11Q22.2) MUTATED AMP PEAK 21(11Q22.2) WILD-TYPE 
                         87.32                         140.81 
  AMP PEAK 21(11Q22.2) MUTATED AMP PEAK 21(11Q22.2) WILD-TYPE 
                          8.35                           9.34 
[1] "0.7 - 87.3 (8.3)"  "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(11Q22.2) MUTATED          0       0       16        15       20
  AMP PEAK 21(11Q22.2) WILD-TYPE        1       2       70        78       72
D21V3, multiclass
           clus
vv          AMP PEAK 21(11Q22.2) MUTATED AMP PEAK 21(11Q22.2) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              0                              2
  STAGE II                            16                             70
  STAGE III                           15                             78
  STAGE IV                            20                             72
[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(11Q22.2) MUTATED         17  24   8
  AMP PEAK 21(11Q22.2) WILD-TYPE       65 112  31
D21V4, multiclass
          clus
vv         AMP PEAK 21(11Q22.2) MUTATED AMP PEAK 21(11Q22.2) WILD-TYPE
  T0+T1+T2                           17                             65
  T3                                 24                            112
  T4                                  8                             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 21(11Q22.2) MUTATED    27   8  11   2
  AMP PEAK 21(11Q22.2) WILD-TYPE 139  20  44   5
D21V5, multiclass
    clus
vv   AMP PEAK 21(11Q22.2) MUTATED AMP PEAK 21(11Q22.2) WILD-TYPE
  N0                           27                            139
  N1                            8                             20
  N2                           11                             44
  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 21(11Q22.2) MUTATED    21   0  30
  AMP PEAK 21(11Q22.2) WILD-TYPE 108   7 111
D21V6, multiclass
    clus
vv   AMP PEAK 21(11Q22.2) MUTATED AMP PEAK 21(11Q22.2) WILD-TYPE
  M0                           21                            108
  M1                            0                              7
  MX                           30                            111
[1] 3 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(11Q22.2) MUTATED    13  38
  AMP PEAK 21(11Q22.2) WILD-TYPE  64 163
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(11Q22.2) MUTATED     13   38
  AMP PEAK 21(11Q22.2) WILD-TYPE   64  163
        clus
vv       AMP PEAK 21(11Q22.2) MUTATED AMP PEAK 21(11Q22.2) WILD-TYPE
  FEMALE                           13                             64
  MALE                             38                            163
[1] 2 2
[1] FALSE
D21V8, continuous
D21V9, continuous
D21V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(11Q22.2) MUTATED       1                         2    45
  AMP PEAK 21(11Q22.2) WILD-TYPE    30                        11   170
D21V11, multiclass
                           clus
vv                          AMP PEAK 21(11Q22.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               45
                           clus
vv                          AMP PEAK 21(11Q22.2) WILD-TYPE
  ASIAN                                                 30
  BLACK OR AFRICAN AMERICAN                             11
  WHITE                                                170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V12, binary
                                cls
clus                               0   1
  AMP PEAK 21(11Q22.2) MUTATED     1  48
  AMP PEAK 21(11Q22.2) WILD-TYPE   4 210
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(11Q22.2) MUTATED      1   48
  AMP PEAK 21(11Q22.2) WILD-TYPE    4  210
                        clus
vv                       AMP PEAK 21(11Q22.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           48
                        clus
vv                       AMP PEAK 21(11Q22.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            210
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(12P12.1) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 22(12P12.1) MUTATED    54  27
  AMP PEAK 22(12P12.1) WILD-TYPE 128  61
  AMP PEAK 22(12P12.1) MUTATED AMP PEAK 22(12P12.1) WILD-TYPE 
                            81                            189 
  AMP PEAK 22(12P12.1) MUTATED AMP PEAK 22(12P12.1) WILD-TYPE 
                            27                             61 
$`AMP PEAK 22(12P12.1) MUTATED`
TCGA-2F-A9KO TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20N 
       22.29        40.08         2.66         6.74        19.04        32.84 
TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD 
       17.88         5.06         5.06         8.25         5.59         3.65 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42E TCGA-C4-A0F0 TCGA-CU-A0YN TCGA-CU-A0YO 
       12.82         2.07         9.99         1.94        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A3IM TCGA-DK-A3IS 
        7.20         5.46        66.41        18.41         7.82        50.27 
TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 
       10.55        48.00        64.18        67.36        15.68        30.67 
TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A6ME TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3NA 
        0.49         0.56        12.99        12.89         6.87        45.93 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A5BS TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ 
        1.97        14.93        37.15         5.36         5.69        27.45 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TF TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        6.28         6.38        18.81         2.07        15.19         7.13 
TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3BM 
        6.48        35.24         0.85        52.67        19.46         2.89 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GU-A762 TCGA-GV-A3JZ TCGA-GV-A3QH 
        2.24        15.81        14.07         2.04         5.69         7.79 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A2OE TCGA-HQ-A2OF 
        4.14         6.67         6.41        19.07        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A83P 
        9.01         8.22         3.45         4.67         6.48         6.38 
TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI TCGA-XF-A9SI TCGA-XF-AAML TCGA-XF-AAMT 
        6.35        13.48        12.23        79.66         7.63         2.96 
TCGA-XF-AAMX TCGA-XF-AAN5 TCGA-YF-AA3M 
        6.77        75.39         9.04 

$`AMP PEAK 22(12P12.1) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A13I 
       11.97        84.00       103.50        98.33         4.83         7.33 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20T 
       12.39         6.58        11.93        12.16        19.50        14.89 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C 
       14.96         8.35        17.16         4.67        15.42        28.70 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
       28.41         8.98        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-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84         9.34         2.53         2.14 
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-A2I4 TCGA-DK-A2I6 
       15.62         1.81        10.59         7.79       123.85        87.32 
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-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 
        9.67         8.28       140.81        17.98        41.56        76.60 
TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       41.06        43.59        15.35        26.17        24.66         0.10 
TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF 
        0.53         0.59         0.66         1.38         0.82        14.33 
TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 
        1.22         0.46        15.68         8.94         4.01        12.43 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       11.93        15.88        24.30        22.45         6.12        12.82 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43S 
        5.52        13.18        46.78        19.79        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BU 
       14.93         3.62        12.13        13.38        11.01         6.87 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TA 
        6.84         6.87        49.68         2.66         4.83        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-FD-A6TK TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.85         3.48         4.08         3.25        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C 
        5.69        26.93        17.26         7.04        20.12         6.94 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 
        4.50        15.91        17.75         1.12         2.66         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        2.10         3.12        20.98         2.20         7.36         6.41 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
        7.59        11.31        27.09         5.62         4.73        10.65 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A6ZA TCGA-H4-A2HO 
        4.41         6.41         6.15         7.63        11.54         1.51 
TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
        6.74         8.75         2.50        10.52         1.74         1.81 
TCGA-K4-A6MB TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
        4.27         3.45        11.80        16.67        14.24         0.85 
TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        3.75        45.04         6.58        88.93        97.45        56.19 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SW TCGA-XF-A9SX 
       15.35         1.87        17.88        64.80        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMR 
       66.64         2.10        92.98        10.82        54.90        91.73 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A89H 
        8.32        56.48        30.94        27.06         3.88        10.36 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
        4.83         0.66         7.96 

  AMP PEAK 22(12P12.1) MUTATED AMP PEAK 22(12P12.1) WILD-TYPE 
                          0.49                           0.07 
  AMP PEAK 22(12P12.1) MUTATED AMP PEAK 22(12P12.1) WILD-TYPE 
                         79.66                         140.81 
  AMP PEAK 22(12P12.1) MUTATED AMP PEAK 22(12P12.1) WILD-TYPE 
                          7.82                          10.49 
[1] "0.5 - 79.7 (7.8)"   "0.1 - 140.8 (10.5)"
[1] "hr=" "1.1"
D22V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 22(12P12.1) MUTATED          0       2       31        26       25
  AMP PEAK 22(12P12.1) WILD-TYPE        1       0       55        67       67
D22V3, multiclass
           clus
vv          AMP PEAK 22(12P12.1) MUTATED AMP PEAK 22(12P12.1) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              2                              0
  STAGE II                            31                             55
  STAGE III                           26                             67
  STAGE IV                            25                             67
[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(12P12.1) MUTATED         32 38 11
  AMP PEAK 22(12P12.1) WILD-TYPE       50 98 28
D22V4, multiclass
          clus
vv         AMP PEAK 22(12P12.1) MUTATED AMP PEAK 22(12P12.1) WILD-TYPE
  T0+T1+T2                           32                             50
  T3                                 38                             98
  T4                                 11                             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 22(12P12.1) MUTATED    50  10  14   3
  AMP PEAK 22(12P12.1) WILD-TYPE 116  18  41   4
D22V5, multiclass
    clus
vv   AMP PEAK 22(12P12.1) MUTATED AMP PEAK 22(12P12.1) WILD-TYPE
  N0                           50                            116
  N1                           10                             18
  N2                           14                             41
  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(12P12.1) MUTATED    45   1  38
  AMP PEAK 22(12P12.1) WILD-TYPE  84   6 103
D22V6, multiclass
    clus
vv   AMP PEAK 22(12P12.1) MUTATED AMP PEAK 22(12P12.1) WILD-TYPE
  M0                           45                             84
  M1                            1                              6
  MX                           38                            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"
D22V7, binary
                                cls
clus                               0   1
  AMP PEAK 22(12P12.1) MUTATED    24  61
  AMP PEAK 22(12P12.1) WILD-TYPE  53 140
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(12P12.1) MUTATED     24   61
  AMP PEAK 22(12P12.1) WILD-TYPE   53  140
        clus
vv       AMP PEAK 22(12P12.1) MUTATED AMP PEAK 22(12P12.1) WILD-TYPE
  FEMALE                           24                             53
  MALE                             61                            140
[1] 2 2
[1] FALSE
D22V8, continuous
D22V9, continuous
D22V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(12P12.1) MUTATED      10                         4    62
  AMP PEAK 22(12P12.1) WILD-TYPE    21                         9   153
D22V11, multiclass
                           clus
vv                          AMP PEAK 22(12P12.1) MUTATED
  ASIAN                                               10
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               62
                           clus
vv                          AMP PEAK 22(12P12.1) WILD-TYPE
  ASIAN                                                 21
  BLACK OR AFRICAN AMERICAN                              9
  WHITE                                                153
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V12, binary
                                cls
clus                               0   1
  AMP PEAK 22(12P12.1) MUTATED     1  75
  AMP PEAK 22(12P12.1) WILD-TYPE   4 183
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(12P12.1) MUTATED      1   75
  AMP PEAK 22(12P12.1) WILD-TYPE    4  183
                        clus
vv                       AMP PEAK 22(12P12.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           75
                        clus
vv                       AMP PEAK 22(12P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            183
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 23(12Q15) MUTATION ANALYSIS
D23V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 23(12Q15) MUTATED    47  26
  AMP PEAK 23(12Q15) WILD-TYPE 135  62
  AMP PEAK 23(12Q15) MUTATED AMP PEAK 23(12Q15) WILD-TYPE 
                          73                          197 
  AMP PEAK 23(12Q15) MUTATED AMP PEAK 23(12Q15) WILD-TYPE 
                          26                           62 
$`AMP PEAK 23(12Q15) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KW TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM 
       22.29        11.97         4.83        40.08         2.66         6.74 
TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20X 
        6.58        19.04        17.88         5.06         5.06         8.25 
TCGA-BT-A2LB TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CU-A0YO 
        5.59         2.07        28.70         9.99        23.01         4.90 
TCGA-CU-A0YR TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        7.20         1.84         2.53         2.14        66.41        18.41 
TCGA-DK-A1AC TCGA-DK-A2I4 TCGA-DK-A3WX TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 
      130.88       123.85        10.55        64.18        67.36        15.68 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6ME TCGA-FD-A43Y TCGA-FD-A5BX TCGA-FD-A5BZ 
        0.59         0.56        12.99        12.13         5.69        27.45 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TG 
       49.68         6.28         6.38        18.81         9.30         2.66 
TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3VY 
       15.19         6.48        61.94         5.69        35.24         0.85 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3QH 
        2.89         2.24        14.07        11.31         6.41         7.79 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        4.14         6.67         6.41         1.51         6.74        38.60 
TCGA-HQ-A2OF TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A83P TCGA-MV-A51V TCGA-S5-A6DX 
        3.06         3.45         4.67         6.38        13.48         0.85 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN4 
       64.80        79.66        11.90         2.96         6.77        27.06 
TCGA-YF-AA3M 
        9.04 

$`AMP PEAK 23(12Q15) WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0YX 
       84.00       103.50        98.33         7.33        12.39        11.93 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W 
       32.84        12.16        19.50        14.89        14.96         8.35 
TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42F 
       17.16         3.65         4.67        12.82        15.42        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S 
        8.98         1.94         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-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB 
        5.46         5.19        16.31         9.34        19.00         8.91 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
        7.79        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-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 
      140.81        48.00        17.98        41.56        76.60        41.06 
TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       30.67        43.59        15.35        26.17        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF 
        0.49         0.53         0.66         1.38         0.82        14.33 
TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
        1.22         0.46        12.89        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-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       22.45         6.12        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-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-A5BY TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TD 
        6.84         6.87         2.66         4.83        50.66         6.71 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 
        4.11         2.07         2.20         4.01        10.85         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2ES 
        3.48         4.08         3.25        30.61        26.93        17.26 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO 
        7.04        20.12        52.67         6.94        19.46        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 
        4.50        15.91        17.75         1.12         2.66         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        2.10         3.12        20.98         2.20         7.36         6.41 
TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
        7.59         2.04        27.09         5.62         4.73        10.65 
TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A40G TCGA-GV-A6ZA 
        4.41         6.15         5.69         7.63        19.07        11.54 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        9.01         8.22         8.75         2.50         6.48        10.52 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
        1.74         1.81         4.27         6.35         3.45        11.80 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC 
       12.23        16.67        14.24         3.75        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI 
       88.93        97.45        56.19        15.35         1.87        17.88 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ 
       16.27        66.64         2.10        92.98        10.82        54.90 
TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN5 
        7.63        91.73         8.32        56.48        30.94        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
        3.88        10.36         4.83         0.66         7.96 

  AMP PEAK 23(12Q15) MUTATED AMP PEAK 23(12Q15) WILD-TYPE 
                        0.56                         0.07 
  AMP PEAK 23(12Q15) MUTATED AMP PEAK 23(12Q15) WILD-TYPE 
                      130.88                       140.81 
  AMP PEAK 23(12Q15) MUTATED AMP PEAK 23(12Q15) WILD-TYPE 
                        7.20                        10.49 
[1] "0.6 - 130.9 (7.2)"  "0.1 - 140.8 (10.5)"
[1] "hr=" "1.2"
D23V2, continuous
                              vv
clus                           STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 23(12Q15) MUTATED          0       1       26        27       23
  AMP PEAK 23(12Q15) WILD-TYPE        1       1       60        66       69
D23V3, multiclass
           clus
vv          AMP PEAK 23(12Q15) MUTATED AMP PEAK 23(12Q15) WILD-TYPE
  STAGE 0A                           0                            1
  STAGE I                            1                            1
  STAGE II                          26                           60
  STAGE III                         27                           66
  STAGE IV                          23                           69
[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(12Q15) MUTATED         23  34  13
  AMP PEAK 23(12Q15) WILD-TYPE       59 102  26
D23V4, multiclass
          clus
vv         AMP PEAK 23(12Q15) MUTATED AMP PEAK 23(12Q15) WILD-TYPE
  T0+T1+T2                         23                           59
  T3                               34                          102
  T4                               13                           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 23(12Q15) MUTATED    46   7  16   0
  AMP PEAK 23(12Q15) WILD-TYPE 120  21  39   7
D23V5, multiclass
    clus
vv   AMP PEAK 23(12Q15) MUTATED AMP PEAK 23(12Q15) WILD-TYPE
  N0                         46                          120
  N1                          7                           21
  N2                         16                           39
  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 23(12Q15) MUTATED    41   1  35
  AMP PEAK 23(12Q15) WILD-TYPE  88   6 106
D23V6, multiclass
    clus
vv   AMP PEAK 23(12Q15) MUTATED AMP PEAK 23(12Q15) WILD-TYPE
  M0                         41                           88
  M1                          1                            6
  MX                         35                          106
[1] 3 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(12Q15) MUTATED    24  54
  AMP PEAK 23(12Q15) WILD-TYPE  53 147
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 23(12Q15) MUTATED     24   54
  AMP PEAK 23(12Q15) WILD-TYPE   53  147
        clus
vv       AMP PEAK 23(12Q15) MUTATED AMP PEAK 23(12Q15) WILD-TYPE
  FEMALE                         24                           53
  MALE                           54                          147
[1] 2 2
[1] FALSE
D23V8, continuous
D23V9, continuous
D23V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(12Q15) MUTATED      11                         4    56
  AMP PEAK 23(12Q15) WILD-TYPE    20                         9   159
D23V11, multiclass
                           clus
vv                          AMP PEAK 23(12Q15) MUTATED
  ASIAN                                             11
  BLACK OR AFRICAN AMERICAN                          4
  WHITE                                             56
                           clus
vv                          AMP PEAK 23(12Q15) WILD-TYPE
  ASIAN                                               20
  BLACK OR AFRICAN AMERICAN                            9
  WHITE                                              159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V12, binary
                              cls
clus                             0   1
  AMP PEAK 23(12Q15) MUTATED     1  70
  AMP PEAK 23(12Q15) WILD-TYPE   4 188
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 23(12Q15) MUTATED      1   70
  AMP PEAK 23(12Q15) WILD-TYPE    4  188
                        clus
vv                       AMP PEAK 23(12Q15) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         70
                        clus
vv                       AMP PEAK 23(12Q15) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          188
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 24(13Q22.1) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 24(13Q22.1) MUTATED    56  25
  AMP PEAK 24(13Q22.1) WILD-TYPE 126  63
  AMP PEAK 24(13Q22.1) MUTATED AMP PEAK 24(13Q22.1) WILD-TYPE 
                            81                            189 
  AMP PEAK 24(13Q22.1) MUTATED AMP PEAK 24(13Q22.1) WILD-TYPE 
                            25                             63 
$`AMP PEAK 24(13Q22.1) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KT TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N 
       22.29        98.33         6.74         6.58        19.04        32.84 
TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-C4-A0F0 TCGA-CF-A1HR 
       19.50        14.96         3.65        12.82         1.94         0.46 
TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3YL TCGA-DK-A2HX TCGA-DK-A2I6 
        0.43        12.92         7.20        16.31         1.81        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-A3X1 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E7-A541 
       48.00        67.36        15.68        41.06        43.59         0.59 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3SM TCGA-FD-A43X TCGA-FD-A5BT 
        8.94         6.87        11.93         6.12         3.62        11.01 
TCGA-FD-A62O TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3ZE 
        4.83         9.30         4.11         2.66         2.20         3.48 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-AA3B TCGA-GC-A3OO TCGA-GC-A3RB 
        6.48        61.94         5.69        52.67        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A42R 
       15.91        17.75         2.10        20.98         6.41        11.31 
TCGA-GU-AATO TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK 
       10.65         6.15         5.69         7.63         7.79         6.67 
TCGA-H4-A2HQ TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC 
        6.74         9.01         8.22         3.45         4.67         6.48 
TCGA-K4-A6MB TCGA-LC-A66R TCGA-MV-A51V TCGA-R3-A69X TCGA-XF-A8HC TCGA-XF-A8HD 
        4.27         6.35        13.48        14.24         6.58        88.93 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9T0 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAML 
       56.19        15.35        26.27         2.10        10.82         7.63 
TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAN0 
       91.73         6.77        56.48 

$`AMP PEAK 24(13Q22.1) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-BL-A0C8 TCGA-BL-A13I 
       11.97        84.00       103.50         4.83        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20R 
        2.66        12.39        11.93        12.16        17.88         5.06 
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-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-A0F6 TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        8.98        23.01         0.69         0.13         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU 
        0.07         0.10         0.10         4.90         5.46         5.19 
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        66.41        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-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IM TCGA-DK-A3IN 
       15.62        10.59         7.79       123.85         7.82         8.22 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV 
        9.67         8.28        10.55       140.81        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       41.56        76.60        30.67        15.35        26.17        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-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 
        0.82        12.99        14.33         1.22         0.46        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
       15.68         4.01        12.43        15.88        45.93        24.30 
TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       22.45        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-A43Y 
        1.97        22.98        14.93        14.96        14.93        12.13 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       13.38        37.15         6.87         5.36         5.69         6.84 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S 
       27.45         6.87        49.68         2.66         6.28         6.38 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TI TCGA-FD-A6TK 
       50.66        18.81         6.71         2.07         4.01        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EL 
       15.19         7.13         4.08         3.25        30.61        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C 
       35.24        17.26         7.04        20.12         0.85         6.94 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 
       19.46         2.89         2.24        14.07         1.12         2.66 
TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A762 
        7.73         3.12         2.20         7.36         7.59         2.04 
TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QI 
       27.09         5.62         4.73         4.41         6.41         4.14 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF 
        6.41        19.07        11.54         1.51        38.60         3.06 
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-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-A6DX TCGA-S5-AA26 
        3.45        11.80        12.23        16.67         0.85         3.75 
TCGA-XF-A8HB TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI 
       45.04        97.45         1.87        17.88        64.80        79.66 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 
       11.90        23.64        21.04        28.24        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-AAME TCGA-XF-AAMJ TCGA-XF-AAMT TCGA-XF-AAMW 
       16.27        66.64        92.98        54.90         2.96         8.32 
TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       30.94        27.06        75.39         3.88        10.36         4.83 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        0.66         7.96         9.04 

  AMP PEAK 24(13Q22.1) MUTATED AMP PEAK 24(13Q22.1) WILD-TYPE 
                          0.43                           0.07 
  AMP PEAK 24(13Q22.1) MUTATED AMP PEAK 24(13Q22.1) WILD-TYPE 
                         98.33                         140.81 
  AMP PEAK 24(13Q22.1) MUTATED AMP PEAK 24(13Q22.1) WILD-TYPE 
                          8.94                           9.67 
[1] "0.4 - 98.3 (8.9)"  "0.1 - 140.8 (9.7)"
[1] "hr=" "1.1"
D24V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 24(13Q22.1) MUTATED          0       0       23        27       31
  AMP PEAK 24(13Q22.1) WILD-TYPE        1       2       63        66       61
D24V3, multiclass
           clus
vv          AMP PEAK 24(13Q22.1) MUTATED AMP PEAK 24(13Q22.1) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              0                              2
  STAGE II                            23                             63
  STAGE III                           27                             66
  STAGE IV                            31                             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 24(13Q22.1) MUTATED         22 42 12
  AMP PEAK 24(13Q22.1) WILD-TYPE       60 94 27
D24V4, multiclass
          clus
vv         AMP PEAK 24(13Q22.1) MUTATED AMP PEAK 24(13Q22.1) WILD-TYPE
  T0+T1+T2                           22                             60
  T3                                 42                             94
  T4                                 12                             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 24(13Q22.1) MUTATED    47   9  20   3
  AMP PEAK 24(13Q22.1) WILD-TYPE 119  19  35   4
D24V5, multiclass
    clus
vv   AMP PEAK 24(13Q22.1) MUTATED AMP PEAK 24(13Q22.1) WILD-TYPE
  N0                           47                            119
  N1                            9                             19
  N2                           20                             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
  AMP PEAK 24(13Q22.1) MUTATED    41   3  39
  AMP PEAK 24(13Q22.1) WILD-TYPE  88   4 102
D24V6, multiclass
    clus
vv   AMP PEAK 24(13Q22.1) MUTATED AMP PEAK 24(13Q22.1) WILD-TYPE
  M0                           41                             88
  M1                            3                              4
  MX                           39                            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"
D24V7, binary
                                cls
clus                               0   1
  AMP PEAK 24(13Q22.1) MUTATED    17  66
  AMP PEAK 24(13Q22.1) WILD-TYPE  60 135
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(13Q22.1) MUTATED     17   66
  AMP PEAK 24(13Q22.1) WILD-TYPE   60  135
        clus
vv       AMP PEAK 24(13Q22.1) MUTATED AMP PEAK 24(13Q22.1) WILD-TYPE
  FEMALE                           17                             60
  MALE                             66                            135
[1] 2 2
[1] FALSE
D24V8, continuous
D24V9, continuous
D24V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(13Q22.1) MUTATED       5                         4    67
  AMP PEAK 24(13Q22.1) WILD-TYPE    26                         9   148
D24V11, multiclass
                           clus
vv                          AMP PEAK 24(13Q22.1) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               67
                           clus
vv                          AMP PEAK 24(13Q22.1) WILD-TYPE
  ASIAN                                                 26
  BLACK OR AFRICAN AMERICAN                              9
  WHITE                                                148
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V12, binary
                                cls
clus                               0   1
  AMP PEAK 24(13Q22.1) MUTATED     0  77
  AMP PEAK 24(13Q22.1) WILD-TYPE   5 181
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(13Q22.1) MUTATED      0   77
  AMP PEAK 24(13Q22.1) WILD-TYPE    5  181
                        clus
vv                       AMP PEAK 24(13Q22.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           77
                        clus
vv                       AMP PEAK 24(13Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            181
[1] 2 2
[1] FALSE

Clustering(25) Variable = AMP PEAK 25(16P13.2) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 25(16P13.2) MUTATED    39  21
  AMP PEAK 25(16P13.2) WILD-TYPE 143  67
  AMP PEAK 25(16P13.2) MUTATED AMP PEAK 25(16P13.2) WILD-TYPE 
                            60                            210 
  AMP PEAK 25(16P13.2) MUTATED AMP PEAK 25(16P13.2) WILD-TYPE 
                            21                             67 
$`AMP PEAK 25(16P13.2) MUTATED`
TCGA-2F-A9KW TCGA-BT-A0S7 TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-C4-A0EZ 
        4.83         6.58         5.06         8.25        17.16         8.98 
TCGA-CF-A47X TCGA-CU-A0YR TCGA-CU-A3QU TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3IM 
        0.10         7.20         5.19         7.79         3.98         7.82 
TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6B1 TCGA-E5-A2PC 
        8.22        50.27         9.67        48.00        67.36        43.59 
TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A6ME TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SR 
       15.35         0.49        12.99        45.93        24.30        19.79 
TCGA-FD-A43U TCGA-FD-A5BY TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI 
       14.93         6.84         6.71         2.07         2.66         4.01 
TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
        3.48         3.25        35.24        20.12         0.85        52.67 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A766 TCGA-GV-A3JV 
        2.89         2.24         7.36         6.41         5.62         4.41 
TCGA-GV-A3JZ TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WU 
        5.69         6.74        38.60         3.06         9.01         3.45 
TCGA-K4-A4AB TCGA-K4-A83P TCGA-LC-A66R TCGA-R3-A69X TCGA-S5-A6DX TCGA-XF-A9SZ 
        2.50         6.38         6.35        14.24         0.85        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMX 
       26.27        66.64         2.10         7.63        91.73         6.77 

$`AMP PEAK 25(16P13.2) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-BL-A0C8 
       22.29        11.97        84.00       103.50        98.33        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         2.66         6.74        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-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
       14.96         8.35         5.59         3.65         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
        2.07        15.42        28.70         9.99        28.41         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-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ 
        0.10         0.07         0.10        12.92         4.90         5.46 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84         9.34         2.53         2.14        66.41 
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-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 
       17.62        15.62         1.81        10.59       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX 
        2.20        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-A6B2 
      140.81        17.98        64.18        41.56        76.60        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       41.06        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-E7-A6MF 
        0.59         0.56         0.66         1.38         0.82        14.33 
TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
        1.22         0.46        12.89        15.68         8.94         6.87 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM 
        4.01        12.43        11.93        15.88        22.45         6.12 
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-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       14.93        14.96         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-A6TA 
       49.68         2.66         4.83         6.28         6.38        50.66 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 
       18.81         9.30         4.11         2.20        10.85        15.19 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        7.13         4.08         6.48        61.94        30.61         5.69 
TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO 
       26.93        17.26         7.04         6.94        19.46        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        4.50        15.91        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-A42Q 
        7.73         2.10         3.12        20.98         2.20         7.59 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JW 
       11.31         2.04        27.09         4.73        10.65         6.41 
TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
        6.15         7.63         7.79         4.14         6.67         6.41 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WV 
       19.07        11.54         1.51         8.22         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-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-XF-A8HB 
       11.80        13.48        12.23        16.67         3.75        45.04 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH 
        6.58        88.93        97.45        56.19        15.35         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
       17.88        64.80        79.66        11.90        23.64        21.04 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ 
       18.90         2.24        16.27        92.98        10.82        54.90 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
        2.96         8.32        56.48        30.94        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        3.88        10.36         4.83         0.66         7.96         9.04 

  AMP PEAK 25(16P13.2) MUTATED AMP PEAK 25(16P13.2) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK 25(16P13.2) MUTATED AMP PEAK 25(16P13.2) WILD-TYPE 
                         91.73                         140.81 
  AMP PEAK 25(16P13.2) MUTATED AMP PEAK 25(16P13.2) WILD-TYPE 
                         7.020                         10.735 
[1] "0.1 - 91.7 (7.0)"   "0.1 - 140.8 (10.7)"
[1] "hr=" "1.3"
D25V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 25(16P13.2) MUTATED          0       0       14        19       26
  AMP PEAK 25(16P13.2) WILD-TYPE        1       2       72        74       66
D25V3, multiclass
           clus
vv          AMP PEAK 25(16P13.2) MUTATED AMP PEAK 25(16P13.2) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              0                              2
  STAGE II                            14                             72
  STAGE III                           19                             74
  STAGE IV                            26                             66
[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(16P13.2) MUTATED         16  24  15
  AMP PEAK 25(16P13.2) WILD-TYPE       66 112  24
D25V4, multiclass
          clus
vv         AMP PEAK 25(16P13.2) MUTATED AMP PEAK 25(16P13.2) WILD-TYPE
  T0+T1+T2                           16                             66
  T3                                 24                            112
  T4                                 15                             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
  AMP PEAK 25(16P13.2) MUTATED    28   9  14   3
  AMP PEAK 25(16P13.2) WILD-TYPE 138  19  41   4
D25V5, multiclass
    clus
vv   AMP PEAK 25(16P13.2) MUTATED AMP PEAK 25(16P13.2) WILD-TYPE
  N0                           28                            138
  N1                            9                             19
  N2                           14                             41
  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(16P13.2) MUTATED    24   4  31
  AMP PEAK 25(16P13.2) WILD-TYPE 105   3 110
D25V6, multiclass
    clus
vv   AMP PEAK 25(16P13.2) MUTATED AMP PEAK 25(16P13.2) WILD-TYPE
  M0                           24                            105
  M1                            4                              3
  MX                           31                            110
[1] 3 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(16P13.2) MUTATED    17  43
  AMP PEAK 25(16P13.2) WILD-TYPE  60 158
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(16P13.2) MUTATED     17   43
  AMP PEAK 25(16P13.2) WILD-TYPE   60  158
        clus
vv       AMP PEAK 25(16P13.2) MUTATED AMP PEAK 25(16P13.2) WILD-TYPE
  FEMALE                           17                             60
  MALE                             43                            158
[1] 2 2
[1] FALSE
D25V8, continuous
D25V9, continuous
D25V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(16P13.2) MUTATED       4                         3    48
  AMP PEAK 25(16P13.2) WILD-TYPE    27                        10   167
D25V11, multiclass
                           clus
vv                          AMP PEAK 25(16P13.2) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               48
                           clus
vv                          AMP PEAK 25(16P13.2) WILD-TYPE
  ASIAN                                                 27
  BLACK OR AFRICAN AMERICAN                             10
  WHITE                                                167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V12, binary
                                cls
clus                               0   1
  AMP PEAK 25(16P13.2) MUTATED     0  55
  AMP PEAK 25(16P13.2) WILD-TYPE   5 203
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(16P13.2) MUTATED      0   55
  AMP PEAK 25(16P13.2) WILD-TYPE    5  203
                        clus
vv                       AMP PEAK 25(16P13.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           55
                        clus
vv                       AMP PEAK 25(16P13.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            203
[1] 2 2
[1] FALSE

Clustering(26) Variable = AMP PEAK 26(16P11.2) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 26(16P11.2) MUTATED    46  25
  AMP PEAK 26(16P11.2) WILD-TYPE 136  63
  AMP PEAK 26(16P11.2) MUTATED AMP PEAK 26(16P11.2) WILD-TYPE 
                            71                            199 
  AMP PEAK 26(16P11.2) MUTATED AMP PEAK 26(16P11.2) WILD-TYPE 
                            25                             63 
$`AMP PEAK 26(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-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3ZE TCGA-FT-A3EE 
        6.71         2.07         2.66         4.01         3.48         3.25 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-AA3B TCGA-GC-A3BM 
        6.48        61.94        35.24        20.12        52.67         2.89 
TCGA-GC-A3I6 TCGA-GC-A3YS TCGA-GD-A76B TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ 
        2.24         1.12         7.36         4.41         6.41         5.69 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
        6.74         3.06         9.01         8.75         3.45         2.50 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-R3-A69X TCGA-S5-A6DX TCGA-XF-A8HC TCGA-XF-A9SZ 
        4.27         6.38        14.24         0.85         6.58        28.24 
TCGA-XF-A9T5 TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAN0 
       66.64         7.63        91.73         6.77        56.48 

$`AMP PEAK 26(16P11.2) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
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        66.41        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        41.56        76.60        67.36 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A541 
       41.06        30.67        24.66         0.10         0.53         0.59 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV 
        0.66         1.38         0.82        12.99        14.33         1.22 
TCGA-E7-A7XN TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
        0.46        15.68         8.94         4.01        12.43        11.93 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       15.88        45.93        22.45         6.12        12.82         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       13.18        46.78         1.97        22.98        14.93        14.96 
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-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
       27.45         6.87        49.68         2.66         4.83         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TH 
        6.38        50.66        18.81         9.30         4.11         2.20 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-G2-A2EJ TCGA-G2-A2EK 
       10.85        15.19         7.13         4.08        30.61         5.69 
TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3F 
       26.93        17.26         7.04         0.85         6.94        19.46 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 
       15.81         4.50        15.91        14.07        17.75         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-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 
        7.59        11.31         2.04        27.09         5.62         4.73 
TCGA-GU-AATO TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       10.65         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-HQ-A5NE 
        6.41        19.07        11.54         1.51        38.60         8.22 
TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-LC-A66R 
        4.67         6.48        10.52         1.74         1.81         6.35 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 
        3.45        11.80        13.48        12.23        16.67         3.75 
TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH 
       45.04        88.93        97.45        56.19        15.35         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
       17.88        64.80        79.66        11.90        23.64        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME 
       26.27        18.90         2.24        16.27         2.10        92.98 
TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN1 TCGA-XF-AAN4 
       10.82        54.90         2.96         8.32        30.94        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39         3.88        10.36         4.83         0.66         7.96 
TCGA-YF-AA3M 
        9.04 

  AMP PEAK 26(16P11.2) MUTATED AMP PEAK 26(16P11.2) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK 26(16P11.2) MUTATED AMP PEAK 26(16P11.2) WILD-TYPE 
                         91.73                         140.81 
  AMP PEAK 26(16P11.2) MUTATED AMP PEAK 26(16P11.2) WILD-TYPE 
                          6.87                          10.82 
[1] "0.1 - 91.7 (6.9)"   "0.1 - 140.8 (10.8)"
[1] "hr=" "1.3"
D26V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 26(16P11.2) MUTATED          0       0       16        21       34
  AMP PEAK 26(16P11.2) WILD-TYPE        1       2       70        72       58
D26V3, multiclass
           clus
vv          AMP PEAK 26(16P11.2) MUTATED AMP PEAK 26(16P11.2) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              0                              2
  STAGE II                            16                             70
  STAGE III                           21                             72
  STAGE IV                            34                             58
[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(16P11.2) MUTATED         16  33  16
  AMP PEAK 26(16P11.2) WILD-TYPE       66 103  23
D26V4, multiclass
          clus
vv         AMP PEAK 26(16P11.2) MUTATED AMP PEAK 26(16P11.2) WILD-TYPE
  T0+T1+T2                           16                             66
  T3                                 33                            103
  T4                                 16                             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 26(16P11.2) MUTATED    33  13  17   3
  AMP PEAK 26(16P11.2) WILD-TYPE 133  15  38   4
D26V5, multiclass
    clus
vv   AMP PEAK 26(16P11.2) MUTATED AMP PEAK 26(16P11.2) WILD-TYPE
  N0                           33                            133
  N1                           13                             15
  N2                           17                             38
  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 26(16P11.2) MUTATED    33   4  34
  AMP PEAK 26(16P11.2) WILD-TYPE  96   3 107
D26V6, multiclass
    clus
vv   AMP PEAK 26(16P11.2) MUTATED AMP PEAK 26(16P11.2) WILD-TYPE
  M0                           33                             96
  M1                            4                              3
  MX                           34                            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"
D26V7, binary
                                cls
clus                               0   1
  AMP PEAK 26(16P11.2) MUTATED    21  50
  AMP PEAK 26(16P11.2) WILD-TYPE  56 151
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(16P11.2) MUTATED     21   50
  AMP PEAK 26(16P11.2) WILD-TYPE   56  151
        clus
vv       AMP PEAK 26(16P11.2) MUTATED AMP PEAK 26(16P11.2) WILD-TYPE
  FEMALE                           21                             56
  MALE                             50                            151
[1] 2 2
[1] FALSE
D26V8, continuous
D26V9, continuous
D26V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 26(16P11.2) MUTATED       4                         3    58
  AMP PEAK 26(16P11.2) WILD-TYPE    27                        10   157
D26V11, multiclass
                           clus
vv                          AMP PEAK 26(16P11.2) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               58
                           clus
vv                          AMP PEAK 26(16P11.2) WILD-TYPE
  ASIAN                                                 27
  BLACK OR AFRICAN AMERICAN                             10
  WHITE                                                157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V12, binary
                                cls
clus                               0   1
  AMP PEAK 26(16P11.2) MUTATED     0  66
  AMP PEAK 26(16P11.2) WILD-TYPE   5 192
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(16P11.2) MUTATED      0   66
  AMP PEAK 26(16P11.2) WILD-TYPE    5  192
                        clus
vv                       AMP PEAK 26(16P11.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           66
                        clus
vv                       AMP PEAK 26(16P11.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            192
[1] 2 2
[1] FALSE

Clustering(27) Variable = AMP PEAK 27(16Q22.1) MUTATION ANALYSIS
D27V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 27(16Q22.1) MUTATED    51  25
  AMP PEAK 27(16Q22.1) WILD-TYPE 131  63
  AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE 
                            76                            194 
  AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE 
                            25                             63 
$`AMP PEAK 27(16Q22.1) MUTATED`
TCGA-2F-A9KP TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20N 
       11.97        98.33         4.83         2.66         6.58        32.84 
TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A42C 
        5.06         5.06         8.25        17.16        12.82        28.70 
TCGA-BT-A42E TCGA-C4-A0EZ TCGA-CF-A1HS TCGA-CF-A47X TCGA-CU-A3KJ TCGA-DK-A1A5 
        9.99         8.98         0.43         0.10         5.46         2.14 
TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3X1 
        7.79         3.98         7.82        50.27         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-A3SJ TCGA-FD-A3SL TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BT TCGA-FD-A5BV 
       24.30        22.45        14.93        12.13        11.01         5.36 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TC 
        6.84        27.45         6.87         6.28         6.38         9.30 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3ZE TCGA-FT-A3EE 
        2.07         2.66         4.01        10.85         3.48         3.25 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GC-A3BM TCGA-GC-A3I6 
       35.24        17.26         0.85        52.67         2.89         2.24 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A762 
        1.12         2.66         7.73        20.98         7.36         2.04 
TCGA-GU-AATO TCGA-GV-A3JW TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
       10.65         6.41         6.74         3.06         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A6MB TCGA-LC-A66R TCGA-R3-A69X 
        8.75         3.45         2.50         4.27         6.35        14.24 
TCGA-S5-A6DX TCGA-XF-A9T3 TCGA-XF-AAMR TCGA-XF-AAMX 
        0.85         2.24        91.73         6.77 

$`AMP PEAK 27(16Q22.1) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM 
       22.29        84.00       103.50        40.08         7.33         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       12.39        11.93        19.04        12.16        17.88        19.50 
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-A3PK TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
        2.07        15.42        28.41         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-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-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
        9.34         2.53        66.41        18.41        19.00         8.91 
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-A3IN TCGA-DK-A3IQ 
       10.59       123.85        87.32         2.20         8.22        10.49 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 
       21.30        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 
       41.56        76.60        67.36        41.06        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-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN 
        0.66         1.38         0.82        12.99        14.33         0.46 
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-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       15.88        45.93         6.12        12.82         5.52        13.18 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       46.78        19.79         1.97        22.98        14.96        14.93 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C1 
        3.62        13.38        37.15         6.87         5.69        49.68 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE 
        2.66         4.83        50.66        18.81         6.71         4.11 
TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF 
        2.20        15.19         7.13         4.08         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C 
       30.61         5.69        26.93         7.04        20.12         6.94 
TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
       19.46        15.81         4.50        15.91        14.07        17.75 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12         2.20         6.41         7.59        11.31 
TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ 
       27.09         5.62         4.73         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-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R 
       11.54         1.51        38.60         4.67         6.48        10.52 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
        1.74         1.81         6.38         3.45        11.80        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
       12.23        16.67         3.75        45.04         6.58        88.93 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH 
       97.45        56.19        15.35         1.87        17.88        64.80 
TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       79.66        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF 
       18.90        16.27        66.64         2.10        92.98        10.82 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 
       54.90         7.63         2.96         8.32        56.48        30.94 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39         3.88        10.36         4.83         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M 
        7.96         9.04 

  AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE 
                         98.33                         140.81 
  AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE 
                         7.545                         11.425 
[1] "0.1 - 98.3 (7.5)"   "0.1 - 140.8 (11.4)"
[1] "hr=" "1.3"
D27V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 27(16Q22.1) MUTATED          0       0       18        28       29
  AMP PEAK 27(16Q22.1) WILD-TYPE        1       2       68        65       63
D27V3, multiclass
           clus
vv          AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              0                              2
  STAGE II                            18                             68
  STAGE III                           28                             65
  STAGE IV                            29                             63
[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(16Q22.1) MUTATED         15 39 16
  AMP PEAK 27(16Q22.1) WILD-TYPE       67 97 23
D27V4, multiclass
          clus
vv         AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE
  T0+T1+T2                           15                             67
  T3                                 39                             97
  T4                                 16                             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 27(16Q22.1) MUTATED    42   9  16   4
  AMP PEAK 27(16Q22.1) WILD-TYPE 124  19  39   3
D27V5, multiclass
    clus
vv   AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE
  N0                           42                            124
  N1                            9                             19
  N2                           16                             39
  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 27(16Q22.1) MUTATED    31   5  39
  AMP PEAK 27(16Q22.1) WILD-TYPE  98   2 102
D27V6, multiclass
    clus
vv   AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE
  M0                           31                             98
  M1                            5                              2
  MX                           39                            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"
D27V7, binary
                                cls
clus                               0   1
  AMP PEAK 27(16Q22.1) MUTATED    27  49
  AMP PEAK 27(16Q22.1) WILD-TYPE  50 152
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(16Q22.1) MUTATED     27   49
  AMP PEAK 27(16Q22.1) WILD-TYPE   50  152
        clus
vv       AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE
  FEMALE                           27                             50
  MALE                             49                            152
[1] 2 2
[1] FALSE
D27V8, continuous
D27V9, continuous
D27V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 27(16Q22.1) MUTATED       4                         5    58
  AMP PEAK 27(16Q22.1) WILD-TYPE    27                         8   157
D27V11, multiclass
                           clus
vv                          AMP PEAK 27(16Q22.1) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               58
                           clus
vv                          AMP PEAK 27(16Q22.1) WILD-TYPE
  ASIAN                                                 27
  BLACK OR AFRICAN AMERICAN                              8
  WHITE                                                157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V12, binary
                                cls
clus                               0   1
  AMP PEAK 27(16Q22.1) MUTATED     0  69
  AMP PEAK 27(16Q22.1) WILD-TYPE   5 189
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(16Q22.1) MUTATED      0   69
  AMP PEAK 27(16Q22.1) WILD-TYPE    5  189
                        clus
vv                       AMP PEAK 27(16Q22.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           69
                        clus
vv                       AMP PEAK 27(16Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            189
[1] 2 2
[1] FALSE

Clustering(28) Variable = AMP PEAK 28(17P11.2) MUTATION ANALYSIS
D28V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 28(17P11.2) MUTATED    36  24
  AMP PEAK 28(17P11.2) WILD-TYPE 146  64
  AMP PEAK 28(17P11.2) MUTATED AMP PEAK 28(17P11.2) WILD-TYPE 
                            60                            210 
  AMP PEAK 28(17P11.2) MUTATED AMP PEAK 28(17P11.2) WILD-TYPE 
                            24                             64 
$`AMP PEAK 28(17P11.2) MUTATED`
TCGA-2F-A9KP TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       11.97         6.74         6.58        19.50         5.06        14.96 
TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C TCGA-C4-A0EZ 
        8.35        17.16         3.65        12.82        28.70         8.98 
TCGA-CF-A1HR TCGA-CU-A0YR TCGA-CU-A3YL TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        0.46         7.20        16.31         2.14        66.41        18.41 
TCGA-DK-A1AD TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A6B1 TCGA-DK-A6B6 
      112.44         7.79         2.20         7.82        67.36        30.67 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-FD-A3B6 TCGA-FD-A3SP TCGA-FD-A3SQ 
        0.59         0.56         1.38         6.87        13.18        46.78 
TCGA-FD-A5BT TCGA-FD-A5C0 TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FJ-A3ZE 
       11.01         6.87         4.11         2.07         2.20         3.48 
TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A3VY TCGA-GC-A3YS TCGA-GD-A3OP 
        3.25        30.61        35.24         0.85         1.12         2.10 
TCGA-GD-A76B TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QH 
        7.36        10.65         4.41         6.41         5.69         7.79 
TCGA-GV-A3QI TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A6FZ TCGA-S5-A6DX TCGA-XF-A8HI 
        4.14         3.45         4.67         1.81         0.85        17.88 
TCGA-XF-A9SI TCGA-XF-A9SX TCGA-XF-A9T0 TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMX 
       79.66        23.64        26.27         7.63         2.96         6.77 

$`AMP PEAK 28(17P11.2) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 
       22.29        84.00       103.50        98.33         4.83        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        7.33         2.66        12.39        11.93        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB 
       12.16        17.88        14.89         5.06         8.25         5.59 
TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
        4.67         2.07        15.42         9.99        28.41         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-A0YO TCGA-CU-A3KJ 
        0.07         0.10         0.10        12.92         4.90         5.46 
TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1AA TCGA-DK-A1AB 
        5.19         1.84         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-A2I1 
      130.88        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
      123.85        87.32         3.98         8.22        10.49        50.27 
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-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 
       48.00        17.98        64.18        41.56        76.60        15.68 
TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       41.06        43.59        15.35        26.17        24.66         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.49         0.53         0.66         0.82        12.99        14.33 
TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 
        1.22         0.46        12.89        15.68         8.94         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-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        6.12        12.82         5.52        19.79         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-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-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-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK 
       18.81         9.30         6.71         2.66         4.01        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EK 
       15.19         7.13         4.08         6.48        61.94         5.69 
TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C 
       26.93        17.26         7.04        20.12        52.67         6.94 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       19.46         2.89         2.24        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS 
       14.07        17.75         2.66         7.73         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        2.20         6.41         7.59        11.31         2.04        27.09 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E 
        5.62         4.73         6.15         7.63         6.67         6.41 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.07        11.54         1.51         6.74        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        9.01         8.22         8.75         2.50         6.48        10.52 
TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
        1.74         4.27         6.38         6.35         3.45        11.80 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 TCGA-XF-A8HB 
       13.48        12.23        16.67        14.24         3.75        45.04 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH 
        6.58        88.93        97.45        56.19        15.35         1.87 
TCGA-XF-A9SH TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 
       64.80        11.90        21.04        28.24        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ 
       16.27        66.64         2.10        92.98        10.82        54.90 
TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
       91.73         8.32        56.48        30.94        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        3.88        10.36         4.83         0.66         7.96         9.04 

  AMP PEAK 28(17P11.2) MUTATED AMP PEAK 28(17P11.2) WILD-TYPE 
                          0.46                           0.07 
  AMP PEAK 28(17P11.2) MUTATED AMP PEAK 28(17P11.2) WILD-TYPE 
                        112.44                         140.81 
  AMP PEAK 28(17P11.2) MUTATED AMP PEAK 28(17P11.2) WILD-TYPE 
                         7.035                         10.570 
[1] "0.5 - 112.4 (7.0)"  "0.1 - 140.8 (10.6)"
[1] "hr=" "1.6"
D28V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 28(17P11.2) MUTATED          0       0       17        17       26
  AMP PEAK 28(17P11.2) WILD-TYPE        1       2       69        76       66
D28V3, multiclass
           clus
vv          AMP PEAK 28(17P11.2) MUTATED AMP PEAK 28(17P11.2) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              0                              2
  STAGE II                            17                             69
  STAGE III                           17                             76
  STAGE IV                            26                             66
[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(17P11.2) MUTATED         15  32   8
  AMP PEAK 28(17P11.2) WILD-TYPE       67 104  31
D28V4, multiclass
          clus
vv         AMP PEAK 28(17P11.2) MUTATED AMP PEAK 28(17P11.2) WILD-TYPE
  T0+T1+T2                           15                             67
  T3                                 32                            104
  T4                                  8                             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 28(17P11.2) MUTATED    30   6  17   4
  AMP PEAK 28(17P11.2) WILD-TYPE 136  22  38   3
D28V5, multiclass
    clus
vv   AMP PEAK 28(17P11.2) MUTATED AMP PEAK 28(17P11.2) WILD-TYPE
  N0                           30                            136
  N1                            6                             22
  N2                           17                             38
  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 28(17P11.2) MUTATED    25   3  32
  AMP PEAK 28(17P11.2) WILD-TYPE 104   4 109
D28V6, multiclass
    clus
vv   AMP PEAK 28(17P11.2) MUTATED AMP PEAK 28(17P11.2) WILD-TYPE
  M0                           25                            104
  M1                            3                              4
  MX                           32                            109
[1] 3 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(17P11.2) MUTATED    19  42
  AMP PEAK 28(17P11.2) WILD-TYPE  58 159
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(17P11.2) MUTATED     19   42
  AMP PEAK 28(17P11.2) WILD-TYPE   58  159
        clus
vv       AMP PEAK 28(17P11.2) MUTATED AMP PEAK 28(17P11.2) WILD-TYPE
  FEMALE                           19                             58
  MALE                             42                            159
[1] 2 2
[1] FALSE
D28V8, continuous
D28V9, continuous
D28V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 28(17P11.2) MUTATED       6                         1    51
  AMP PEAK 28(17P11.2) WILD-TYPE    25                        12   164
D28V11, multiclass
                           clus
vv                          AMP PEAK 28(17P11.2) MUTATED
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               51
                           clus
vv                          AMP PEAK 28(17P11.2) WILD-TYPE
  ASIAN                                                 25
  BLACK OR AFRICAN AMERICAN                             12
  WHITE                                                164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V12, binary
                                cls
clus                               0   1
  AMP PEAK 28(17P11.2) MUTATED     0  56
  AMP PEAK 28(17P11.2) WILD-TYPE   5 202
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(17P11.2) MUTATED      0   56
  AMP PEAK 28(17P11.2) WILD-TYPE    5  202
                        clus
vv                       AMP PEAK 28(17P11.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           56
                        clus
vv                       AMP PEAK 28(17P11.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            202
[1] 2 2
[1] FALSE

Clustering(29) Variable = AMP PEAK 29(17Q11.2) MUTATION ANALYSIS
D29V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 29(17Q11.2) MUTATED    75  44
  AMP PEAK 29(17Q11.2) WILD-TYPE 107  44
  AMP PEAK 29(17Q11.2) MUTATED AMP PEAK 29(17Q11.2) WILD-TYPE 
                           119                            151 
  AMP PEAK 29(17Q11.2) MUTATED AMP PEAK 29(17Q11.2) WILD-TYPE 
                            44                             44 
$`AMP PEAK 29(17Q11.2) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       22.29        11.97         2.66         6.74        12.39         6.58 
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-A2LD TCGA-BT-A3PH TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A47X 
        3.65         4.67        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        66.41        18.41 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IM 
      130.88       112.44        10.59         7.79         2.20         7.82 
TCGA-DK-A3IS TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 
       50.27        48.00        17.98        67.36        41.06        30.67 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE 
       43.59        15.35        26.17         0.49         0.59         0.56 
TCGA-E7-A677 TCGA-E7-A6ME TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3NA 
        1.38        12.99         8.94         6.87        11.93        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43U 
       24.30        13.18        46.78        22.98        14.93        14.93 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5C1 TCGA-FD-A62O 
        3.62        13.38        11.01         5.36        49.68         4.83 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
       50.66        18.81         4.11         2.07         2.66         2.20 
TCGA-FJ-A3Z7 TCGA-FT-A3EE TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       15.19         3.25        35.24        20.12         0.85        52.67 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP 
       19.46         2.89         4.50         1.12         7.73         2.10 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A767 TCGA-GU-AATO 
        2.20         7.36         6.41        11.31         4.73        10.65 
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-A40E TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
        6.67         6.41        19.07         6.74        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A6FZ TCGA-K4-A6MB 
        9.01         8.22         3.45         4.67         1.81         4.27 
TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
       12.23        14.24         0.85        88.93        56.19        15.35 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9T0 TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT 
        1.87        17.88        26.27         7.63        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-YF-AA3L TCGA-YF-AA3M 
        8.32         6.77        56.48         7.96         9.04 

$`AMP PEAK 29(17Q11.2) WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 TCGA-BL-A13I 
       84.00       103.50        98.33         4.83        40.08         7.33 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20V TCGA-BT-A20X 
       11.93        19.04        32.84        12.16         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E 
       17.16         5.59        12.82         2.07        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-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A2I6 
       16.14        17.62        15.62         1.81       123.85        87.32 
TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        3.98         8.22        10.49        21.30        20.02         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
        8.28        10.55       140.81        64.18        41.56        76.60 
TCGA-DK-A6B2 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A678 
       15.68        24.66         0.10         0.53         0.66         0.82 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B7 
       14.33         1.22         0.46        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         6.12        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-FD-A6TK TCGA-FJ-A3Z9 
        6.38         9.30         6.71         4.01        10.85         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-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO 
       26.93        17.26         7.04         6.94         2.24        15.81 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A3OS 
       15.91        14.07        17.75         2.66         3.12        20.98 
TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GV-A3JX TCGA-GV-A6ZA 
        7.59         2.04        27.09         5.62         6.15        11.54 
TCGA-H4-A2HO TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ 
        1.51         8.75         2.50         6.48        10.52         1.74 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN 
        6.38         6.35         3.45        11.80        13.48        16.67 
TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A9SH TCGA-XF-A9SI 
        3.75        45.04         6.58        97.45        64.80        79.66 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 
       11.90        23.64        21.04        28.24        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ 
       16.27        66.64         2.10        92.98        10.82        54.90 
TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       30.94        27.06        75.39         3.88        10.36         4.83 
TCGA-YC-A9TC 
        0.66 

  AMP PEAK 29(17Q11.2) MUTATED AMP PEAK 29(17Q11.2) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK 29(17Q11.2) MUTATED AMP PEAK 29(17Q11.2) WILD-TYPE 
                        130.88                         140.81 
  AMP PEAK 29(17Q11.2) MUTATED AMP PEAK 29(17Q11.2) WILD-TYPE 
                          8.35                          10.36 
[1] "0.1 - 130.9 (8.3)"  "0.1 - 140.8 (10.4)"
[1] "hr=" "1.3"
D29V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 29(17Q11.2) MUTATED          0       0       37        34       49
  AMP PEAK 29(17Q11.2) WILD-TYPE        1       2       49        59       43
D29V3, multiclass
           clus
vv          AMP PEAK 29(17Q11.2) MUTATED AMP PEAK 29(17Q11.2) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              0                              2
  STAGE II                            37                             49
  STAGE III                           34                             59
  STAGE IV                            49                             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
  AMP PEAK 29(17Q11.2) MUTATED         38 59 17
  AMP PEAK 29(17Q11.2) WILD-TYPE       44 77 22
D29V4, multiclass
          clus
vv         AMP PEAK 29(17Q11.2) MUTATED AMP PEAK 29(17Q11.2) WILD-TYPE
  T0+T1+T2                           38                             44
  T3                                 59                             77
  T4                                 17                             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 29(17Q11.2) MUTATED    62  14  33   2
  AMP PEAK 29(17Q11.2) WILD-TYPE 104  14  22   5
D29V5, multiclass
    clus
vv   AMP PEAK 29(17Q11.2) MUTATED AMP PEAK 29(17Q11.2) WILD-TYPE
  N0                           62                            104
  N1                           14                             14
  N2                           33                             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
  AMP PEAK 29(17Q11.2) MUTATED   52  3 66
  AMP PEAK 29(17Q11.2) WILD-TYPE 77  4 75
D29V6, multiclass
    clus
vv   AMP PEAK 29(17Q11.2) MUTATED AMP PEAK 29(17Q11.2) WILD-TYPE
  M0                           52                             77
  M1                            3                              4
  MX                           66                             75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                                cls
clus                               0   1
  AMP PEAK 29(17Q11.2) MUTATED    31  91
  AMP PEAK 29(17Q11.2) WILD-TYPE  46 110
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(17Q11.2) MUTATED     31   91
  AMP PEAK 29(17Q11.2) WILD-TYPE   46  110
        clus
vv       AMP PEAK 29(17Q11.2) MUTATED AMP PEAK 29(17Q11.2) WILD-TYPE
  FEMALE                           31                             46
  MALE                             91                            110
[1] 2 2
[1] FALSE
D29V8, continuous
D29V9, continuous
D29V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 29(17Q11.2) MUTATED      10                         5    96
  AMP PEAK 29(17Q11.2) WILD-TYPE    21                         8   119
D29V11, multiclass
                           clus
vv                          AMP PEAK 29(17Q11.2) MUTATED
  ASIAN                                               10
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               96
                           clus
vv                          AMP PEAK 29(17Q11.2) WILD-TYPE
  ASIAN                                                 21
  BLACK OR AFRICAN AMERICAN                              8
  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"
D29V12, binary
                                cls
clus                               0   1
  AMP PEAK 29(17Q11.2) MUTATED     2 110
  AMP PEAK 29(17Q11.2) WILD-TYPE   3 148
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(17Q11.2) MUTATED      2  110
  AMP PEAK 29(17Q11.2) WILD-TYPE    3  148
                        clus
vv                       AMP PEAK 29(17Q11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          110
                        clus
vv                       AMP PEAK 29(17Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            148
[1] 2 2
[1] FALSE

Clustering(30) Variable = AMP PEAK 30(17Q12) MUTATION ANALYSIS
D30V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 30(17Q12) MUTATED    65  44
  AMP PEAK 30(17Q12) WILD-TYPE 117  44
  AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE 
                         109                          161 
  AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE 
                          44                           44 
$`AMP PEAK 30(17Q12) MUTATED`
TCGA-2F-A9KP TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20O 
       11.97         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        66.41        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-E7-A6ME TCGA-FD-A3B5 
        0.49         0.59         0.56         1.38        12.99         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SP TCGA-FD-A3SQ 
        6.87         4.01        45.93        24.30        13.18        46.78 
TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5C1 
       14.93        14.93         3.62        13.38         5.36        49.68 
TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        4.83        50.66        18.81         9.30         6.71         4.11 
TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FT-A3EE TCGA-G2-A3IE TCGA-G2-AA3B 
        2.07         2.20        15.19         3.25        20.12        52.67 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GD-A3OP TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R 
       19.46         2.89         2.10         7.36         6.41        11.31 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        4.73        10.65         4.41         5.69         7.63         7.79 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ 
        4.14         6.67         6.41        19.07         1.51         6.74 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV 
       38.60         3.06         9.01         8.22         3.45         4.67 
TCGA-K4-A6FZ TCGA-MV-A51V TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX TCGA-XF-A8HC 
        1.81        13.48        12.23        14.24         0.85         6.58 
TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9T0 
       88.93        56.19        15.35         1.87        17.88        26.27 
TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-YF-AA3L 
        7.63        91.73         2.96         8.32        56.48         7.96 
TCGA-YF-AA3M 
        9.04 

$`AMP PEAK 30(17Q12) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 
       22.29        84.00       103.50        98.33         4.83        40.08 
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        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       76.60        15.68        41.06        26.17        24.66         0.10 
TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN 
        0.53         0.66         0.82        14.33         1.22         0.46 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SL 
       12.89        15.68        12.43        11.93        15.88        22.45 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        6.12        12.82         5.52        19.79         1.97        22.98 
TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
       14.96        12.13        37.15        11.01         6.87         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S 
        6.84        27.45         6.87         2.66         6.28         6.38 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        2.66         4.01        10.85         7.13         3.48         4.08 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        6.48        61.94        30.61         5.69        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO 
       17.26         7.04         0.85         6.94         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        4.50        15.91        14.07        17.75         1.12         2.66 
TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 
        7.73         3.12        20.98         2.20         7.59         2.04 
TCGA-GU-A763 TCGA-GU-A766 TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A6ZA TCGA-K4-A3WS 
       27.09         5.62         6.41         6.15        11.54         8.75 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P 
        2.50         6.48        10.52         1.74         4.27         6.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-XF-A8HB 
        6.35         3.45        11.80        16.67         3.75        45.04 
TCGA-XF-A8HE TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
       97.45        64.80        79.66        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       28.24        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMX TCGA-XF-AAN1 TCGA-XF-AAN4 
       92.98        10.82        54.90         6.77        30.94        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       75.39         3.88        10.36         4.83         0.66 

  AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE 
                        0.10                         0.07 
  AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE 
                      112.44                       140.81 
  AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE 
                        8.35                        10.49 
[1] "0.1 - 112.4 (8.3)"  "0.1 - 140.8 (10.5)"
[1] "hr=" "1.6"
D30V2, continuous
                              vv
clus                           STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 30(17Q12) MUTATED          0       0       34        33       43
  AMP PEAK 30(17Q12) WILD-TYPE        1       2       52        60       49
D30V3, multiclass
           clus
vv          AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE
  STAGE 0A                           0                            1
  STAGE I                            0                            2
  STAGE II                          34                           52
  STAGE III                         33                           60
  STAGE IV                          43                           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 30(17Q12) MUTATED         37 49 19
  AMP PEAK 30(17Q12) WILD-TYPE       45 87 20
D30V4, multiclass
          clus
vv         AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE
  T0+T1+T2                         37                           45
  T3                               49                           87
  T4                               19                           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 30(17Q12) MUTATED    60  11  30   2
  AMP PEAK 30(17Q12) WILD-TYPE 106  17  25   5
D30V5, multiclass
    clus
vv   AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE
  N0                         60                          106
  N1                         11                           17
  N2                         30                           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 30(17Q12) MUTATED   47  3 62
  AMP PEAK 30(17Q12) WILD-TYPE 82  4 79
D30V6, multiclass
    clus
vv   AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE
  M0                         47                           82
  M1                          3                            4
  MX                         62                           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"
D30V7, binary
                              cls
clus                             0   1
  AMP PEAK 30(17Q12) MUTATED    30  82
  AMP PEAK 30(17Q12) WILD-TYPE  47 119
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 30(17Q12) MUTATED     30   82
  AMP PEAK 30(17Q12) WILD-TYPE   47  119
        clus
vv       AMP PEAK 30(17Q12) MUTATED AMP PEAK 30(17Q12) WILD-TYPE
  FEMALE                         30                           47
  MALE                           82                          119
[1] 2 2
[1] FALSE
D30V8, continuous
D30V9, continuous
D30V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 30(17Q12) MUTATED      10                         4    87
  AMP PEAK 30(17Q12) WILD-TYPE    21                         9   128
D30V11, multiclass
                           clus
vv                          AMP PEAK 30(17Q12) MUTATED
  ASIAN                                             10
  BLACK OR AFRICAN AMERICAN                          4
  WHITE                                             87
                           clus
vv                          AMP PEAK 30(17Q12) WILD-TYPE
  ASIAN                                               21
  BLACK OR AFRICAN AMERICAN                            9
  WHITE                                              128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V12, binary
                              cls
clus                             0   1
  AMP PEAK 30(17Q12) MUTATED     2 101
  AMP PEAK 30(17Q12) WILD-TYPE   3 157
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 30(17Q12) MUTATED      2  101
  AMP PEAK 30(17Q12) WILD-TYPE    3  157
                        clus
vv                       AMP PEAK 30(17Q12) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                        101
                        clus
vv                       AMP PEAK 30(17Q12) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          157
[1] 2 2
[1] FALSE

Clustering(31) Variable = AMP PEAK 31(17Q23.3) MUTATION ANALYSIS
D31V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 31(17Q23.3) MUTATED    81  47
  AMP PEAK 31(17Q23.3) WILD-TYPE 101  41
  AMP PEAK 31(17Q23.3) MUTATED AMP PEAK 31(17Q23.3) WILD-TYPE 
                           128                            142 
  AMP PEAK 31(17Q23.3) MUTATED AMP PEAK 31(17Q23.3) WILD-TYPE 
                            47                             41 
$`AMP PEAK 31(17Q23.3) MUTATED`
TCGA-2F-A9KR TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
      103.50        40.08         2.66         6.74        12.39         6.58 
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-A2LA TCGA-BT-A2LD 
       14.96         5.06         8.35         8.25        17.16         3.65 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47X 
       28.70         8.98         0.46         0.43         0.69         0.10 
TCGA-CU-A0YN TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD 
       12.92        16.31         1.84        66.41        18.41       112.44 
TCGA-DK-A1AE TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IQ 
       16.14        10.59         7.79        87.32         7.82        10.49 
TCGA-DK-A3IS TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 
       50.27        10.55        48.00        17.98        64.18        67.36 
TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 
       30.67        43.59         0.49         0.59         0.56         1.38 
TCGA-E7-A6ME TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA 
       12.99        15.68         8.94         6.87         4.01        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR 
       24.30        13.18        46.78        14.93         3.62        13.38 
TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TB 
        5.36        27.45        49.68         4.83        50.66        18.81 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 
        4.11         2.07         2.66         2.20         4.01        15.19 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EO 
        3.48         4.08         3.25         6.48        30.61        35.24 
TCGA-G2-A3VY TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 
        0.85        19.46         2.89         7.73         2.10         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW 
        7.36         6.41        11.31        10.65         4.41         6.41 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
        5.69         7.63         7.79         6.67         6.41        19.07 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV 
        6.74        38.60         9.01         8.22         3.45         4.67 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI TCGA-R3-A69X 
        1.81         4.27         6.35        13.48        12.23        14.24 
TCGA-S5-A6DX TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH 
        0.85         6.58        88.93        56.19        15.35         1.87 
TCGA-XF-A8HI TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-AAMF 
       17.88        21.04        26.27         2.24         2.10        10.82 
TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
        7.63        91.73         2.96         8.32         6.77        56.48 
TCGA-YF-AA3L TCGA-YF-AA3M 
        7.96         9.04 

$`AMP PEAK 31(17Q23.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A13I 
       22.29        11.97        84.00        98.33         4.83         7.33 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
       11.93        19.04         5.59         4.67        12.82         2.07 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A47S 
       15.42         9.99        28.41         1.94        23.01         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-A3QU TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AA 
        5.46         5.19         9.34         2.53         2.14        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I4 
        8.91       130.88        17.62        15.62         1.81       123.85 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        2.20         3.98         8.22        21.30        20.02         9.67 
TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 
        8.28       140.81        41.56        76.60        15.68        41.06 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KF 
       15.35        26.17        24.66         0.10         0.53         0.66 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B8 
        0.82        14.33         1.22         0.46        12.89        12.43 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       11.93        15.88        22.45         6.12        12.82         5.52 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43Y 
       19.79         1.97        22.98        14.93        14.96        12.13 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       37.15        11.01         6.87         5.69         6.84         6.87 
TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TK 
        2.66         6.28         6.38         9.30         6.71        10.85 
TCGA-FJ-A3Z9 TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB 
        7.13        61.94         5.69        26.93        17.26         7.04 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       20.12        52.67         6.94         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OQ 
       15.91        14.07        17.75         1.12         2.66         3.12 
TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 
       20.98         7.59         2.04        27.09         5.62         4.73 
TCGA-GV-A3JX TCGA-GV-A3QI TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-K4-A3WS 
        6.15         4.14        11.54         1.51         3.06         8.75 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A83P TCGA-LT-A5Z6 
        2.50         6.48        10.52         1.74         6.38         3.45 
TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HE TCGA-XF-A9SH 
       11.80        16.67         3.75        45.04        97.45        64.80 
TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T4 
       79.66        11.90        23.64        28.24        18.90        16.27 
TCGA-XF-A9T5 TCGA-XF-AAME TCGA-XF-AAMJ TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
       66.64        92.98        54.90        30.94        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
        3.88        10.36         4.83         0.66 

  AMP PEAK 31(17Q23.3) MUTATED AMP PEAK 31(17Q23.3) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK 31(17Q23.3) MUTATED AMP PEAK 31(17Q23.3) WILD-TYPE 
                        112.44                         140.81 
  AMP PEAK 31(17Q23.3) MUTATED AMP PEAK 31(17Q23.3) WILD-TYPE 
                         8.645                         10.175 
[1] "0.1 - 112.4 (8.6)"  "0.1 - 140.8 (10.2)"
[1] "hr=" "1.3"
D31V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 31(17Q23.3) MUTATED          0       1       33        41       53
  AMP PEAK 31(17Q23.3) WILD-TYPE        1       1       53        52       39
D31V3, multiclass
           clus
vv          AMP PEAK 31(17Q23.3) MUTATED AMP PEAK 31(17Q23.3) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              1                              1
  STAGE II                            33                             53
  STAGE III                           41                             52
  STAGE IV                            53                             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 31(17Q23.3) MUTATED         35 66 21
  AMP PEAK 31(17Q23.3) WILD-TYPE       47 70 18
D31V4, multiclass
          clus
vv         AMP PEAK 31(17Q23.3) MUTATED AMP PEAK 31(17Q23.3) WILD-TYPE
  T0+T1+T2                           35                             47
  T3                                 66                             70
  T4                                 21                             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 31(17Q23.3) MUTATED   68 15 34  4
  AMP PEAK 31(17Q23.3) WILD-TYPE 98 13 21  3
D31V5, multiclass
    clus
vv   AMP PEAK 31(17Q23.3) MUTATED AMP PEAK 31(17Q23.3) WILD-TYPE
  N0                           68                             98
  N1                           15                             13
  N2                           34                             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 31(17Q23.3) MUTATED   58  4 69
  AMP PEAK 31(17Q23.3) WILD-TYPE 71  3 72
D31V6, multiclass
    clus
vv   AMP PEAK 31(17Q23.3) MUTATED AMP PEAK 31(17Q23.3) WILD-TYPE
  M0                           58                             71
  M1                            4                              3
  MX                           69                             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"
D31V7, binary
                                cls
clus                               0   1
  AMP PEAK 31(17Q23.3) MUTATED    40  92
  AMP PEAK 31(17Q23.3) WILD-TYPE  37 109
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(17Q23.3) MUTATED     40   92
  AMP PEAK 31(17Q23.3) WILD-TYPE   37  109
        clus
vv       AMP PEAK 31(17Q23.3) MUTATED AMP PEAK 31(17Q23.3) WILD-TYPE
  FEMALE                           40                             37
  MALE                             92                            109
[1] 2 2
[1] FALSE
D31V8, continuous
D31V9, continuous
D31V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 31(17Q23.3) MUTATED      14                         6   101
  AMP PEAK 31(17Q23.3) WILD-TYPE    17                         7   114
D31V11, multiclass
                           clus
vv                          AMP PEAK 31(17Q23.3) MUTATED
  ASIAN                                               14
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                              101
                           clus
vv                          AMP PEAK 31(17Q23.3) WILD-TYPE
  ASIAN                                                 17
  BLACK OR AFRICAN AMERICAN                              7
  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"
D31V12, binary
                                cls
clus                               0   1
  AMP PEAK 31(17Q23.3) MUTATED     2 120
  AMP PEAK 31(17Q23.3) WILD-TYPE   3 138
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(17Q23.3) MUTATED      2  120
  AMP PEAK 31(17Q23.3) WILD-TYPE    3  138
                        clus
vv                       AMP PEAK 31(17Q23.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          120
                        clus
vv                       AMP PEAK 31(17Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            138
[1] 2 2
[1] FALSE

Clustering(32) Variable = AMP PEAK 32(19Q12) MUTATION ANALYSIS
D32V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 32(19Q12) MUTATED    74  31
  AMP PEAK 32(19Q12) WILD-TYPE 108  57
  AMP PEAK 32(19Q12) MUTATED AMP PEAK 32(19Q12) WILD-TYPE 
                         105                          165 
  AMP PEAK 32(19Q12) MUTATED AMP PEAK 32(19Q12) WILD-TYPE 
                          31                           57 
$`AMP PEAK 32(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-A0YN TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
       12.92         5.46        16.31         2.53        66.41        18.41 
TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IL 
        8.91       112.44         1.81       123.85        87.32         3.98 
TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A2PC 
       48.00        64.18        67.36        15.68        30.67        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A6ME TCGA-FD-A3B3 
       15.35        26.17         0.49         0.56        12.99        12.89 
TCGA-FD-A3B8 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
       12.43        24.30        22.45        19.79         1.97        22.98 
TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       14.93        14.93         3.62         6.84        27.45         6.87 
TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 
        6.28        18.81         2.66         2.20        10.85        15.19 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-A3VY 
        4.08         3.25        61.94        35.24        20.12         0.85 
TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS 
       52.67        19.46         4.50        15.91        14.07         1.12 
TCGA-GD-A2C5 TCGA-GD-A76B TCGA-GU-A42R TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW 
        7.73         7.36        11.31         4.73         4.41         6.41 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE 
        5.69         7.63         7.79        19.07         6.74        38.60 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A5RJ TCGA-K4-A6MB 
        9.01         8.22         8.75         2.50         1.74         4.27 
TCGA-MV-A51V TCGA-R3-A69X TCGA-S5-A6DX TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG 
       13.48        14.24         0.85         6.58        56.19        15.35 
TCGA-XF-A9SI TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T3 TCGA-XF-AAMX TCGA-XF-AAN0 
       79.66        21.04        28.24         2.24         6.77        56.48 
TCGA-XF-AAN5 TCGA-YC-A8S6 TCGA-YF-AA3M 
       75.39         4.83         9.04 

$`AMP PEAK 32(19Q12) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
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-A0YO TCGA-CU-A0YR 
        0.07         0.10         0.07         0.10         4.90         7.20 
TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AC 
        5.19         1.84         9.34         2.14        19.00       130.88 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK 
       16.14        17.62        15.62        10.59         7.79         2.20 
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-A3X2 TCGA-DK-A6AW 
        9.67         8.28        10.55       140.81        17.98        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A541 
       76.60        41.06        24.66         0.10         0.53         0.59 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN 
        0.66         1.38         0.82        14.33         1.22         0.46 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3N6 
       15.68         8.94         6.87         4.01        11.93        15.88 
TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       45.93         6.12        12.82         5.52        13.18        46.78 
TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       14.96        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-A62S 
        5.36         5.69        49.68         2.66         4.83         6.38 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TI 
       50.66         9.30         6.71         4.11         2.07         4.01 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        7.13         3.48         6.48        30.61         5.69        26.93 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
       17.26         7.04         6.94         2.89         2.24        15.81 
TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       17.75         2.66         2.10         3.12        20.98         2.20 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-AATO 
        6.41         7.59         2.04        27.09         5.62        10.65 
TCGA-GV-A3JX TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO 
        6.15         4.14         6.67         6.41        11.54         1.51 
TCGA-HQ-A2OF TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A6FZ 
        3.06         3.45         4.67         6.48        10.52         1.81 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN 
        6.38         6.35         3.45        11.80        12.23        16.67 
TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI 
        3.75        45.04        88.93        97.45         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 
       64.80        11.90        23.64        26.27        18.90        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML 
       66.64         2.10        92.98        10.82        54.90         7.63 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN8 
       91.73         2.96         8.32        30.94        27.06         3.88 
TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L 
       10.36         0.66         7.96 

  AMP PEAK 32(19Q12) MUTATED AMP PEAK 32(19Q12) WILD-TYPE 
                        0.10                         0.07 
  AMP PEAK 32(19Q12) MUTATED AMP PEAK 32(19Q12) WILD-TYPE 
                      123.85                       140.81 
  AMP PEAK 32(19Q12) MUTATED AMP PEAK 32(19Q12) WILD-TYPE 
                       10.85                         8.94 
[1] "0.1 - 123.8 (10.8)" "0.1 - 140.8 (8.9)" 
[1] "hr=" "1.3"
D32V2, continuous
                              vv
clus                           STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 32(19Q12) MUTATED          0       0       32        32       41
  AMP PEAK 32(19Q12) WILD-TYPE        1       2       54        61       51
D32V3, multiclass
           clus
vv          AMP PEAK 32(19Q12) MUTATED AMP PEAK 32(19Q12) WILD-TYPE
  STAGE 0A                           0                            1
  STAGE I                            0                            2
  STAGE II                          32                           54
  STAGE III                         32                           61
  STAGE IV                          41                           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 32(19Q12) MUTATED         30 53 16
  AMP PEAK 32(19Q12) WILD-TYPE       52 83 23
D32V4, multiclass
          clus
vv         AMP PEAK 32(19Q12) MUTATED AMP PEAK 32(19Q12) WILD-TYPE
  T0+T1+T2                         30                           52
  T3                               53                           83
  T4                               16                           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 32(19Q12) MUTATED    57  11  27   2
  AMP PEAK 32(19Q12) WILD-TYPE 109  17  28   5
D32V5, multiclass
    clus
vv   AMP PEAK 32(19Q12) MUTATED AMP PEAK 32(19Q12) WILD-TYPE
  N0                         57                          109
  N1                         11                           17
  N2                         27                           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 32(19Q12) MUTATED   52  2 53
  AMP PEAK 32(19Q12) WILD-TYPE 77  5 88
D32V6, multiclass
    clus
vv   AMP PEAK 32(19Q12) MUTATED AMP PEAK 32(19Q12) WILD-TYPE
  M0                         52                           77
  M1                          2                            5
  MX                         53                           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"
D32V7, binary
                              cls
clus                             0   1
  AMP PEAK 32(19Q12) MUTATED    27  81
  AMP PEAK 32(19Q12) WILD-TYPE  50 120
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 32(19Q12) MUTATED     27   81
  AMP PEAK 32(19Q12) WILD-TYPE   50  120
        clus
vv       AMP PEAK 32(19Q12) MUTATED AMP PEAK 32(19Q12) WILD-TYPE
  FEMALE                         27                           50
  MALE                           81                          120
[1] 2 2
[1] FALSE
D32V8, continuous
D32V9, continuous
D32V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 32(19Q12) MUTATED      13                         4    82
  AMP PEAK 32(19Q12) WILD-TYPE    18                         9   133
D32V11, multiclass
                           clus
vv                          AMP PEAK 32(19Q12) MUTATED
  ASIAN                                             13
  BLACK OR AFRICAN AMERICAN                          4
  WHITE                                             82
                           clus
vv                          AMP PEAK 32(19Q12) WILD-TYPE
  ASIAN                                               18
  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"
D32V12, binary
                              cls
clus                             0   1
  AMP PEAK 32(19Q12) MUTATED     2  97
  AMP PEAK 32(19Q12) WILD-TYPE   3 161
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 32(19Q12) MUTATED      2   97
  AMP PEAK 32(19Q12) WILD-TYPE    3  161
                        clus
vv                       AMP PEAK 32(19Q12) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         97
                        clus
vv                       AMP PEAK 32(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          161
[1] 2 2
[1] FALSE

Clustering(33) Variable = AMP PEAK 33(19Q13.43) MUTATION ANALYSIS
D33V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 33(19Q13.43) MUTATED    68  30
  AMP PEAK 33(19Q13.43) WILD-TYPE 114  58
  AMP PEAK 33(19Q13.43) MUTATED AMP PEAK 33(19Q13.43) WILD-TYPE 
                             98                             172 
  AMP PEAK 33(19Q13.43) MUTATED AMP PEAK 33(19Q13.43) WILD-TYPE 
                             30                              58 
$`AMP PEAK 33(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        66.41        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-E5-A2PC 
        9.67        17.98        64.18        67.36        15.68        43.59 
TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A7DV 
       15.35         0.49         0.59         0.56        12.99         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-A6TB 
        3.62        12.13        11.01         6.84        27.45        18.81 
TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A3EE 
        2.07         2.20        10.85        15.19         4.08         3.25 
TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-AA3B TCGA-GC-A3RC TCGA-GC-A3RD 
       61.94        35.24        20.12        52.67        15.91        14.07 
TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42R 
        1.12         7.73         3.12        20.98         7.36        11.31 
TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       10.65         4.41         6.41         5.69         7.63         7.79 
TCGA-GV-A3QI TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-K4-A4AB 
        4.14        19.07         6.74        38.60         9.01         2.50 
TCGA-K4-A6MB TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HF TCGA-XF-A8HG 
        4.27         0.85         3.75        45.04        56.19        15.35 
TCGA-XF-A9SI TCGA-XF-A9SX TCGA-XF-A9T3 TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN5 
       79.66        23.64         2.24         6.77        56.48        75.39 
TCGA-YC-A89H TCGA-YC-A8S6 
       10.36         4.83 

$`AMP PEAK 33(19Q13.43) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
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        41.56        76.60 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       41.06        30.67        26.17        24.66         0.10         0.53 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B4 
        0.66         1.38         0.82        14.33         0.46        15.68 
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-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       24.30         6.12        12.82         5.52        13.18        46.78 
TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BU 
       19.79        14.93        14.96        13.38        37.15         6.87 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        5.36         5.69         6.87        49.68         2.66         4.83 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28         6.38        50.66         9.30         6.71         4.11 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A61P TCGA-G2-A2EJ 
        2.66         4.01         7.13         3.48         6.48        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3C 
        5.69        26.93        17.26         7.04         0.85         6.94 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC 
       19.46         2.89         2.24        15.81         4.50        17.75 
TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A762 
        2.66         2.10         2.20         6.41         7.59         2.04 
TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JX TCGA-GV-A3QK TCGA-GV-A40E 
       27.09         5.62         4.73         6.15         6.67         6.41 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       11.54         1.51         3.06         8.22         8.75         3.45 
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-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        6.35         3.45        11.80        13.48        12.23        16.67 
TCGA-R3-A69X TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI 
       14.24         6.58        88.93        97.45         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       64.80        11.90        21.04        28.24        26.27        18.90 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ 
       16.27        66.64         2.10        92.98        10.82        54.90 
TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN1 TCGA-XF-AAN4 
        7.63        91.73         2.96         8.32        30.94        27.06 
TCGA-XF-AAN8 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        3.88         0.66         7.96         9.04 

  AMP PEAK 33(19Q13.43) MUTATED AMP PEAK 33(19Q13.43) WILD-TYPE 
                           0.10                            0.07 
  AMP PEAK 33(19Q13.43) MUTATED AMP PEAK 33(19Q13.43) WILD-TYPE 
                         130.88                          140.81 
  AMP PEAK 33(19Q13.43) MUTATED AMP PEAK 33(19Q13.43) WILD-TYPE 
                           9.34                            9.17 
[1] "0.1 - 130.9 (9.3)" "0.1 - 140.8 (9.2)"
[1] "hr=" "1.1"
D33V2, continuous
                                 vv
clus                              STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 33(19Q13.43) MUTATED          0       0       28        30       40
  AMP PEAK 33(19Q13.43) WILD-TYPE        1       2       58        63       52
D33V3, multiclass
           clus
vv          AMP PEAK 33(19Q13.43) MUTATED AMP PEAK 33(19Q13.43) WILD-TYPE
  STAGE 0A                              0                               1
  STAGE I                               0                               2
  STAGE II                             28                              58
  STAGE III                            30                              63
  STAGE IV                             40                              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 33(19Q13.43) MUTATED         25 47 19
  AMP PEAK 33(19Q13.43) WILD-TYPE       57 89 20
D33V4, multiclass
          clus
vv         AMP PEAK 33(19Q13.43) MUTATED AMP PEAK 33(19Q13.43) WILD-TYPE
  T0+T1+T2                            25                              57
  T3                                  47                              89
  T4                                  19                              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 33(19Q13.43) MUTATED    50  12  24   4
  AMP PEAK 33(19Q13.43) WILD-TYPE 116  16  31   3
D33V5, multiclass
    clus
vv   AMP PEAK 33(19Q13.43) MUTATED AMP PEAK 33(19Q13.43) WILD-TYPE
  N0                            50                             116
  N1                            12                              16
  N2                            24                              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
  AMP PEAK 33(19Q13.43) MUTATED   47  4 50
  AMP PEAK 33(19Q13.43) WILD-TYPE 82  3 91
D33V6, multiclass
    clus
vv   AMP PEAK 33(19Q13.43) MUTATED AMP PEAK 33(19Q13.43) WILD-TYPE
  M0                            47                              82
  M1                             4                               3
  MX                            50                              91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                                 cls
clus                                0   1
  AMP PEAK 33(19Q13.43) MUTATED    30  71
  AMP PEAK 33(19Q13.43) WILD-TYPE  47 130
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 33(19Q13.43) MUTATED     30   71
  AMP PEAK 33(19Q13.43) WILD-TYPE   47  130
        clus
vv       AMP PEAK 33(19Q13.43) MUTATED AMP PEAK 33(19Q13.43) WILD-TYPE
  FEMALE                            30                              47
  MALE                              71                             130
[1] 2 2
[1] FALSE
D33V8, continuous
D33V9, continuous
D33V10, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 33(19Q13.43) MUTATED      11                         5    78
  AMP PEAK 33(19Q13.43) WILD-TYPE    20                         8   137
D33V11, multiclass
                           clus
vv                          AMP PEAK 33(19Q13.43) MUTATED
  ASIAN                                                11
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                78
                           clus
vv                          AMP PEAK 33(19Q13.43) WILD-TYPE
  ASIAN                                                  20
  BLACK OR AFRICAN AMERICAN                               8
  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"
D33V12, binary
                                 cls
clus                                0   1
  AMP PEAK 33(19Q13.43) MUTATED     1  91
  AMP PEAK 33(19Q13.43) WILD-TYPE   4 167
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 33(19Q13.43) MUTATED      1   91
  AMP PEAK 33(19Q13.43) WILD-TYPE    4  167
                        clus
vv                       AMP PEAK 33(19Q13.43) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            91
                        clus
vv                       AMP PEAK 33(19Q13.43) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             167
[1] 2 2
[1] FALSE

Clustering(34) Variable = AMP PEAK 34(20Q11.21) MUTATION ANALYSIS
D34V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 34(20Q11.21) MUTATED   115  54
  AMP PEAK 34(20Q11.21) WILD-TYPE  67  34
  AMP PEAK 34(20Q11.21) MUTATED AMP PEAK 34(20Q11.21) WILD-TYPE 
                            169                             101 
  AMP PEAK 34(20Q11.21) MUTATED AMP PEAK 34(20Q11.21) WILD-TYPE 
                             54                              34 
$`AMP PEAK 34(20Q11.21) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KT TCGA-BL-A0C8 TCGA-BL-A13J 
       22.29        11.97       103.50        98.33        40.08         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q 
        6.74         6.58        19.04        32.84        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LD 
        5.06        14.89         5.06         8.35         8.25         3.65 
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-A1HS TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47X 
       23.01         0.46         0.43         0.13         0.07         0.10 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A1A5 
       12.92         4.90         7.20         5.46         1.84         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 
       66.41        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-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WX 
        8.22        10.49        50.27        20.02         9.67        10.55 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       48.00        17.98        64.18        67.36        15.68        41.06 
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-A6ME TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 
        0.56        12.99         1.22        12.89         6.87         4.01 
TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SP TCGA-FD-A3SQ 
       11.93        45.93        24.30        22.45        13.18        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR 
       19.79         1.97        22.98        14.93         3.62        13.38 
TCGA-FD-A5BT TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62S 
       11.01        27.45         6.87        49.68         4.83         6.38 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH 
       18.81         9.30         6.71         4.11         2.07         2.20 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P 
        4.01        10.85        15.19         3.48         3.25         6.48 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B 
       61.94        30.61         5.69        35.24         0.85        52.67 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       19.46         2.89         2.24        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS 
       14.07         1.12         2.66         7.73         2.10        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A766 TCGA-GU-AATO 
        2.20         7.36         7.59        11.31         5.62        10.65 
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-A40E TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
        4.14         6.41        19.07         6.74        38.60         3.06 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A6FZ 
        8.22         8.75         3.45         4.67         6.48         1.81 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-A6DX TCGA-XF-A8HB 
        3.45        13.48        12.23        16.67         0.85        45.04 
TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SI TCGA-XF-A9SX 
       88.93        56.19        15.35         1.87        79.66        23.64 
TCGA-XF-A9SY TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMF 
       21.04         2.24        16.27        66.64         2.10        10.82 
TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN1 TCGA-YC-A89H 
        7.63        91.73         2.96         6.77        30.94        10.36 
TCGA-YF-AA3M 
        9.04 

$`AMP PEAK 34(20Q11.21) WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20O 
       84.00         4.83         7.33        12.39        11.93        12.16 
TCGA-BT-A20U TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B 
       14.96        17.16         5.59         4.67        12.82        15.42 
TCGA-CF-A27C TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A3QU TCGA-CU-A3YL 
        0.69         0.10         0.07         0.10         5.19        16.31 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF 
        9.34         2.53        19.00         8.91        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A3IT TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 
       15.62        21.30         8.28       140.81        41.56        76.60 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       24.66         0.10         0.53         0.66         1.38         0.82 
TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 
       14.33         0.46        15.68         8.94        12.43        15.88 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y 
        6.12        12.82         5.52        14.96        14.93        12.13 
TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62N 
       37.15         6.87         5.36         5.69         6.84         2.66 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TG TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-G2-A2EL 
        6.28        50.66         2.66         7.13         4.08        26.93 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3WC TCGA-GD-A3OQ 
       17.26         7.04        20.12         6.94        17.75         3.12 
TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A767 TCGA-GV-A3QK TCGA-GV-A6ZA 
        6.41         2.04        27.09         4.73         6.67        11.54 
TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB 
        1.51         9.01         2.50        10.52         1.74         4.27 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A8JT TCGA-R3-A69X TCGA-S5-AA26 TCGA-XF-A8HC 
        6.38         6.35        11.80        14.24         3.75         6.58 
TCGA-XF-A8HE TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SW TCGA-XF-A9SZ TCGA-XF-A9T0 
       97.45        17.88        64.80        11.90        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-AAME TCGA-XF-AAMJ TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN4 
       18.90        92.98        54.90         8.32        56.48        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39         3.88         4.83         0.66         7.96 

  AMP PEAK 34(20Q11.21) MUTATED AMP PEAK 34(20Q11.21) WILD-TYPE 
                           0.07                            0.07 
  AMP PEAK 34(20Q11.21) MUTATED AMP PEAK 34(20Q11.21) WILD-TYPE 
                         130.88                          140.81 
  AMP PEAK 34(20Q11.21) MUTATED AMP PEAK 34(20Q11.21) WILD-TYPE 
                           9.30                            9.01 
[1] "0.1 - 130.9 (9.3)" "0.1 - 140.8 (9.0)"
[1] "hr=" "1.1"
D34V2, continuous
                                 vv
clus                              STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 34(20Q11.21) MUTATED          0       1       56        53       60
  AMP PEAK 34(20Q11.21) WILD-TYPE        1       1       30        40       32
D34V3, multiclass
           clus
vv          AMP PEAK 34(20Q11.21) MUTATED AMP PEAK 34(20Q11.21) WILD-TYPE
  STAGE 0A                              0                               1
  STAGE I                               1                               1
  STAGE II                             56                              30
  STAGE III                            53                              40
  STAGE IV                             60                              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
  AMP PEAK 34(20Q11.21) MUTATED         51 83 24
  AMP PEAK 34(20Q11.21) WILD-TYPE       31 53 15
D34V4, multiclass
          clus
vv         AMP PEAK 34(20Q11.21) MUTATED AMP PEAK 34(20Q11.21) WILD-TYPE
  T0+T1+T2                            51                              31
  T3                                  83                              53
  T4                                  24                              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 34(20Q11.21) MUTATED   97 17 38  6
  AMP PEAK 34(20Q11.21) WILD-TYPE 69 11 17  1
D34V5, multiclass
    clus
vv   AMP PEAK 34(20Q11.21) MUTATED AMP PEAK 34(20Q11.21) WILD-TYPE
  N0                            97                              69
  N1                            17                              11
  N2                            38                              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
  AMP PEAK 34(20Q11.21) MUTATED   78  5 89
  AMP PEAK 34(20Q11.21) WILD-TYPE 51  2 52
D34V6, multiclass
    clus
vv   AMP PEAK 34(20Q11.21) MUTATED AMP PEAK 34(20Q11.21) WILD-TYPE
  M0                            78                              51
  M1                             5                               2
  MX                            89                              52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                                 cls
clus                                0   1
  AMP PEAK 34(20Q11.21) MUTATED    51 122
  AMP PEAK 34(20Q11.21) WILD-TYPE  26  79
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 34(20Q11.21) MUTATED     51  122
  AMP PEAK 34(20Q11.21) WILD-TYPE   26   79
        clus
vv       AMP PEAK 34(20Q11.21) MUTATED AMP PEAK 34(20Q11.21) WILD-TYPE
  FEMALE                            51                              26
  MALE                             122                              79
[1] 2 2
[1] FALSE
D34V8, continuous
D34V9, continuous
D34V10, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 34(20Q11.21) MUTATED      14                         7   136
  AMP PEAK 34(20Q11.21) WILD-TYPE    17                         6    79
D34V11, multiclass
                           clus
vv                          AMP PEAK 34(20Q11.21) MUTATED
  ASIAN                                                14
  BLACK OR AFRICAN AMERICAN                             7
  WHITE                                               136
                           clus
vv                          AMP PEAK 34(20Q11.21) WILD-TYPE
  ASIAN                                                  17
  BLACK OR AFRICAN AMERICAN                               6
  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"
D34V12, binary
                                 cls
clus                                0   1
  AMP PEAK 34(20Q11.21) MUTATED     2 157
  AMP PEAK 34(20Q11.21) WILD-TYPE   3 101
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 34(20Q11.21) MUTATED      2  157
  AMP PEAK 34(20Q11.21) WILD-TYPE    3  101
                        clus
vv                       AMP PEAK 34(20Q11.21) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           157
                        clus
vv                       AMP PEAK 34(20Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             101
[1] 2 2
[1] FALSE

Clustering(35) Variable = AMP PEAK 35(22Q12.2) MUTATION ANALYSIS
D35V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 35(22Q12.2) MUTATED    36  16
  AMP PEAK 35(22Q12.2) WILD-TYPE 146  72
  AMP PEAK 35(22Q12.2) MUTATED AMP PEAK 35(22Q12.2) WILD-TYPE 
                            52                            218 
  AMP PEAK 35(22Q12.2) MUTATED AMP PEAK 35(22Q12.2) WILD-TYPE 
                            16                             72 
$`AMP PEAK 35(22Q12.2) MUTATED`
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-BL-A0C8 TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A3PJ 
      103.50         4.83        40.08         8.35         5.59        12.82 
TCGA-C4-A0F6 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I6 TCGA-DK-A3IN 
       23.01        66.41        18.41       112.44        87.32         8.22 
TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3WX TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE 
       50.27        20.02        10.55         0.49         0.59         0.56 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A43P TCGA-FD-A5BT 
        6.87         4.01        22.45        12.82        14.93        11.01 
TCGA-FD-A5BV TCGA-FD-A62O TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-AA3B 
        5.36         4.83        61.94        35.24        17.26        52.67 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GD-A2C5 TCGA-GU-A767 TCGA-GV-A3JV 
        2.89         2.24        14.07         7.73         4.73         4.41 
TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
        5.69         7.79         4.14         6.67         6.41        19.07 
TCGA-HQ-A2OE TCGA-LT-A5Z6 TCGA-S5-A6DX TCGA-XF-A9SI TCGA-XF-A9T0 TCGA-XF-A9T6 
       38.60         3.45         0.85        79.66        26.27         2.10 
TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX 
        7.63        91.73         8.32         6.77 

$`AMP PEAK 35(22Q12.2) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-BL-A13I TCGA-BL-A13J 
       22.29        11.97        84.00        98.33         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        11.93        19.04        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-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK 
        5.06         8.25        17.16         3.65         4.67         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-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-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        0.07         0.10         0.10        12.92         4.90         7.20 
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-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF 
        2.14        19.00         8.91       130.88        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       15.62         1.81        10.59         7.79       123.85         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW 
        3.98         7.82        10.49        21.30         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        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ 
       67.36        15.68        41.06        30.67        43.59        15.35 
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-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 
        0.82        12.99        14.33         1.22         0.46        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       15.68         8.94        12.43        11.93        15.88        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       24.30         6.12         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-A5BR TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       13.38        37.15         6.87         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-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       18.81         9.30         6.71         4.11         2.07         2.66 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        2.20         4.01        10.85        15.19         7.13         3.48 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        4.08         3.25         6.48        30.61         5.69        26.93 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO 
        7.04        20.12         0.85         6.94        19.46        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OP 
        4.50        15.91        17.75         1.12         2.66         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36         6.41         7.59 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JW 
       11.31         2.04        27.09         5.62        10.65         6.41 
TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF 
        6.15         7.63        11.54         1.51         6.74         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        9.01         8.22         8.75         3.45         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-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
        6.35        11.80        13.48        12.23        16.67        14.24 
TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        3.75        45.04         6.58        88.93        97.45        56.19 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SW TCGA-XF-A9SX 
       15.35         1.87        17.88        64.80        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       21.04        28.24        18.90         2.24        16.27        66.64 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMT TCGA-XF-AAN0 TCGA-XF-AAN1 
       92.98        10.82        54.90         2.96        56.48        30.94 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39         3.88        10.36         4.83         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M 
        7.96         9.04 

  AMP PEAK 35(22Q12.2) MUTATED AMP PEAK 35(22Q12.2) WILD-TYPE 
                          0.49                           0.07 
  AMP PEAK 35(22Q12.2) MUTATED AMP PEAK 35(22Q12.2) WILD-TYPE 
                        112.44                         140.81 
  AMP PEAK 35(22Q12.2) MUTATED AMP PEAK 35(22Q12.2) WILD-TYPE 
                         8.335                          9.320 
[1] "0.5 - 112.4 (8.3)" "0.1 - 140.8 (9.3)"
[1] "hr=" "1.2"
D35V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 35(22Q12.2) MUTATED          0       1       18        20       13
  AMP PEAK 35(22Q12.2) WILD-TYPE        1       1       68        73       79
D35V3, multiclass
           clus
vv          AMP PEAK 35(22Q12.2) MUTATED AMP PEAK 35(22Q12.2) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              1                              1
  STAGE II                            18                             68
  STAGE III                           20                             73
  STAGE IV                            13                             79
[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 35(22Q12.2) MUTATED         18  26   5
  AMP PEAK 35(22Q12.2) WILD-TYPE       64 110  34
D35V4, multiclass
          clus
vv         AMP PEAK 35(22Q12.2) MUTATED AMP PEAK 35(22Q12.2) WILD-TYPE
  T0+T1+T2                           18                             64
  T3                                 26                            110
  T4                                  5                             34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 35(22Q12.2) MUTATED    34   3   9   2
  AMP PEAK 35(22Q12.2) WILD-TYPE 132  25  46   5
D35V5, multiclass
    clus
vv   AMP PEAK 35(22Q12.2) MUTATED AMP PEAK 35(22Q12.2) WILD-TYPE
  N0                           34                            132
  N1                            3                             25
  N2                            9                             46
  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 35(22Q12.2) MUTATED    25   1  27
  AMP PEAK 35(22Q12.2) WILD-TYPE 104   6 114
D35V6, multiclass
    clus
vv   AMP PEAK 35(22Q12.2) MUTATED AMP PEAK 35(22Q12.2) WILD-TYPE
  M0                           25                            104
  M1                            1                              6
  MX                           27                            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"
D35V7, binary
                                cls
clus                               0   1
  AMP PEAK 35(22Q12.2) MUTATED    16  37
  AMP PEAK 35(22Q12.2) WILD-TYPE  61 164
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 35(22Q12.2) MUTATED     16   37
  AMP PEAK 35(22Q12.2) WILD-TYPE   61  164
        clus
vv       AMP PEAK 35(22Q12.2) MUTATED AMP PEAK 35(22Q12.2) WILD-TYPE
  FEMALE                           16                             61
  MALE                             37                            164
[1] 2 2
[1] FALSE
D35V8, continuous
D35V9, continuous
D35V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 35(22Q12.2) MUTATED       4                         3    43
  AMP PEAK 35(22Q12.2) WILD-TYPE    27                        10   172
D35V11, multiclass
                           clus
vv                          AMP PEAK 35(22Q12.2) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               43
                           clus
vv                          AMP PEAK 35(22Q12.2) WILD-TYPE
  ASIAN                                                 27
  BLACK OR AFRICAN AMERICAN                             10
  WHITE                                                172
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V12, binary
                                cls
clus                               0   1
  AMP PEAK 35(22Q12.2) MUTATED     1  47
  AMP PEAK 35(22Q12.2) WILD-TYPE   4 211
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 35(22Q12.2) MUTATED      1   47
  AMP PEAK 35(22Q12.2) WILD-TYPE    4  211
                        clus
vv                       AMP PEAK 35(22Q12.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           47
                        clus
vv                       AMP PEAK 35(22Q12.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            211
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK  1(1P36.11) MUTATION ANALYSIS
D36V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.11) MUTATED    36  18
  DEL PEAK  1(1P36.11) WILD-TYPE 146  70
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            54                            216 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            18                             70 
$`DEL PEAK  1(1P36.11) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KW TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20T TCGA-BT-A20W 
       22.29         4.83         6.58        19.04        14.89         8.35 
TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-CF-A1HR TCGA-CF-A1HS 
        3.65         2.07        15.42         9.99         0.46         0.43 
TCGA-CF-A47X TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A1A7 TCGA-DK-A1AE 
        0.10         7.20         5.46         1.84        18.41        16.14 
TCGA-DK-A2I2 TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3WX TCGA-DK-A6B6 TCGA-E5-A2PC 
        7.79        10.49        21.30        10.55        30.67        43.59 
TCGA-FD-A3B5 TCGA-FD-A3SO TCGA-FD-A43Y TCGA-FD-A5BU TCGA-FD-A5C1 TCGA-FD-A6TE 
        8.94         5.52        12.13         6.87        49.68         4.11 
TCGA-FD-A6TG TCGA-FJ-A3ZE TCGA-G2-A2EL TCGA-G2-AA3F TCGA-GU-A763 TCGA-GU-A766 
        2.66         3.48        26.93        19.46        27.09         5.62 
TCGA-GV-A3JV TCGA-GV-A3QI TCGA-GV-A6ZA TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A3WV 
        4.41         4.14        11.54         3.06         8.75         4.67 
TCGA-K4-A4AC TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
        6.48         1.74         4.27         3.45        13.48        12.23 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SX TCGA-XF-AAMX TCGA-XF-AAN1 TCGA-XF-AAN5 
       56.19        15.35        23.64         6.77        30.94        75.39 

$`DEL PEAK  1(1P36.11) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-BL-A0C8 TCGA-BL-A13I 
       11.97        84.00       103.50        98.33        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O 
        2.66         6.74        12.39        11.93        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       17.88        19.50         5.06        14.96         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42C TCGA-BT-A42F 
       17.16         5.59         4.67        12.82        28.70        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        8.98         1.94        23.01         0.69         0.13         0.07 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3QU 
        0.10         0.07         0.10        12.92         4.90         5.19 
TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA 
       16.31         9.34         2.53         2.14        66.41        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-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY 
        8.22        50.27        20.02         9.67         8.28       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        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       15.68        41.06        15.35        26.17        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-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 
        0.82        12.99        14.33         1.22         0.46        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-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP 
       45.93        24.30        22.45         6.12        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-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV 
       14.93         3.62        13.38        37.15        11.01         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O 
        5.69         6.84        27.45         6.87         2.66         4.83 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        6.28         6.38        50.66        18.81         9.30         6.71 
TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        2.07         2.20         4.01        10.85        15.19         7.13 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        4.08         3.25         6.48        61.94        30.61         5.69 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       35.24        17.26         7.04        20.12         0.85        52.67 
TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
        6.94         2.89         2.24        15.81         4.50        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-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36         6.41         7.59 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JW TCGA-GV-A3JX 
       11.31         2.04         4.73        10.65         6.41         6.15 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
        5.69         7.63         7.79         6.67         6.41        19.07 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU 
        1.51         6.74        38.60         9.01         8.22         3.45 
TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A8JT 
        2.50        10.52         1.81         6.38         6.35        11.80 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC 
       16.67        14.24         0.85         3.75        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI 
       88.93        97.45         1.87        17.88        64.80        79.66 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       11.90        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ 
       16.27        66.64         2.10        92.98        10.82        54.90 
TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN4 
        7.63        91.73         2.96         8.32        56.48        27.06 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        3.88        10.36         4.83         0.66         7.96         9.04 

  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 
                         75.39                         140.81 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                         8.550                          9.505 
[1] "0.1 - 75.4 (8.6)"  "0.1 - 140.8 (9.5)"
[1] "hr=" "1.2"
D36V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  1(1P36.11) MUTATED          1       0       14        21       18
  DEL PEAK  1(1P36.11) WILD-TYPE        0       2       72        72       74
D36V3, 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                            14                             72
  STAGE III                           21                             72
  STAGE IV                            18                             74
[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         15  32   5
  DEL PEAK  1(1P36.11) WILD-TYPE       67 104  34
D36V4, multiclass
          clus
vv         DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  T0+T1+T2                           15                             67
  T3                                 32                            104
  T4                                  5                             34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK  1(1P36.11) MUTATED    36  10   5   3
  DEL PEAK  1(1P36.11) WILD-TYPE 130  18  50   4
D36V5, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                           36                            130
  N1                           10                             18
  N2                            5                             50
  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    25   1  30
  DEL PEAK  1(1P36.11) WILD-TYPE 104   6 111
D36V6, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  M0                           25                            104
  M1                            1                              6
  MX                           30                            111
[1] 3 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  1(1P36.11) MUTATED    15  41
  DEL PEAK  1(1P36.11) WILD-TYPE  62 160
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     15   41
  DEL PEAK  1(1P36.11) WILD-TYPE   62  160
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  FEMALE                           15                             62
  MALE                             41                            160
[1] 2 2
[1] FALSE
D36V8, continuous
D36V9, continuous
D36V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.11) MUTATED       4                         3    45
  DEL PEAK  1(1P36.11) WILD-TYPE    27                        10   170
D36V11, multiclass
                           clus
vv                          DEL PEAK  1(1P36.11) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               45
                           clus
vv                          DEL PEAK  1(1P36.11) WILD-TYPE
  ASIAN                                                 27
  BLACK OR AFRICAN AMERICAN                             10
  WHITE                                                170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V12, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED     0  53
  DEL PEAK  1(1P36.11) WILD-TYPE   5 205
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      0   53
  DEL PEAK  1(1P36.11) WILD-TYPE    5  205
                        clus
vv                       DEL PEAK  1(1P36.11) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           53
                        clus
vv                       DEL PEAK  1(1P36.11) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            205
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK  2(1Q32.1) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1Q32.1) MUTATED    33  17
  DEL PEAK  2(1Q32.1) WILD-TYPE 149  71
  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE 
                           50                           220 
  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE 
                           17                            71 
$`DEL PEAK  2(1Q32.1) MUTATED`
TCGA-2F-A9KO TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A3PJ TCGA-BT-A3PK 
       22.29        32.84        14.89         8.35        12.82         2.07 
TCGA-CF-A1HS TCGA-CU-A0YO TCGA-CU-A3YL TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IK 
        0.43         4.90        16.31         1.81        87.32         2.20 
TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3X1 TCGA-DK-A6B2 TCGA-DK-A6B6 
        7.82        10.49        50.27        48.00        15.68        30.67 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-FD-A3SL TCGA-FD-A3SR TCGA-FD-A5C0 TCGA-FD-A62P 
        0.49         0.53        22.45        19.79         6.87         6.28 
TCGA-FD-A62S TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-G2-A2EK TCGA-G2-A3IE 
        6.38         4.11         2.20        15.19         5.69        20.12 
TCGA-G2-A3VY TCGA-GC-A3RC TCGA-GU-A766 TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QH 
        0.85        15.91         5.62         6.41         5.69         7.79 
TCGA-GV-A40E TCGA-GV-A6ZA TCGA-K4-A3WU TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-S5-A6DX 
        6.41        11.54         3.45         3.45        13.48         0.85 
TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMX 
        6.58        56.19         1.87         2.10        10.82         6.77 
TCGA-YF-AA3L TCGA-YF-AA3M 
        7.96         9.04 

$`DEL PEAK  2(1Q32.1) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 
       11.97        84.00       103.50        98.33         4.83        40.08 
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-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-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-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-A47X TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3KJ 
        0.07         0.10         0.10        12.92         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
        5.19         1.84         9.34         2.53         2.14        66.41 
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-A3IL 
       17.62        15.62        10.59         7.79       123.85         3.98 
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-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
      140.81        17.98        64.18        41.56        76.60        67.36 
TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       41.06        43.59        15.35        26.17        24.66         0.10 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
        0.59         0.56         0.66         1.38         0.82        12.99 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       14.33         1.22         0.46        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-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       24.30         6.12        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-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-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        5.69         6.84        27.45        49.68         2.66         4.83 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG 
       50.66        18.81         9.30         6.71         2.07         2.66 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
        4.01        10.85         7.13         3.48         4.08         3.25 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
        6.48        61.94        30.61        26.93        35.24        17.26 
TCGA-G2-A3IB TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
        7.04        52.67         6.94        19.46         2.89         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-GD-A76B 
        7.73         2.10         3.12        20.98         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A767 
        6.41         7.59        11.31         2.04        27.09         4.73 
TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK 
       10.65         4.41         6.15         7.63         4.14         6.67 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       19.07         1.51         6.74        38.60         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        8.22         8.75         4.67         2.50         6.48        10.52 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A8JT 
        1.74         1.81         4.27         6.38         6.35        11.80 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HD 
       12.23        16.67        14.24         3.75        45.04        88.93 
TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW 
       97.45        15.35        17.88        64.80        79.66        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-AAME TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR 
       16.27        66.64        92.98        54.90         7.63        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
        2.96         8.32        56.48        30.94        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
        3.88        10.36         4.83         0.66 

  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 
                         7.33                         10.44 
[1] "0.4 - 87.3 (7.3)"   "0.1 - 140.8 (10.4)"
[1] "hr=" "1.3"
D37V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  2(1Q32.1) MUTATED          1       0       18        12       18
  DEL PEAK  2(1Q32.1) WILD-TYPE        0       2       68        81       74
D37V3, 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                           18                            68
  STAGE III                          12                            81
  STAGE IV                           18                            74
[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         13  22   8
  DEL PEAK  2(1Q32.1) WILD-TYPE       69 114  31
D37V4, multiclass
          clus
vv         DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE
  T0+T1+T2                          13                            69
  T3                                22                           114
  T4                                 8                            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
  DEL PEAK  2(1Q32.1) MUTATED    22   4  13   2
  DEL PEAK  2(1Q32.1) WILD-TYPE 144  24  42   5
D37V5, multiclass
    clus
vv   DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE
  N0                          22                           144
  N1                           4                            24
  N2                          13                            42
  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    21   1  27
  DEL PEAK  2(1Q32.1) WILD-TYPE 108   6 114
D37V6, multiclass
    clus
vv   DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE
  M0                          21                           108
  M1                           1                             6
  MX                          27                           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"
D37V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1Q32.1) MUTATED     8  42
  DEL PEAK  2(1Q32.1) WILD-TYPE  69 159
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1Q32.1) MUTATED      8   42
  DEL PEAK  2(1Q32.1) WILD-TYPE   69  159
        clus
vv       DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE
  FEMALE                           8                            69
  MALE                            42                           159
[1] 2 2
[1] FALSE
D37V8, continuous
D37V9, continuous
D37V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1Q32.1) MUTATED       5                         2    39
  DEL PEAK  2(1Q32.1) WILD-TYPE    26                        11   176
D37V11, multiclass
                           clus
vv                          DEL PEAK  2(1Q32.1) MUTATED
  ASIAN                                               5
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              39
                           clus
vv                          DEL PEAK  2(1Q32.1) WILD-TYPE
  ASIAN                                                26
  BLACK OR AFRICAN AMERICAN                            11
  WHITE                                               176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V12, binary
                               cls
clus                              0   1
  DEL PEAK  2(1Q32.1) MUTATED     2  46
  DEL PEAK  2(1Q32.1) WILD-TYPE   3 212
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1Q32.1) MUTATED      2   46
  DEL PEAK  2(1Q32.1) WILD-TYPE    3  212
                        clus
vv                       DEL PEAK  2(1Q32.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          46
                        clus
vv                       DEL PEAK  2(1Q32.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           212
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK  3(2Q22.1) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2Q22.1) MUTATED    57  29
  DEL PEAK  3(2Q22.1) WILD-TYPE 125  59
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           86                           184 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           29                            59 
$`DEL PEAK  3(2Q22.1) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-BL-A13I TCGA-BT-A20P 
       22.29        84.00       103.50         4.83         7.33        17.88 
TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A3PJ 
       14.89         5.06         8.35        17.16         4.67        12.82 
TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A47X TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU 
        8.98        23.01         0.10        12.92         5.46         5.19 
TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IS 
        2.53        18.41         1.81        10.59         2.20        50.27 
TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A4U1 
        9.67        17.98        64.18        67.36        30.67        26.17 
TCGA-E7-A541 TCGA-FD-A3B5 TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SR TCGA-FD-A5BR 
        0.59         8.94        15.88        24.30        19.79        13.38 
TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A6TE TCGA-FD-A6TF 
        5.36        27.45         6.87         2.66         4.11         2.07 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
        2.66         2.20         4.08         6.48        61.94        30.61 
TCGA-G2-A2EL TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3OO TCGA-GC-A3RD 
       26.93         0.85        52.67         6.94        15.81        14.07 
TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A763 
        2.66         2.10        20.98         2.20         7.59        27.09 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QK 
        4.73        10.65         4.41         6.41         5.69         6.67 
TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-LT-A5Z6 
        8.22         3.45         6.48         1.74         1.81         3.45 
TCGA-MV-A51V TCGA-S5-AA26 TCGA-XF-A8HC TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9T0 
       13.48         3.75         6.58        15.35         1.87        26.27 
TCGA-XF-A9T5 TCGA-XF-AAMF TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN5 TCGA-YC-A9TC 
       66.64        10.82         2.96         6.77        75.39         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M 
        7.96         9.04 

$`DEL PEAK  3(2Q22.1) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KT TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       11.97        98.33        40.08         2.66         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20Q 
        6.58        11.93        19.04        32.84        12.16        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PK 
        5.06        14.96         8.25         5.59         3.65         2.07 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR 
       15.42        28.70         9.99        28.41         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-A47Y TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        0.10         4.90         7.20        16.31         1.84         9.34 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
        2.14        66.41        19.00         8.91       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       16.14        17.62        15.62         7.79       123.85        87.32 
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-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 
        8.28        10.55       140.81        48.00        41.56        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 
       15.68        41.06        43.59        15.35        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-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 
       12.99        14.33         1.22         0.46        12.89        15.68 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SL 
        6.87         4.01        12.43        11.93        45.93        22.45 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS 
        6.12        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-A43Y 
       22.98        14.93        14.96        14.93         3.62        12.13 
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-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        4.83         6.28         6.38        50.66        18.81         9.30 
TCGA-FD-A6TD TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        6.71         4.01        10.85        15.19         7.13         3.48 
TCGA-FT-A3EE TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
        3.25         5.69        35.24        17.26         7.04        20.12 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC 
       19.46         2.89         2.24         4.50        15.91        17.75 
TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R 
        1.12         7.73         3.12         7.36         6.41        11.31 
TCGA-GU-A762 TCGA-GU-A766 TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
        2.04         5.62         6.15         7.63         7.79         4.14 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        6.41        19.07        11.54         1.51         6.74        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R 
        3.06         9.01         8.75         4.67         2.50        10.52 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN 
        4.27         6.38         6.35        11.80        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       14.24         0.85        45.04        88.93        97.45        56.19 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
       17.88        64.80        79.66        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME 
       28.24        18.90         2.24        16.27         2.10        92.98 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 
       54.90         7.63        91.73         8.32        56.48        30.94 
TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       27.06         3.88        10.36         4.83 

  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 
                       103.50                        140.81 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                        8.090                        10.505 
[1] "0.1 - 103.5 (8.1)"  "0.1 - 140.8 (10.5)"
[1] "hr=" "1.2"
D38V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  3(2Q22.1) MUTATED          0       0       27        27       34
  DEL PEAK  3(2Q22.1) WILD-TYPE        1       2       59        66       58
D38V3, 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                           27                            59
  STAGE III                          27                            66
  STAGE IV                           34                            58
[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         22 47  9
  DEL PEAK  3(2Q22.1) WILD-TYPE       60 89 30
D38V4, multiclass
          clus
vv         DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  T0+T1+T2                          22                            60
  T3                                47                            89
  T4                                 9                            30
[1] 3 2
[1] 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    46   9  23   2
  DEL PEAK  3(2Q22.1) WILD-TYPE 120  19  32   5
D38V5, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  N0                          46                           120
  N1                           9                            19
  N2                          23                            32
  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   42  3 42
  DEL PEAK  3(2Q22.1) WILD-TYPE 87  4 99
D38V6, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  M0                          42                            87
  M1                           3                             4
  MX                          42                            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"
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED    29  59
  DEL PEAK  3(2Q22.1) WILD-TYPE  48 142
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     29   59
  DEL PEAK  3(2Q22.1) WILD-TYPE   48  142
        clus
vv       DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  FEMALE                          29                            48
  MALE                            59                           142
[1] 2 2
[1] FALSE
D38V8, continuous
D38V9, continuous
D38V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(2Q22.1) MUTATED       7                         5    68
  DEL PEAK  3(2Q22.1) WILD-TYPE    24                         8   147
D38V11, multiclass
                           clus
vv                          DEL PEAK  3(2Q22.1) MUTATED
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              68
                           clus
vv                          DEL PEAK  3(2Q22.1) WILD-TYPE
  ASIAN                                                24
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                               147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V12, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     2  81
  DEL PEAK  3(2Q22.1) WILD-TYPE   3 177
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      2   81
  DEL PEAK  3(2Q22.1) WILD-TYPE    3  177
                        clus
vv                       DEL PEAK  3(2Q22.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          81
                        clus
vv                       DEL PEAK  3(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           177
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK  4(2Q34) MUTATION ANALYSIS
D39V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  4(2Q34) MUTATED    73  35
  DEL PEAK  4(2Q34) WILD-TYPE 109  53
  DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE 
                        108                         162 
  DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE 
                         35                          53 
$`DEL PEAK  4(2Q34) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A13J 
       22.29        11.97        84.00        98.33         4.83         2.66 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LA 
       19.04        32.84        14.89         5.06         8.35        17.16 
TCGA-BT-A3PH TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ TCGA-CF-A1HS TCGA-CF-A47X 
        4.67        28.70         9.99         8.98         0.43         0.10 
TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A5 TCGA-DK-A1AC 
       12.92         5.46         5.19        16.31         2.14       130.88 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        1.81        10.59         7.79         2.20         3.98         7.82 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       50.27        21.30         9.67        17.98        64.18        41.56 
TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A4IJ 
       67.36        41.06        30.67        15.35        24.66         0.49 
TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A3SJ 
        0.59         1.22        15.68         8.94        11.93        24.30 
TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ 
       12.82        19.79        13.38         5.36         6.84        27.45 
TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
        6.87         2.66         6.71         4.11         2.07         2.66 
TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EL 
        2.20         4.08         6.48        61.94         5.69        26.93 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC 
        0.85        52.67        15.81         4.50        14.07        17.75 
TCGA-GC-A3YS TCGA-GD-A3OP TCGA-GU-A42P TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV 
        1.12         2.10         6.41         4.73        10.65         4.41 
TCGA-GV-A3JW TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA 
        6.41         7.79         4.14         6.67        19.07        11.54 
TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC 
       38.60         8.22         8.75         3.45         4.67         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-A6FN TCGA-S5-AA26 TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SW TCGA-XF-A9SX 
       16.67         3.75        15.35         1.87        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-AAMF TCGA-XF-AAMT TCGA-YF-AA3L 
       21.04        26.27         2.24        10.82         2.96         7.96 

$`DEL PEAK  4(2Q34) WILD-TYPE`
TCGA-2F-A9KR TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
      103.50        40.08         7.33         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-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
        8.25         5.59         3.65        12.82         2.07        15.42 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47S 
       28.41         1.94        23.01         0.46         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-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
        1.84         9.34         2.53        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I4 
        8.91       112.44        16.14        17.62        15.62       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX 
       87.32         8.22        10.49        20.02         8.28        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-E5-A2PC TCGA-E5-A4U1 
      140.81        48.00        76.60        15.68        43.59        26.17 
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-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 
       12.99        14.33         0.46        12.89         6.87         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO 
       12.43        15.88        45.93        22.45         6.12         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       13.18        46.78         1.97        22.98        14.93        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       14.93         3.62        12.13        37.15        11.01         6.87 
TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
        5.69        49.68         4.83         6.28         6.38        50.66 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
       18.81         9.30         4.01        10.85        15.19         7.13 
TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
        3.48         3.25        30.61        35.24        17.26         7.04 
TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RC 
       20.12         6.94        19.46         2.89         2.24        15.91 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
        2.66         7.73         3.12        20.98         2.20         7.36 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GV-A3JX 
        7.59        11.31         2.04        27.09         5.62         6.15 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A40E TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF 
        5.69         7.63         6.41         1.51         6.74         3.06 
TCGA-HQ-A5ND TCGA-K4-A4AB TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A8JT TCGA-PQ-A6FI 
        9.01         2.50         4.27         6.38        11.80        12.23 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
       14.24         0.85        45.04         6.58        88.93        97.45 
TCGA-XF-A8HF TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SZ TCGA-XF-A9T2 
       56.19        17.88        64.80        79.66        28.24        18.90 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMJ TCGA-XF-AAML 
       16.27        66.64         2.10        92.98        54.90         7.63 
TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 
       91.73         8.32         6.77        56.48        30.94        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3M 
       75.39         3.88        10.36         4.83         0.66         9.04 

  DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE 
                       0.10                        0.07 
  DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE 
                     130.88                      140.81 
  DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE 
                      8.550                      10.425 
[1] "0.1 - 130.9 (8.6)"  "0.1 - 140.8 (10.4)"
[1] "hr=" "1.1"
D39V2, continuous
                             vv
clus                          STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  4(2Q34) MUTATED          1       0       34        31       42
  DEL PEAK  4(2Q34) WILD-TYPE        0       2       52        62       50
D39V3, multiclass
           clus
vv          DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE
  STAGE 0A                          1                           0
  STAGE I                           0                           2
  STAGE II                         34                          52
  STAGE III                        31                          62
  STAGE IV                         42                          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  4(2Q34) MUTATED         30 56 14
  DEL PEAK  4(2Q34) WILD-TYPE       52 80 25
D39V4, multiclass
          clus
vv         DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE
  T0+T1+T2                        30                          52
  T3                              56                          80
  T4                              14                          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  4(2Q34) MUTATED    60   9  31   2
  DEL PEAK  4(2Q34) WILD-TYPE 106  19  24   5
D39V5, multiclass
    clus
vv   DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE
  N0                        60                         106
  N1                         9                          19
  N2                        31                          24
  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(2Q34) MUTATED   49  2 58
  DEL PEAK  4(2Q34) WILD-TYPE 80  5 83
D39V6, multiclass
    clus
vv   DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE
  M0                        49                          80
  M1                         2                           5
  MX                        58                          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"
D39V7, binary
                             cls
clus                            0   1
  DEL PEAK  4(2Q34) MUTATED    28  82
  DEL PEAK  4(2Q34) WILD-TYPE  49 119
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2Q34) MUTATED     28   82
  DEL PEAK  4(2Q34) WILD-TYPE   49  119
        clus
vv       DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE
  FEMALE                        28                          49
  MALE                          82                         119
[1] 2 2
[1] FALSE
D39V8, continuous
D39V9, continuous
D39V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q34) MUTATED       8                         5    89
  DEL PEAK  4(2Q34) WILD-TYPE    23                         8   126
D39V11, multiclass
                           clus
vv                          DEL PEAK  4(2Q34) MUTATED
  ASIAN                                             8
  BLACK OR AFRICAN AMERICAN                         5
  WHITE                                            89
                           clus
vv                          DEL PEAK  4(2Q34) WILD-TYPE
  ASIAN                                              23
  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"
D39V12, binary
                             cls
clus                            0   1
  DEL PEAK  4(2Q34) MUTATED     2 100
  DEL PEAK  4(2Q34) WILD-TYPE   3 158
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2Q34) MUTATED      2  100
  DEL PEAK  4(2Q34) WILD-TYPE    3  158
                        clus
vv                       DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE
  HISPANIC OR LATINO                             2                           3
  NOT HISPANIC OR LATINO                       100                         158
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK  5(2Q37.1) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  5(2Q37.1) MUTATED   89 45
  DEL PEAK  5(2Q37.1) WILD-TYPE 93 43
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                          134                           136 
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                           45                            43 
$`DEL PEAK  5(2Q37.1) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A13J 
       22.29        11.97        84.00        98.33         4.83         2.66 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W 
       19.04        32.84        19.50        14.89         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        8.25        17.16         4.67        15.42        28.70         9.99 
TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47X TCGA-CU-A0YN TCGA-CU-A0YR 
        8.98         0.46         0.43         0.10        12.92         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1AC 
        5.46         5.19        16.31         1.84         2.14       130.88 
TCGA-DK-A1AD TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IL 
      112.44        15.62         1.81        10.59         2.20         3.98 
TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X2 
        7.82        50.27        21.30        20.02         9.67        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4TZ 
       64.18        41.56        67.36        41.06        30.67        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A7DV 
       26.17        24.66         0.49         0.59         0.56         1.22 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SR 
       15.68         8.94        11.93        24.30        12.82        19.79 
TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ 
        1.97         3.62        13.38         5.36         6.84        27.45 
TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
        6.87         2.66         9.30         6.71         4.11         2.07 
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-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB 
       26.93         0.85        52.67        19.46        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A3OP TCGA-GU-A42P 
       15.91        14.07        17.75         1.12         2.10         6.41 
TCGA-GU-A762 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
        2.04         4.73        10.65         4.41         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-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       38.60         9.01         8.22         8.75         3.45         4.67 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-LC-A66R 
        6.48        10.52         1.74         1.81         4.27         6.35 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB 
        3.45        13.48        16.67         0.85         3.75        45.04 
TCGA-XF-A8HC TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        6.58        15.35         1.87        11.90        23.64        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-AAMF TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN1 
       26.27         2.24        10.82         2.96         8.32        30.94 
TCGA-YF-AA3L TCGA-YF-AA3M 
        7.96         9.04 

$`DEL PEAK  5(2Q37.1) WILD-TYPE`
TCGA-2F-A9KR TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
      103.50        40.08         7.33         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A2LB 
       11.93        12.16        17.88         5.06        14.96         5.59 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 
        3.65        12.82         2.07        28.41         1.94        23.01 
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-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
        4.90         9.34         2.53        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
        8.91        16.14        17.62         7.79       123.85        87.32 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
        8.22        10.49         8.28        10.55       140.81        48.00 
TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-E5-A2PC TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KF 
       76.60        15.68        43.59         0.10         0.53         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B3 
        1.38         0.82        12.99        14.33         0.46        12.89 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL 
        6.87         4.01        12.43        15.88        45.93        22.45 
TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43P 
        6.12         5.52        13.18        46.78        22.98        14.93 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       14.96        14.93        12.13        37.15        11.01         6.87 
TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
        5.69        49.68         4.83         6.28         6.38        50.66 
TCGA-FD-A6TB TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
       18.81         4.01        10.85        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-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ 
        6.94         2.89         2.24         2.66         7.73         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 
       20.98         2.20         7.36         7.59        11.31        27.09 
TCGA-GU-A766 TCGA-GV-A3JZ TCGA-GV-A40E TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF 
        5.62         5.69         6.41         1.51         6.74         3.06 
TCGA-K4-A4AB TCGA-K4-A83P TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-R3-A69X TCGA-XF-A8HD 
        2.50         6.38        11.80        12.23        14.24        88.93 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SZ 
       97.45        56.19        17.88        64.80        79.66        28.24 
TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMJ 
       18.90        16.27        66.64         2.10        92.98        54.90 
TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 
        7.63        91.73         6.77        56.48        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
        3.88        10.36         4.83         0.66 

  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                       130.88                        140.81 
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                         8.55                         10.93 
[1] "0.1 - 130.9 (8.6)"  "0.1 - 140.8 (10.9)"
[1] "hr=" "1.3"
D40V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  5(2Q37.1) MUTATED          1       0       42        36       55
  DEL PEAK  5(2Q37.1) WILD-TYPE        0       2       44        57       37
D40V3, multiclass
           clus
vv          DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             0                             2
  STAGE II                           42                            44
  STAGE III                          36                            57
  STAGE IV                           55                            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  5(2Q37.1) MUTATED         40 66 21
  DEL PEAK  5(2Q37.1) WILD-TYPE       42 70 18
D40V4, multiclass
          clus
vv         DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  T0+T1+T2                          40                            42
  T3                                66                            70
  T4                                21                            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  5(2Q37.1) MUTATED   74 13 39  2
  DEL PEAK  5(2Q37.1) WILD-TYPE 92 15 16  5
D40V5, multiclass
    clus
vv   DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  N0                          74                            92
  N1                          13                            15
  N2                          39                            16
  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  5(2Q37.1) MUTATED   63  2 71
  DEL PEAK  5(2Q37.1) WILD-TYPE 66  5 70
D40V6, multiclass
    clus
vv   DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  M0                          63                            66
  M1                           2                             5
  MX                          71                            70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.1) MUTATED    32 105
  DEL PEAK  5(2Q37.1) WILD-TYPE  45  96
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.1) MUTATED     32  105
  DEL PEAK  5(2Q37.1) WILD-TYPE   45   96
        clus
vv       DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  FEMALE                          32                            45
  MALE                           105                            96
[1] 2 2
[1] FALSE
D40V8, continuous
D40V9, continuous
D40V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(2Q37.1) MUTATED      12                         5   106
  DEL PEAK  5(2Q37.1) WILD-TYPE    19                         8   109
D40V11, multiclass
                           clus
vv                          DEL PEAK  5(2Q37.1) MUTATED
  ASIAN                                              12
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                             106
                           clus
vv                          DEL PEAK  5(2Q37.1) WILD-TYPE
  ASIAN                                                19
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                               109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V12, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.1) MUTATED     4 123
  DEL PEAK  5(2Q37.1) WILD-TYPE   1 135
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.1) MUTATED      4  123
  DEL PEAK  5(2Q37.1) WILD-TYPE    1  135
                        clus
vv                       DEL PEAK  5(2Q37.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         123
                        clus
vv                       DEL PEAK  5(2Q37.1) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           135
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK  6(3P14.2) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(3P14.2) MUTATED    55  23
  DEL PEAK  6(3P14.2) WILD-TYPE 127  65
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           78                           192 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           23                            65 
$`DEL PEAK  6(3P14.2) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KW TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W 
       22.29       103.50         4.83        14.89         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F0 
        8.25        15.42        28.70         9.99         8.98         1.94 
TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-DK-A1A6 
        0.43        12.92         7.20         5.46        16.31        66.41 
TCGA-DK-A1AB TCGA-DK-A2I2 TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3WX 
        8.91         7.79         7.82        10.49        50.27        10.55 
TCGA-DK-A3X1 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B4 
       48.00        41.06        43.59         0.59         1.22        15.68 
TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A43N TCGA-FD-A43Y 
        6.87        11.93        24.30        12.82        22.98        12.13 
TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TF 
        5.36         6.84        27.45        49.68         6.28         2.07 
TCGA-FD-A6TG TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2ES TCGA-G2-A3IB 
        2.66         3.48        61.94        30.61        17.26         7.04 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RB 
       20.12         0.85        52.67        19.46         2.24         4.50 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A767 TCGA-GV-A3JW 
       17.75         1.12         2.20         7.59         4.73         6.41 
TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WV 
       11.54         6.74        38.60         9.01         8.75         4.67 
TCGA-K4-A4AC TCGA-K4-A6MB TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD TCGA-XF-A8HI 
        6.48         4.27        12.23        16.67        88.93        17.88 
TCGA-XF-A9T0 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMT TCGA-XF-AAMW TCGA-YF-AA3M 
       26.27        66.64         2.10         2.96         8.32         9.04 

$`DEL PEAK  6(3P14.2) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       11.97        84.00        98.33        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        11.93        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A2LA 
       12.16        17.88        19.50         5.06        14.96        17.16 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42F 
        5.59         3.65         4.67        12.82         2.07        28.41 
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-A47X TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A3QU TCGA-CU-A5W6 
        0.07         0.10         0.10         4.90         5.19         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AC 
        9.34         2.53         2.14        18.41        19.00       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IT 
      123.85        87.32         2.20         3.98         8.22        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV 
       20.02         9.67         8.28       140.81        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A4TZ 
       41.56        76.60        67.36        15.68        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-A6ME TCGA-E7-A6MF TCGA-E7-A7XN 
        0.66         1.38         0.82        12.99        14.33         0.46 
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         6.12         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-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        4.83         6.38        50.66        18.81         9.30         6.71 
TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        4.11         2.20         4.01        10.85        15.19         7.13 
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-AA3C TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 
        6.94         2.89        15.81        15.91        14.07         2.66 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P 
        7.73         2.10         3.12        20.98         7.36         6.41 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JV 
       11.31         2.04        27.09         5.62        10.65         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-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WU 
        6.41        19.07         1.51         3.06         8.22         3.45 
TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R 
        2.50        10.52         1.74         1.81         6.38         6.35 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
        3.45        11.80        13.48        14.24         0.85         3.75 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH 
       45.04         6.58        97.45        56.19        15.35         1.87 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       64.80        79.66        11.90        23.64        21.04        28.24 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ 
       18.90         2.24        16.27        92.98        10.82        54.90 
TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 
        7.63        91.73         6.77        56.48        30.94        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39         3.88        10.36         4.83         0.66         7.96 

  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 
                       103.50                        140.81 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                        9.025                         9.320 
[1] "0.4 - 103.5 (9.0)" "0.1 - 140.8 (9.3)"
[1] "hr=" "1.2"
D41V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  6(3P14.2) MUTATED          1       0       20        26       30
  DEL PEAK  6(3P14.2) WILD-TYPE        0       2       66        67       62
D41V3, 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                           20                            66
  STAGE III                          26                            67
  STAGE IV                           30                            62
[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         21 42  8
  DEL PEAK  6(3P14.2) WILD-TYPE       61 94 31
D41V4, multiclass
          clus
vv         DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  T0+T1+T2                          21                            61
  T3                                42                            94
  T4                                 8                            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
  DEL PEAK  6(3P14.2) MUTATED    45  12  11   4
  DEL PEAK  6(3P14.2) WILD-TYPE 121  16  44   3
D41V5, multiclass
    clus
vv   DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  N0                          45                           121
  N1                          12                            16
  N2                          11                            44
  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   32  4 42
  DEL PEAK  6(3P14.2) WILD-TYPE 97  3 99
D41V6, multiclass
    clus
vv   DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  M0                          32                            97
  M1                           4                             3
  MX                          42                            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"
D41V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P14.2) MUTATED    27  52
  DEL PEAK  6(3P14.2) WILD-TYPE  50 149
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED     27   52
  DEL PEAK  6(3P14.2) WILD-TYPE   50  149
        clus
vv       DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  FEMALE                          27                            50
  MALE                            52                           149
[1] 2 2
[1] FALSE
D41V8, continuous
D41V9, continuous
D41V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(3P14.2) MUTATED       2                         5    64
  DEL PEAK  6(3P14.2) WILD-TYPE    29                         8   151
D41V11, multiclass
                           clus
vv                          DEL PEAK  6(3P14.2) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              64
                           clus
vv                          DEL PEAK  6(3P14.2) WILD-TYPE
  ASIAN                                                29
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                               151
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V12, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P14.2) MUTATED     2  69
  DEL PEAK  6(3P14.2) WILD-TYPE   3 189
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED      2   69
  DEL PEAK  6(3P14.2) WILD-TYPE    3  189
                        clus
vv                       DEL PEAK  6(3P14.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          69
                        clus
vv                       DEL PEAK  6(3P14.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           189
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK  7(4Q22.1) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(4Q22.1) MUTATED    71  31
  DEL PEAK  7(4Q22.1) WILD-TYPE 111  57
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                          102                           168 
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                           31                            57 
$`DEL PEAK  7(4Q22.1) MUTATED`
TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A13I TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V 
       98.33         4.83         7.33         5.06        14.96         5.06 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C 
        5.59         3.65         4.67        12.82        15.42        28.70 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47V 
       28.41         1.94        23.01         0.46         0.43         0.10 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AD 
       12.92         4.90         7.20         2.53        18.41       112.44 
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-A3IQ TCGA-DK-A3IT TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B2 
        8.22        10.49        21.30        17.98        64.18        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       41.06        30.67        43.59        15.35        26.17        24.66 
TCGA-E7-A541 TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SL 
        0.59        12.89         6.87         4.01        24.30        22.45 
TCGA-FD-A3SO TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62N 
        5.52        12.13        13.38         6.84        49.68         2.66 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TH 
        4.83         6.28         6.38         9.30         2.66         2.20 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A2EF TCGA-G2-A2EL TCGA-G2-A2EO 
       10.85        15.19         4.08        61.94        26.93        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A6I1 
       17.26         7.04         2.89        15.81         4.50         2.66 
TCGA-GD-A2C5 TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 TCGA-GV-A3JV TCGA-GV-A3QH 
        7.73         2.20         7.59         2.04         4.41         7.79 
TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AC 
       11.54         6.74         3.06         8.75         4.67         6.48 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-PQ-A6FI TCGA-PQ-A6FN 
       10.52         1.74         1.81         4.27        12.23        16.67 
TCGA-R3-A69X TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SX TCGA-XF-A9T0 
       14.24         6.58        56.19        15.35        23.64        26.27 
TCGA-XF-A9T5 TCGA-XF-AAMJ TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-YF-AA3M 
       66.64        54.90         2.96         8.32        56.48         9.04 

$`DEL PEAK  7(4Q22.1) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-BL-A0C8 TCGA-BL-A13J 
       22.29        11.97        84.00       103.50        40.08         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        11.93        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A20X 
       12.16        17.88        19.50        14.89         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A3PK TCGA-BT-A42E TCGA-C4-A0EZ TCGA-CF-A27C TCGA-CF-A47S 
       17.16         2.07         9.99         8.98         0.69         0.13 
TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A3KJ TCGA-CU-A3QU 
        0.07         0.07         0.10         0.10         5.46         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA 
       16.31         1.84         9.34         2.14        66.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I4 
        8.91       130.88        16.14        17.62        15.62       123.85 
TCGA-DK-A3IL TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
        3.98        50.27        20.02         9.67         8.28        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-E7-A3Y1 
      140.81        48.00        41.56        76.60        67.36         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-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.99        14.33         1.22         0.46        15.68         8.94 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SN 
       12.43        11.93        15.88        45.93         6.12        12.82 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       13.18        46.78        19.79         1.97        22.98        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-A6TA TCGA-FD-A6TB 
        5.36         5.69        27.45         6.87        50.66        18.81 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        6.71         4.11         2.07         4.01         7.13         3.48 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A3IE TCGA-G2-A3VY 
        3.25         6.48        30.61         5.69        20.12         0.85 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD 
       52.67         6.94        19.46         2.24        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B 
       17.75         1.12         2.10         3.12        20.98         7.36 
TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
        6.41        11.31        27.09         5.62         4.73        10.65 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK 
        6.41         6.15         5.69         7.63         4.14         6.67 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE 
        6.41        19.07         1.51        38.60         9.01         8.22 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
        3.45         2.50         6.38         6.35         3.45        11.80 
TCGA-MV-A51V TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE 
       13.48         0.85         3.75        45.04        88.93        97.45 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SY 
        1.87        17.88        64.80        79.66        11.90        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME 
       28.24        18.90         2.24        16.27         2.10        92.98 
TCGA-XF-AAMF TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAN1 TCGA-XF-AAN4 
       10.82         7.63        91.73         6.77        30.94        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39         3.88        10.36         4.83         0.66         7.96 

  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                       112.44                        140.81 
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                        8.535                         9.830 
[1] "0.1 - 112.4 (8.5)" "0.1 - 140.8 (9.8)"
[1] "hr=" "1.1"
D42V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  7(4Q22.1) MUTATED          1       0       29        35       37
  DEL PEAK  7(4Q22.1) WILD-TYPE        0       2       57        58       55
D42V3, multiclass
           clus
vv          DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             0                             2
  STAGE II                           29                            57
  STAGE III                          35                            58
  STAGE IV                           37                            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
  DEL PEAK  7(4Q22.1) MUTATED         28 57 11
  DEL PEAK  7(4Q22.1) WILD-TYPE       54 79 28
D42V4, multiclass
          clus
vv         DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  T0+T1+T2                          28                            54
  T3                                57                            79
  T4                                11                            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
  DEL PEAK  7(4Q22.1) MUTATED    61  11  24   2
  DEL PEAK  7(4Q22.1) WILD-TYPE 105  17  31   5
D42V5, multiclass
    clus
vv   DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  N0                          61                           105
  N1                          11                            17
  N2                          24                            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  7(4Q22.1) MUTATED   50  2 52
  DEL PEAK  7(4Q22.1) WILD-TYPE 79  5 89
D42V6, multiclass
    clus
vv   DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  M0                          50                            79
  M1                           2                             5
  MX                          52                            89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q22.1) MUTATED    31  73
  DEL PEAK  7(4Q22.1) WILD-TYPE  46 128
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED     31   73
  DEL PEAK  7(4Q22.1) WILD-TYPE   46  128
        clus
vv       DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  FEMALE                          31                            46
  MALE                            73                           128
[1] 2 2
[1] FALSE
D42V8, continuous
D42V9, continuous
D42V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(4Q22.1) MUTATED       9                         5    82
  DEL PEAK  7(4Q22.1) WILD-TYPE    22                         8   133
D42V11, multiclass
                           clus
vv                          DEL PEAK  7(4Q22.1) MUTATED
  ASIAN                                               9
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              82
                           clus
vv                          DEL PEAK  7(4Q22.1) WILD-TYPE
  ASIAN                                                22
  BLACK OR AFRICAN AMERICAN                             8
  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"
D42V12, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q22.1) MUTATED     1  97
  DEL PEAK  7(4Q22.1) WILD-TYPE   4 161
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED      1   97
  DEL PEAK  7(4Q22.1) WILD-TYPE    4  161
                        clus
vv                       DEL PEAK  7(4Q22.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          97
                        clus
vv                       DEL PEAK  7(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           161
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK  8(4Q34.2) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  8(4Q34.2) MUTATED   83 33
  DEL PEAK  8(4Q34.2) WILD-TYPE 99 55
  DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE 
                          116                           154 
  DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE 
                           33                            55 
$`DEL PEAK  8(4Q34.2) MUTATED`
TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A13J TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20T 
       98.33         4.83         2.66        32.84         5.06        14.89 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A42B 
        5.06         8.35         5.59         3.65         4.67        15.42 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS 
       28.70         9.99        28.41         1.94         0.46         0.43 
TCGA-CF-A47S TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A1A3 TCGA-DK-A1A7 
        0.13        12.92         4.90         7.20         2.53        18.41 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 
      112.44        16.14         1.81        10.59         7.79        87.32 
TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A6AV TCGA-DK-A6B2 
        2.20         7.82         8.22        21.30        64.18        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A541 TCGA-FD-A3B3 
       41.06        30.67        43.59        15.35         0.59        12.89 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A43N 
        6.87         4.01        22.45        12.82         5.52        22.98 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
       12.13        13.38         6.84        49.68         2.66         4.83 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28         6.38        50.66         9.30         6.71         4.11 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
        2.07         2.66         2.20        10.85        15.19         4.08 
TCGA-G2-A2EF TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       61.94        26.93         7.04        20.12         0.85        52.67 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC 
       19.46         2.89        15.81         4.50        15.91        17.75 
TCGA-GD-A2C5 TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 TCGA-GV-A3JV TCGA-GV-A3JW 
        7.73         2.20         7.59         2.04         4.41         6.41 
TCGA-GV-A3QH TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
        7.79        19.07        11.54         6.74        38.60         3.06 
TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
        8.75         4.67         6.48        10.52         1.74         1.81 
TCGA-K4-A6MB TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-XF-A8HB 
        4.27         3.45        13.48        16.67        14.24        45.04 
TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 
        6.58        56.19        15.35        23.64        21.04        26.27 
TCGA-XF-A9T5 TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       66.64        10.82        54.90         2.96         8.32         6.77 
TCGA-XF-AAN0 TCGA-YF-AA3M 
       56.48         9.04 

$`DEL PEAK  8(4Q34.2) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-BL-A0C8 TCGA-BL-A13I 
       22.29        11.97        84.00       103.50        40.08         7.33 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        6.74        12.39         6.58        11.93        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ 
       17.88        19.50        14.96         8.25        17.16        12.82 
TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47T TCGA-CF-A47V 
        2.07         8.98        23.01         0.69         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
        0.07         0.10         0.10         5.46         5.19        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB 
        1.84         9.34         2.14        66.41        19.00         8.91 
TCGA-DK-A1AC TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IQ 
      130.88        17.62        15.62       123.85         3.98        10.49 
TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       50.27        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-E5-A4U1 
       48.00        17.98        41.56        76.60        67.36        26.17 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF 
       24.66         0.10         0.49         0.53         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN 
        1.38         0.82        12.99        14.33         1.22         0.46 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       15.68         8.94        12.43        11.93        15.88        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       24.30         6.12        13.18        46.78        19.79         1.97 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT 
       14.93        14.96        14.93         3.62        37.15        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A6TB 
        6.87         5.36         5.69        27.45         6.87        18.81 
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-A2EO TCGA-G2-A2ES TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3RD 
        5.69        35.24        17.26         6.94         2.24        14.07 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B 
        1.12         2.66         2.10         3.12        20.98         7.36 
TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
        6.41        11.31        27.09         5.62         4.73        10.65 
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-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A83P 
        1.51         9.01         8.22         3.45         2.50         6.38 
TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HD 
        6.35        11.80        12.23         0.85         3.75        88.93 
TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW 
       97.45         1.87        17.88        64.80        79.66        11.90 
TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME 
       28.24        18.90         2.24        16.27         2.10        92.98 
TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
        7.63        91.73        30.94        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       10.36         4.83         0.66         7.96 

  DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE 
                         0.13                          0.07 
  DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE 
                       112.44                        140.81 
  DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE 
                        8.550                        10.015 
[1] "0.1 - 112.4 (8.6)"  "0.1 - 140.8 (10.0)"
[1] "hr=" "1.2"
D43V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  8(4Q34.2) MUTATED          1       0       33        37       44
  DEL PEAK  8(4Q34.2) WILD-TYPE        0       2       53        56       48
D43V3, multiclass
           clus
vv          DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             0                             2
  STAGE II                           33                            53
  STAGE III                          37                            56
  STAGE IV                           44                            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  8(4Q34.2) MUTATED         30 64 13
  DEL PEAK  8(4Q34.2) WILD-TYPE       52 72 26
D43V4, multiclass
          clus
vv         DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE
  T0+T1+T2                          30                            52
  T3                                64                            72
  T4                                13                            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  8(4Q34.2) MUTATED    66  13  29   1
  DEL PEAK  8(4Q34.2) WILD-TYPE 100  15  26   6
D43V5, multiclass
    clus
vv   DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE
  N0                          66                           100
  N1                          13                            15
  N2                          29                            26
  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  8(4Q34.2) MUTATED   49  3 65
  DEL PEAK  8(4Q34.2) WILD-TYPE 80  4 76
D43V6, multiclass
    clus
vv   DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE
  M0                          49                            80
  M1                           3                             4
  MX                          65                            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"
D43V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q34.2) MUTATED    33  85
  DEL PEAK  8(4Q34.2) WILD-TYPE  44 116
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q34.2) MUTATED     33   85
  DEL PEAK  8(4Q34.2) WILD-TYPE   44  116
        clus
vv       DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE
  FEMALE                          33                            44
  MALE                            85                           116
[1] 2 2
[1] FALSE
D43V8, continuous
D43V9, continuous
D43V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(4Q34.2) MUTATED      10                         6    92
  DEL PEAK  8(4Q34.2) WILD-TYPE    21                         7   123
D43V11, multiclass
                           clus
vv                          DEL PEAK  8(4Q34.2) MUTATED
  ASIAN                                              10
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                              92
                           clus
vv                          DEL PEAK  8(4Q34.2) WILD-TYPE
  ASIAN                                                21
  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"
D43V12, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q34.2) MUTATED     3 108
  DEL PEAK  8(4Q34.2) WILD-TYPE   2 150
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q34.2) MUTATED      3  108
  DEL PEAK  8(4Q34.2) WILD-TYPE    2  150
                        clus
vv                       DEL PEAK  8(4Q34.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         108
                        clus
vv                       DEL PEAK  8(4Q34.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           150
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK  9(5Q12.1) MUTATION ANALYSIS
D44V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  9(5Q12.1) MUTATED   86 47
  DEL PEAK  9(5Q12.1) WILD-TYPE 96 41
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                          133                           137 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           47                            41 
$`DEL PEAK  9(5Q12.1) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 TCGA-BL-A13I 
       22.29        11.97        98.33         4.83        40.08         7.33 
TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V 
        6.58        19.04        32.84         5.06        14.89         5.06 
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-A42B TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CU-A3QU 
       15.42         9.99        23.01         0.46         0.43         5.19 
TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 
        2.14        18.41       112.44        10.59       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        2.20         3.98         7.82         8.22        10.49        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A3X2 
       21.30        20.02         9.67        10.55        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       64.18        15.68        41.06        43.59        15.35        26.17 
TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A6ME TCGA-E7-A7DV TCGA-FD-A3B5 
       24.66         0.49         0.59        12.99         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         6.12        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-A6TB 
       27.45         6.87         2.66         4.83         6.38        18.81 
TCGA-FD-A6TC TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZE 
        9.30         2.07         2.66        10.85        15.19         3.48 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3VY 
        4.08         6.48        61.94        26.93         7.04         0.85 
TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 
       52.67        19.46        15.81         1.12         2.66         7.73 
TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A767 
        2.10         2.20         7.36         6.41         2.04         4.73 
TCGA-GU-AATO TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       10.65         6.41         6.15         7.63         7.79         4.14 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
        6.41        19.07        11.54         6.74        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        9.01         8.22         3.45         4.67         2.50         6.48 
TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X 
       10.52         1.81         4.27        13.48        16.67        14.24 
TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T3 
        6.58        56.19        15.35        23.64        28.24         2.24 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-YF-AA3L 
       54.90         7.63         2.96         6.77        56.48         7.96 
TCGA-YF-AA3M 
        9.04 

$`DEL PEAK  9(5Q12.1) WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX 
       84.00       103.50         2.66         6.74        12.39        11.93 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A3PK 
       12.16        17.88        19.50        14.96         8.25         2.07 
TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A27C TCGA-CF-A47S 
       28.70        28.41         8.98         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-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        4.90         7.20         5.46        16.31         1.84         9.34 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE 
        2.53        66.41        19.00         8.91       130.88        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A3WW TCGA-DK-A3WY 
       17.62        15.62         1.81         7.79         8.28       140.81 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       41.56        76.60        67.36        30.67         0.10         0.53 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN 
        0.56         0.66         1.38         0.82        14.33         0.46 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA 
       12.89        15.68         4.01        12.43        15.88        45.93 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       12.82         5.52        46.78        22.98        14.93        14.96 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
        3.62        12.13        37.15        11.01         6.87         5.69 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH 
       49.68         6.28        50.66         6.71         4.11         2.20 
TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO 
        4.01         7.13         3.25        30.61         5.69        35.24 
TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB 
       17.26        20.12         6.94         2.89         2.24         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q 
       15.91        14.07        17.75         3.12        20.98         7.59 
TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A766 TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QK 
       11.31        27.09         5.62         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-LT-A8JT TCGA-PQ-A6FI TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HD 
       11.80        12.23         0.85         3.75        45.04        88.93 
TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW 
       97.45         1.87        17.88        64.80        79.66        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       21.04        26.27        18.90        16.27        66.64         2.10 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAN1 TCGA-XF-AAN4 
       92.98        10.82        91.73         8.32        30.94        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       75.39         3.88        10.36         4.83         0.66 

  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                         0.43                          0.07 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                       123.85                        140.81 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                         8.94                         10.82 
[1] "0.4 - 123.8 (8.9)"  "0.1 - 140.8 (10.8)"
[1] "hr=" "1.3"
D44V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  9(5Q12.1) MUTATED          1       1       37        41       53
  DEL PEAK  9(5Q12.1) WILD-TYPE        0       1       49        52       39
D44V3, multiclass
           clus
vv          DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             1                             1
  STAGE II                           37                            49
  STAGE III                          41                            52
  STAGE IV                           53                            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  9(5Q12.1) MUTATED         38 70 18
  DEL PEAK  9(5Q12.1) WILD-TYPE       44 66 21
D44V4, multiclass
          clus
vv         DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  T0+T1+T2                          38                            44
  T3                                70                            66
  T4                                18                            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  9(5Q12.1) MUTATED   69 16 34  5
  DEL PEAK  9(5Q12.1) WILD-TYPE 97 12 21  2
D44V5, multiclass
    clus
vv   DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  N0                          69                            97
  N1                          16                            12
  N2                          34                            21
  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  9(5Q12.1) MUTATED   59  5 71
  DEL PEAK  9(5Q12.1) WILD-TYPE 70  2 70
D44V6, multiclass
    clus
vv   DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  M0                          59                            70
  M1                           5                             2
  MX                          71                            70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(5Q12.1) MUTATED    36 100
  DEL PEAK  9(5Q12.1) WILD-TYPE  41 101
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED     36  100
  DEL PEAK  9(5Q12.1) WILD-TYPE   41  101
        clus
vv       DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  FEMALE                          36                            41
  MALE                           100                           101
[1] 2 2
[1] FALSE
D44V8, continuous
D44V9, continuous
D44V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(5Q12.1) MUTATED      11                         7   106
  DEL PEAK  9(5Q12.1) WILD-TYPE    20                         6   109
D44V11, multiclass
                           clus
vv                          DEL PEAK  9(5Q12.1) MUTATED
  ASIAN                                              11
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                             106
                           clus
vv                          DEL PEAK  9(5Q12.1) WILD-TYPE
  ASIAN                                                20
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                               109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V12, binary
                               cls
clus                              0   1
  DEL PEAK  9(5Q12.1) MUTATED     2 125
  DEL PEAK  9(5Q12.1) WILD-TYPE   3 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED      2  125
  DEL PEAK  9(5Q12.1) WILD-TYPE    3  133
                        clus
vv                       DEL PEAK  9(5Q12.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         125
                        clus
vv                       DEL PEAK  9(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           133
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 10(6P25.3) MUTATION ANALYSIS
D45V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(6P25.3) MUTATED    42  25
  DEL PEAK 10(6P25.3) WILD-TYPE 140  63
  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                           67                           203 
  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                           25                            63 
$`DEL PEAK 10(6P25.3) MUTATED`
TCGA-2F-A9KW TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        4.83         5.06         8.25        17.16         5.59         3.65 
TCGA-BT-A3PH TCGA-CU-A0YR TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1AB 
        4.67         7.20         1.84         9.34        66.41         8.91 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL 
      130.88         1.81        10.59         7.79       123.85         3.98 
TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A4TZ 
       21.30        48.00        17.98        67.36        30.67        15.35 
TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA 
       26.17         0.49        15.68         6.87         4.01        45.93 
TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A62O TCGA-FD-A62P 
       22.45        12.82        14.93         5.36         4.83         6.28 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A2EO TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GV-A3JZ 
       15.19         4.08        35.24         2.10        20.98         5.69 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HQ 
        7.63         7.79         4.14         6.67         6.41         6.74 
TCGA-HQ-A2OF TCGA-K4-A4AB TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
        3.06         2.50         1.81         3.45        13.48        12.23 
TCGA-R3-A69X TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-AAMF 
       14.24        15.35         1.87        28.24        26.27        10.82 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN5 
       54.90         7.63         8.32         6.77        56.48        75.39 
TCGA-YF-AA3M 
        9.04 

$`DEL PEAK 10(6P25.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-BL-A0C8 
       22.29        11.97        84.00       103.50        98.33        40.08 
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-A20W TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
       14.89        14.96         8.35        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-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-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AA 
        5.19        16.31         2.53         2.14        18.41        19.00 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I6 TCGA-DK-A3IK 
      112.44        16.14        17.62        15.62        87.32         2.20 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV 
        7.82         8.22        10.49        50.27        20.02         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
        8.28        10.55       140.81        64.18        41.56        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       15.68        41.06        43.59        24.66         0.10         0.53 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
        0.59         0.56         0.66         1.38         0.82        12.99 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B8 
       14.33         1.22         0.46        12.89         8.94        12.43 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP 
       11.93        15.88        24.30         6.12         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-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-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        5.69         6.84        27.45         6.87        49.68         2.66 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.38        50.66        18.81         9.30         6.71         4.11 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 
        2.07         2.66         2.20         4.01        10.85         7.13 
TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.48         3.25         6.48        61.94        30.61         5.69 
TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       26.93        17.26         7.04        20.12         0.85        52.67 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
        6.94        19.46         2.89         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 
       15.91        14.07        17.75         1.12         2.66         7.73 
TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
        3.12         2.20         7.36         6.41         7.59        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV 
        2.04        27.09         5.62         4.73        10.65         4.41 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE 
        6.41         6.15        19.07        11.54         1.51        38.60 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC 
        9.01         8.22         8.75         3.45         4.67         6.48 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A8JT 
       10.52         1.74         4.27         6.38         6.35        11.80 
TCGA-PQ-A6FN TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
       16.67         0.85         3.75        45.04         6.58        88.93 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW 
       97.45        56.19        17.88        64.80        79.66        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       23.64        21.04        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAN1 TCGA-XF-AAN4 
        2.10        92.98        91.73         2.96        30.94        27.06 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
        3.88        10.36         4.83         0.66         7.96 

  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                         0.49                          0.07 
  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                       130.88                        140.81 
  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                         8.32                          9.99 
[1] "0.5 - 130.9 (8.3)"  "0.1 - 140.8 (10.0)"
[1] "hr=" "1.2"
D45V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 10(6P25.3) MUTATED          0       0       16        25       27
  DEL PEAK 10(6P25.3) WILD-TYPE        1       2       70        68       65
D45V3, multiclass
           clus
vv          DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE
  STAGE 0A                            0                             1
  STAGE I                             0                             2
  STAGE II                           16                            70
  STAGE III                          25                            68
  STAGE IV                           27                            65
[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(6P25.3) MUTATED         14  32  15
  DEL PEAK 10(6P25.3) WILD-TYPE       68 104  24
D45V4, multiclass
          clus
vv         DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE
  T0+T1+T2                          14                            68
  T3                                32                           104
  T4                                15                            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 10(6P25.3) MUTATED    35   2  20   2
  DEL PEAK 10(6P25.3) WILD-TYPE 131  26  35   5
D45V5, multiclass
    clus
vv   DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE
  N0                          35                           131
  N1                           2                            26
  N2                          20                            35
  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 10(6P25.3) MUTATED    32   2  34
  DEL PEAK 10(6P25.3) WILD-TYPE  97   5 107
D45V6, multiclass
    clus
vv   DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE
  M0                          32                            97
  M1                           2                             5
  MX                          34                           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"
D45V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(6P25.3) MUTATED    22  46
  DEL PEAK 10(6P25.3) WILD-TYPE  55 155
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(6P25.3) MUTATED     22   46
  DEL PEAK 10(6P25.3) WILD-TYPE   55  155
        clus
vv       DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE
  FEMALE                          22                            55
  MALE                            46                           155
[1] 2 2
[1] FALSE
D45V8, continuous
D45V9, continuous
D45V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(6P25.3) MUTATED       3                         5    57
  DEL PEAK 10(6P25.3) WILD-TYPE    28                         8   158
D45V11, multiclass
                           clus
vv                          DEL PEAK 10(6P25.3) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              57
                           clus
vv                          DEL PEAK 10(6P25.3) WILD-TYPE
  ASIAN                                                28
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                               158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V12, binary
                               cls
clus                              0   1
  DEL PEAK 10(6P25.3) MUTATED     2  63
  DEL PEAK 10(6P25.3) WILD-TYPE   3 195
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(6P25.3) MUTATED      2   63
  DEL PEAK 10(6P25.3) WILD-TYPE    3  195
                        clus
vv                       DEL PEAK 10(6P25.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          63
                        clus
vv                       DEL PEAK 10(6P25.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           195
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 11(6Q21) MUTATION ANALYSIS
D46V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 11(6Q21) MUTATED   85 43
  DEL PEAK 11(6Q21) WILD-TYPE 97 45
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                        128                         142 
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                         43                          45 
$`DEL PEAK 11(6Q21) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BT-A20J 
       22.29        84.00       103.50        98.33         4.83        19.04 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
       32.84        14.89         5.06         5.59         3.65         4.67 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A27C 
        2.07        15.42        28.70         1.94         0.46         0.69 
TCGA-CF-A47X TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
        0.10         5.19         1.84         2.53        66.41        18.41 
TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
        8.91         1.81        10.59         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X1 
        2.20         3.98        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        41.06        30.67        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A7DV 
       26.17         0.49         0.59         0.56        12.99         1.22 
TCGA-FD-A3B5 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR 
        8.94        24.30        22.45        12.82        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BU 
        1.97        14.93        14.93        13.38        11.01         6.87 
TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O 
        5.36         6.84        27.45         6.87        49.68         4.83 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
        6.28         6.38         9.30         4.11         2.66         2.20 
TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY 
       15.19         6.48        35.24        17.26        20.12         0.85 
TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A3OP 
       52.67        19.46         2.24        14.07         2.66         2.10 
TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A767 TCGA-GV-A3JW TCGA-GV-A3JX 
        6.41        11.31         2.04         4.73         6.41         6.15 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ 
        7.63         7.79         6.41        19.07        11.54         6.74 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A6FZ TCGA-LT-A5Z6 
       38.60         3.06         4.67         2.50         1.81         3.45 
TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-XF-A8HB TCGA-XF-A8HC 
       13.48        16.67        14.24         0.85        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SI 
       88.93        56.19        15.35         1.87        17.88        79.66 
TCGA-XF-A9SW TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-AAMJ 
       11.90        28.24        26.27         2.24         2.10        54.90 
TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN5 
        7.63        91.73         8.32         6.77        56.48        75.39 
TCGA-YF-AA3L TCGA-YF-AA3M 
        7.96         9.04 

$`DEL PEAK 11(6Q21) WILD-TYPE`
TCGA-2F-A9KP TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       11.97        40.08         7.33         2.66         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
        6.58        11.93        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A42E 
       14.96         8.35         8.25        17.16        12.82         9.99 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T 
       28.41         8.98        23.01         0.43         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-A3KJ TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AC 
        5.46        16.31         9.34         2.14        19.00       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IM TCGA-DK-A3IN 
      112.44        16.14        17.62        15.62         7.82         8.22 
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        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       76.60        67.36        15.68        24.66         0.10         0.53 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B3 
        0.66         1.38         0.82        14.33         0.46        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-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S 
       45.93         6.12         5.52        13.18        22.98        14.96 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BX TCGA-FD-A62N TCGA-FD-A6TA 
        3.62        12.13        37.15         5.69         2.66        50.66 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 
       18.81         6.71         2.07         4.01        10.85         7.13 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.48         4.08         3.25        61.94        30.61         5.69 
TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB 
       26.93         7.04         6.94         2.89        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS 
       15.91        17.75         1.12         7.73         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-AATO 
        2.20         7.36         7.59        27.09         5.62        10.65 
TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A3QK TCGA-H4-A2HO TCGA-HQ-A5ND 
        4.41         5.69         4.14         6.67         1.51         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ 
        8.22         8.75         3.45         6.48        10.52         1.74 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-S5-AA26 
        4.27         6.38         6.35        11.80        12.23         3.75 
TCGA-XF-A8HE TCGA-XF-A9SH TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T4 
       97.45        64.80        23.64        21.04        18.90        16.27 
TCGA-XF-A9T5 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMT TCGA-XF-AAN1 TCGA-XF-AAN4 
       66.64        92.98        10.82         2.96        30.94        27.06 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
        3.88        10.36         4.83         0.66 

  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                       0.10                        0.07 
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                     123.85                      140.81 
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                      9.895                       8.995 
[1] "0.1 - 123.8 (9.9)" "0.1 - 140.8 (9.0)"
[1] "hr=" "1.1"
D46V2, continuous
                             vv
clus                          STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 11(6Q21) MUTATED          1       0       38        36       52
  DEL PEAK 11(6Q21) WILD-TYPE        0       2       48        57       40
D46V3, multiclass
           clus
vv          DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  STAGE 0A                          1                           0
  STAGE I                           0                           2
  STAGE II                         38                          48
  STAGE III                        36                          57
  STAGE IV                         52                          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
  DEL PEAK 11(6Q21) MUTATED         39 65 17
  DEL PEAK 11(6Q21) WILD-TYPE       43 71 22
D46V4, multiclass
          clus
vv         DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  T0+T1+T2                        39                          43
  T3                              65                          71
  T4                              17                          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 11(6Q21) MUTATED   67 12 35  3
  DEL PEAK 11(6Q21) WILD-TYPE 99 16 20  4
D46V5, multiclass
    clus
vv   DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  N0                        67                          99
  N1                        12                          16
  N2                        35                          20
  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 11(6Q21) MUTATED   53  2 74
  DEL PEAK 11(6Q21) WILD-TYPE 76  5 67
D46V6, multiclass
    clus
vv   DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  M0                        53                          76
  M1                         2                           5
  MX                        74                          67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                             cls
clus                            0   1
  DEL PEAK 11(6Q21) MUTATED    41  89
  DEL PEAK 11(6Q21) WILD-TYPE  36 112
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q21) MUTATED     41   89
  DEL PEAK 11(6Q21) WILD-TYPE   36  112
        clus
vv       DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  FEMALE                        41                          36
  MALE                          89                         112
[1] 2 2
[1] FALSE
D46V8, continuous
D46V9, continuous
D46V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(6Q21) MUTATED      13                         7    99
  DEL PEAK 11(6Q21) WILD-TYPE    18                         6   116
D46V11, multiclass
                           clus
vv                          DEL PEAK 11(6Q21) MUTATED
  ASIAN                                            13
  BLACK OR AFRICAN AMERICAN                         7
  WHITE                                            99
                           clus
vv                          DEL PEAK 11(6Q21) WILD-TYPE
  ASIAN                                              18
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                             116
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V12, binary
                             cls
clus                            0   1
  DEL PEAK 11(6Q21) MUTATED     4 119
  DEL PEAK 11(6Q21) WILD-TYPE   1 139
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q21) MUTATED      4  119
  DEL PEAK 11(6Q21) WILD-TYPE    1  139
                        clus
vv                       DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  HISPANIC OR LATINO                             4                           1
  NOT HISPANIC OR LATINO                       119                         139
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 12(6Q27) MUTATION ANALYSIS
D47V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 12(6Q27) MUTATED   84 42
  DEL PEAK 12(6Q27) WILD-TYPE 98 46
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                        126                         144 
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                         42                          46 
$`DEL PEAK 12(6Q27) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BT-A20J TCGA-BT-A20N 
       22.29       103.50        98.33         4.83        19.04        32.84 
TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42C 
        5.06         5.59         3.65         4.67         2.07        28.70 
TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A47X TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A5W6 
        1.94         0.46         0.10         7.20         5.19         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 
        2.53        66.41         8.91       112.44         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN 
        7.79       123.85        87.32         2.20         3.98         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       10.49        50.27        21.30        48.00        17.98        64.18 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A5KE 
       41.06        30.67        43.59        15.35         0.49         0.56 
TCGA-E7-A6ME TCGA-E7-A7DV TCGA-FD-A3B5 TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SQ 
       12.99         1.22         8.94        22.45        12.82        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BU 
       19.79         1.97        12.13        13.38        11.01         6.87 
TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O 
        5.36         6.84        27.45         6.87        49.68         4.83 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG 
        6.28         6.38        50.66         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-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A6I1 
        0.85        19.46         2.24         4.50        14.07         2.66 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A767 
        7.73         2.10         6.41        11.31         2.04         4.73 
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-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
        6.41        19.07        11.54         6.74        38.60         3.06 
TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-MV-A51V 
        8.75         2.50        10.52         1.81         3.45        13.48 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
       16.67        14.24         0.85        45.04         6.58        88.93 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SI TCGA-XF-A9SW 
       56.19        15.35         1.87        17.88        79.66        11.90 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR 
       28.24        26.27         2.24        54.90         7.63        91.73 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN5 TCGA-YF-AA3L TCGA-YF-AA3M 
        8.32         6.77        56.48        75.39         7.96         9.04 

$`DEL PEAK 12(6Q27) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       11.97        84.00        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       12.39         6.58        11.93        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
        5.06        14.89        14.96         8.35         8.25        17.16 
TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 
       12.82        15.42         9.99        28.41         8.98        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-A0YO TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A72E 
        0.10        12.92         4.90         5.46        16.31         9.34 
TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF 
        2.14        18.41        19.00       130.88        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A3IM TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       15.62         7.82        20.02         9.67         8.28        10.55 
TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-E5-A4U1 
      140.81        41.56        76.60        67.36        15.68        26.17 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 
       24.66         0.10         0.53         0.59         0.66         1.38 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 
        0.82        14.33         0.46        12.89        15.68         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-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
        6.12         5.52        13.18        22.98        14.93        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BX TCGA-FD-A62N TCGA-FD-A6TB 
       14.93         3.62        37.15         5.69         2.66        18.81 
TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        6.71         2.07         4.01        10.85         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-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RC 
        7.04        52.67         6.94         2.89        15.81        15.91 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
       17.75         1.12         3.12        20.98         2.20         7.36 
TCGA-GU-A42Q TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3QK 
        7.59        27.09         5.62        10.65         4.41         6.67 
TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC 
        1.51         9.01         8.22         3.45         4.67         6.48 
TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FI 
        1.74         4.27         6.38         6.35        11.80        12.23 
TCGA-S5-AA26 TCGA-XF-A8HE TCGA-XF-A9SH TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T2 
        3.75        97.45        64.80        23.64        21.04        18.90 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMT 
       16.27        66.64         2.10        92.98        10.82         2.96 
TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       30.94        27.06         3.88        10.36         4.83         0.66 

  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                       0.10                        0.07 
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                     123.85                      140.81 
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                      8.830                      10.175 
[1] "0.1 - 123.8 (8.8)"  "0.1 - 140.8 (10.2)"
[1] "hr=" "1"  
D47V2, continuous
                             vv
clus                          STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 12(6Q27) MUTATED          1       0       34        39       52
  DEL PEAK 12(6Q27) WILD-TYPE        0       2       52        54       40
D47V3, multiclass
           clus
vv          DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE
  STAGE 0A                          1                           0
  STAGE I                           0                           2
  STAGE II                         34                          52
  STAGE III                        39                          54
  STAGE IV                         52                          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
  DEL PEAK 12(6Q27) MUTATED         35 65 19
  DEL PEAK 12(6Q27) WILD-TYPE       47 71 20
D47V4, multiclass
          clus
vv         DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE
  T0+T1+T2                        35                          47
  T3                              65                          71
  T4                              19                          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 12(6Q27) MUTATED    65  10  36   4
  DEL PEAK 12(6Q27) WILD-TYPE 101  18  19   3
D47V5, multiclass
    clus
vv   DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE
  N0                        65                         101
  N1                        10                          18
  N2                        36                          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 12(6Q27) MUTATED   51  2 74
  DEL PEAK 12(6Q27) WILD-TYPE 78  5 67
D47V6, multiclass
    clus
vv   DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE
  M0                        51                          78
  M1                         2                           5
  MX                        74                          67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q27) MUTATED    38  90
  DEL PEAK 12(6Q27) WILD-TYPE  39 111
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q27) MUTATED     38   90
  DEL PEAK 12(6Q27) WILD-TYPE   39  111
        clus
vv       DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE
  FEMALE                        38                          39
  MALE                          90                         111
[1] 2 2
[1] FALSE
D47V8, continuous
D47V9, continuous
D47V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(6Q27) MUTATED      12                         6    99
  DEL PEAK 12(6Q27) WILD-TYPE    19                         7   116
D47V11, multiclass
                           clus
vv                          DEL PEAK 12(6Q27) MUTATED
  ASIAN                                            12
  BLACK OR AFRICAN AMERICAN                         6
  WHITE                                            99
                           clus
vv                          DEL PEAK 12(6Q27) WILD-TYPE
  ASIAN                                              19
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                             116
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V12, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q27) MUTATED     4 116
  DEL PEAK 12(6Q27) WILD-TYPE   1 142
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q27) MUTATED      4  116
  DEL PEAK 12(6Q27) WILD-TYPE    1  142
                        clus
vv                       DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE
  HISPANIC OR LATINO                             4                           1
  NOT HISPANIC OR LATINO                       116                         142
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 13(7Q36.3) MUTATION ANALYSIS
D48V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(7Q36.3) MUTATED    30   9
  DEL PEAK 13(7Q36.3) WILD-TYPE 152  79
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                           39                           231 
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                            9                            79 
$`DEL PEAK 13(7Q36.3) MUTATED`
TCGA-2F-A9KW TCGA-BT-A20N TCGA-BT-A20X TCGA-CF-A1HS TCGA-CF-A47X TCGA-DK-A2I4 
        4.83        32.84         8.25         0.43         0.10       123.85 
TCGA-DK-A3IK TCGA-DK-A3IM TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A6ME TCGA-FD-A3N6 
        2.20         7.82        15.35        26.17        12.99        15.88 
TCGA-FD-A3NA TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A6TA TCGA-FD-A6TE 
       45.93         6.84        27.45         6.87        50.66         4.11 
TCGA-FD-A6TF TCGA-FJ-A3ZF TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3YS 
        2.07         4.08         2.24         4.50        14.07         1.12 
TCGA-GC-A6I1 TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3QI TCGA-K4-A3WS 
        2.66         2.04         5.62        10.65         4.14         8.75 
TCGA-K4-A6MB TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-XF-A8HD 
        4.27         6.35         3.45        12.23        16.67        88.93 
TCGA-XF-AAML TCGA-XF-AAMT TCGA-YF-AA3M 
        7.63         2.96         9.04 

$`DEL PEAK 13(7Q36.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-BL-A0C8 
       22.29        11.97        84.00       103.50        98.33        40.08 
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-A20T 
       19.04        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
       14.96         5.06         8.35        17.16         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-A27C 
       28.41         8.98         1.94        23.01         0.46         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-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-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
        9.34         2.53         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
        8.91       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IN 
        1.81        10.59         7.79        87.32         3.98         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-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        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC 
       76.60        67.36        15.68        41.06        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-A6MF TCGA-E7-A7DV TCGA-E7-A7XN 
        0.66         1.38         0.82        14.33         1.22         0.46 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       12.89        15.68         8.94         6.87         4.01        12.43 
TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       11.93        24.30        22.45         6.12        12.82         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       13.18        46.78        19.79         1.97        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-A5C1 TCGA-FD-A62N 
       11.01         6.87         5.36         5.69        49.68         2.66 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        4.83         6.28         6.38        18.81         9.30         6.71 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        2.66         2.20         4.01        10.85        15.19         7.13 
TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.48         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-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RC 
       52.67         6.94        19.46         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-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A767 
        7.36         6.41         7.59        11.31        27.09         4.73 
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-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-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV 
       38.60         3.06         9.01         8.22         3.45         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-LT-A8JT TCGA-MV-A51V TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB 
       11.80        13.48        14.24         0.85         3.75        45.04 
TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI 
        6.58        97.45        56.19        15.35         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       64.80        79.66        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX 
       92.98        10.82        54.90        91.73         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
       56.48        30.94        27.06        75.39         3.88        10.36 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
        4.83         0.66         7.96 

  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                       123.85                        140.81 
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                         6.87                         10.49 
[1] "0.1 - 123.8 (6.9)"  "0.1 - 140.8 (10.5)"
[1] "hr=" "1.2"
D48V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 13(7Q36.3) MUTATED          0       0       11        13       14
  DEL PEAK 13(7Q36.3) WILD-TYPE        1       2       75        80       78
D48V3, multiclass
           clus
vv          DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE
  STAGE 0A                            0                             1
  STAGE I                             0                             2
  STAGE II                           11                            75
  STAGE III                          13                            80
  STAGE IV                           14                            78
[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(7Q36.3) MUTATED         10  22   5
  DEL PEAK 13(7Q36.3) WILD-TYPE       72 114  34
D48V4, multiclass
          clus
vv         DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE
  T0+T1+T2                          10                            72
  T3                                22                           114
  T4                                 5                            34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 13(7Q36.3) MUTATED    22   3  11   0
  DEL PEAK 13(7Q36.3) WILD-TYPE 144  25  44   7
D48V5, multiclass
    clus
vv   DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE
  N0                          22                           144
  N1                           3                            25
  N2                          11                            44
  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 13(7Q36.3) MUTATED    12   1  26
  DEL PEAK 13(7Q36.3) WILD-TYPE 117   6 115
D48V6, multiclass
    clus
vv   DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE
  M0                          12                           117
  M1                           1                             6
  MX                          26                           115
[1] 3 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 13(7Q36.3) MUTATED    10  29
  DEL PEAK 13(7Q36.3) WILD-TYPE  67 172
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7Q36.3) MUTATED     10   29
  DEL PEAK 13(7Q36.3) WILD-TYPE   67  172
        clus
vv       DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE
  FEMALE                          10                            67
  MALE                            29                           172
[1] 2 2
[1] FALSE
D48V8, continuous
D48V9, continuous
D48V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(7Q36.3) MUTATED       3                         1    30
  DEL PEAK 13(7Q36.3) WILD-TYPE    28                        12   185
D48V11, multiclass
                           clus
vv                          DEL PEAK 13(7Q36.3) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              30
                           clus
vv                          DEL PEAK 13(7Q36.3) WILD-TYPE
  ASIAN                                                28
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                               185
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V12, binary
                               cls
clus                              0   1
  DEL PEAK 13(7Q36.3) MUTATED     1  36
  DEL PEAK 13(7Q36.3) WILD-TYPE   4 222
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7Q36.3) MUTATED      1   36
  DEL PEAK 13(7Q36.3) WILD-TYPE    4  222
                        clus
vv                       DEL PEAK 13(7Q36.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          36
                        clus
vv                       DEL PEAK 13(7Q36.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           222
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 14(8P23.1) MUTATION ANALYSIS
D49V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(8P23.1) MUTATED   108  47
  DEL PEAK 14(8P23.1) WILD-TYPE  74  41
  DEL PEAK 14(8P23.1) MUTATED DEL PEAK 14(8P23.1) WILD-TYPE 
                          155                           115 
  DEL PEAK 14(8P23.1) MUTATED DEL PEAK 14(8P23.1) WILD-TYPE 
                           47                            41 
$`DEL PEAK 14(8P23.1) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 
       22.29        11.97       103.50        98.33         4.83        40.08 
TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A3PJ 
        2.66        19.04         5.06         8.35         5.59        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-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3KJ 
        0.43         0.69         0.13        12.92         7.20         5.46 
TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD 
        5.19         2.53         2.14        18.41       130.88       112.44 
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-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        41.06        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-A3NA 
       15.68         8.94         6.87         4.01        11.93        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR 
       24.30        22.45         6.12         5.52        13.18        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BU 
        1.97        22.98        14.93        12.13        13.38         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-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
        6.38        50.66         9.30         6.71         4.11         2.07 
TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        2.20        10.85        15.19         7.13         3.48         4.08 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C 
        6.48        61.94         5.69        20.12         0.85         6.94 
TCGA-G2-AA3F TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       19.46         4.50        15.91        14.07        17.75         1.12 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A762 
        7.73         2.10         3.12         7.36         6.41         2.04 
TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JX TCGA-GV-A3JZ 
       27.09         5.62         4.73        10.65         6.15         5.69 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ 
        7.63         7.79         6.41        19.07        11.54         6.74 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        3.06         9.01         8.22         8.75         3.45         4.67 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        2.50         6.48        10.52         1.81         4.27         6.38 
TCGA-LC-A66R TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
        6.35        11.80        13.48        12.23        16.67        14.24 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SI TCGA-XF-A9SW 
       45.04         6.58        15.35         1.87        79.66        11.90 
TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT 
       26.27         2.24        66.64        54.90         7.63         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN5 TCGA-YC-A89H 
        8.32         6.77        56.48        75.39        10.36 

$`DEL PEAK 14(8P23.1) WILD-TYPE`
TCGA-2F-A9KQ TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       84.00         7.33         6.74        12.39         6.58        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-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A42B 
       14.96         8.25        17.16         3.65         4.67        15.42 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
       23.01         0.46         0.07         0.10         0.07         0.10 
TCGA-CF-A47Y TCGA-CU-A0YO TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A6 
        0.10         4.90        16.31         1.84         9.34        66.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2I2 TCGA-DK-A3IS 
       19.00         8.91        16.14        17.62         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        41.56 
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-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B3 
        0.66         0.82        12.99        14.33         0.46        12.89 
TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A43S TCGA-FD-A43U 
       12.43        15.88        12.82        46.78        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-A6TB TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EL 
       18.81         2.66         4.01         3.25        30.61        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-AA3B TCGA-GC-A3BM TCGA-GC-A3I6 
       35.24        17.26         7.04        52.67         2.89         2.24 
TCGA-GC-A3OO TCGA-GC-A6I1 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
       15.81         2.66        20.98         2.20         7.59        11.31 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QI TCGA-GV-A3QK TCGA-H4-A2HO TCGA-HQ-A2OE 
        4.41         6.41         4.14         6.67         1.51        38.60 
TCGA-K4-A5RJ TCGA-LT-A5Z6 TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HD TCGA-XF-A8HE 
        1.74         3.45         0.85         3.75        88.93        97.45 
TCGA-XF-A8HF TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       56.19        17.88        64.80        23.64        21.04        28.24 
TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMR 
       18.90        16.27         2.10        92.98        10.82        91.73 
TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       30.94        27.06         3.88         4.83         0.66         7.96 
TCGA-YF-AA3M 
        9.04 

  DEL PEAK 14(8P23.1) MUTATED DEL PEAK 14(8P23.1) WILD-TYPE 
                         0.13                          0.07 
  DEL PEAK 14(8P23.1) MUTATED DEL PEAK 14(8P23.1) WILD-TYPE 
                       130.88                        140.81 
  DEL PEAK 14(8P23.1) MUTATED DEL PEAK 14(8P23.1) WILD-TYPE 
                         8.22                         12.39 
[1] "0.1 - 130.9 (8.2)"  "0.1 - 140.8 (12.4)"
[1] "hr=" "1"  
D49V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 14(8P23.1) MUTATED          1       2       44        45       62
  DEL PEAK 14(8P23.1) WILD-TYPE        0       0       42        48       30
D49V3, multiclass
           clus
vv          DEL PEAK 14(8P23.1) MUTATED DEL PEAK 14(8P23.1) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             2                             0
  STAGE II                           44                            42
  STAGE III                          45                            48
  STAGE IV                           62                            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 14(8P23.1) MUTATED         44 75 25
  DEL PEAK 14(8P23.1) WILD-TYPE       38 61 14
D49V4, multiclass
          clus
vv         DEL PEAK 14(8P23.1) MUTATED DEL PEAK 14(8P23.1) WILD-TYPE
  T0+T1+T2                          44                            38
  T3                                75                            61
  T4                                25                            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
  DEL PEAK 14(8P23.1) MUTATED   85 19 36  6
  DEL PEAK 14(8P23.1) WILD-TYPE 81  9 19  1
D49V5, multiclass
    clus
vv   DEL PEAK 14(8P23.1) MUTATED DEL PEAK 14(8P23.1) WILD-TYPE
  N0                          85                            81
  N1                          19                             9
  N2                          36                            19
  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 14(8P23.1) MUTATED   65  6 84
  DEL PEAK 14(8P23.1) WILD-TYPE 64  1 57
D49V6, multiclass
    clus
vv   DEL PEAK 14(8P23.1) MUTATED DEL PEAK 14(8P23.1) WILD-TYPE
  M0                          65                            64
  M1                           6                             1
  MX                          84                            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"
D49V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.1) MUTATED    40 116
  DEL PEAK 14(8P23.1) WILD-TYPE  37  85
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.1) MUTATED     40  116
  DEL PEAK 14(8P23.1) WILD-TYPE   37   85
        clus
vv       DEL PEAK 14(8P23.1) MUTATED DEL PEAK 14(8P23.1) WILD-TYPE
  FEMALE                          40                            37
  MALE                           116                            85
[1] 2 2
[1] FALSE
D49V8, continuous
D49V9, continuous
D49V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(8P23.1) MUTATED      12                        10   121
  DEL PEAK 14(8P23.1) WILD-TYPE    19                         3    94
D49V11, multiclass
                           clus
vv                          DEL PEAK 14(8P23.1) MUTATED
  ASIAN                                              12
  BLACK OR AFRICAN AMERICAN                          10
  WHITE                                             121
                           clus
vv                          DEL PEAK 14(8P23.1) WILD-TYPE
  ASIAN                                                19
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V12, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.1) MUTATED     1 144
  DEL PEAK 14(8P23.1) WILD-TYPE   4 114
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.1) MUTATED      1  144
  DEL PEAK 14(8P23.1) WILD-TYPE    4  114
                        clus
vv                       DEL PEAK 14(8P23.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         144
                        clus
vv                       DEL PEAK 14(8P23.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           114
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 15(9P23) MUTATION ANALYSIS
D50V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 15(9P23) MUTATED    80  34
  DEL PEAK 15(9P23) WILD-TYPE 102  54
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                        114                         156 
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                         34                          54 
$`DEL PEAK 15(9P23) MUTATED`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 
       11.97        84.00       103.50        98.33         4.83        40.08 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20W 
       11.93        19.04        32.84        19.50        14.89         8.35 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0F0 
       17.16         5.59         2.07        28.70         9.99         1.94 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A47X TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3YL 
        0.46         0.69         0.10         4.90         5.46        16.31 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AF 
        1.84         9.34         2.53        19.00         8.91        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
       15.62        10.59         2.20         8.22        10.49        50.27 
TCGA-DK-A3IT TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B2 
       21.30        10.55        48.00        17.98        64.18        15.68 
TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A541 TCGA-E7-A5KE 
       41.06        43.59        26.17        24.66         0.59         0.56 
TCGA-E7-A5KF TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ 
        0.66        15.68         8.94         6.12        12.82        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BZ 
       19.79         1.97        22.98        13.38         5.36        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-A6TB TCGA-FD-A6TG TCGA-FD-A6TK TCGA-FJ-A3ZE TCGA-FT-A61P TCGA-G2-A2EJ 
       18.81         2.66        10.85         3.48         6.48        30.61 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3RD 
       35.24         7.04         0.85        52.67        19.46        14.07 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
        1.12         2.66         3.12        20.98         2.20         7.36 
TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JW TCGA-GV-A3QH 
        7.59         2.04         4.73        10.65         6.41         7.79 
TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WS 
        6.67        11.54         6.74        38.60         3.06         8.75 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A6MB TCGA-LT-A8JT TCGA-PQ-A6FI 
        3.45         4.67         2.50         4.27        11.80        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HI TCGA-XF-A9SW 
       16.67        14.24         0.85         3.75        17.88        11.90 
TCGA-XF-A9T0 TCGA-XF-A9T4 TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAN1 TCGA-YF-AA3L 
       26.27        16.27        91.73         6.77        30.94         7.96 

$`DEL PEAK 15(9P23) WILD-TYPE`
TCGA-2F-A9KO TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       22.29         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       12.16        17.88         5.06        14.96         5.06         8.25 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0EZ 
        3.65         4.67        12.82        15.42        28.41         8.98 
TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       23.01         0.43         0.13         0.07         0.10         0.07 
TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3QU TCGA-DK-A1A5 TCGA-DK-A1A6 
        0.10        12.92         7.20         5.19         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A2HX TCGA-DK-A2I2 
       18.41       130.88       112.44        16.14         1.81         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IU TCGA-DK-A3IV 
      123.85        87.32         3.98         7.82        20.02         9.67 
TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 
        8.28       140.81        41.56        76.60        67.36        30.67 
TCGA-E5-A4TZ TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A677 TCGA-E7-A678 
       15.35         0.10         0.49         0.53         1.38         0.82 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B6 
       12.99        14.33         1.22         0.46        12.89         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-A3SL TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       22.45         5.52        13.18        14.93        14.96        14.93 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
        3.62        12.13        37.15        11.01         6.87         5.69 
TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
        6.84         2.66         9.30         6.71         4.11         2.07 
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-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-AA3C 
       61.94         5.69        26.93        17.26        20.12         6.94 
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-GU-A763 TCGA-GU-A766 
        7.73         2.10         6.41        11.31        27.09         5.62 
TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A40E 
        4.41         6.15         5.69         7.63         4.14         6.41 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A4AC TCGA-K4-A54R 
       19.07         1.51         9.01         8.22         6.48        10.52 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
        1.74         1.81         6.38         6.35         3.45        13.48 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       45.04         6.58        88.93        97.45        56.19        15.35 
TCGA-XF-A8HH TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
        1.87        64.80        79.66        23.64        21.04        28.24 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF 
       18.90         2.24        66.64         2.10        92.98        10.82 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN4 
       54.90         7.63         2.96         8.32        56.48        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3M 
       75.39         3.88        10.36         4.83         0.66         9.04 

  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                       0.10                        0.07 
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                     103.50                      140.81 
  DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE 
                      10.57                        8.30 
[1] "0.1 - 103.5 (10.6)" "0.1 - 140.8 (8.3)" 
[1] "hr=" "1.2"
D50V2, continuous
                             vv
clus                          STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 15(9P23) MUTATED          1       1       35        42       38
  DEL PEAK 15(9P23) WILD-TYPE        0       1       51        51       54
D50V3, multiclass
           clus
vv          DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  STAGE 0A                          1                           0
  STAGE I                           1                           1
  STAGE II                         35                          51
  STAGE III                        42                          51
  STAGE IV                         38                          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 15(9P23) MUTATED         36 60 16
  DEL PEAK 15(9P23) WILD-TYPE       46 76 23
D50V4, multiclass
          clus
vv         DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  T0+T1+T2                        36                          46
  T3                              60                          76
  T4                              16                          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 15(9P23) MUTATED   74 10 25  2
  DEL PEAK 15(9P23) WILD-TYPE 92 18 30  5
D50V5, multiclass
    clus
vv   DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  N0                        74                          92
  N1                        10                          18
  N2                        25                          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
  DEL PEAK 15(9P23) MUTATED   58  3 58
  DEL PEAK 15(9P23) WILD-TYPE 71  4 83
D50V6, multiclass
    clus
vv   DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  M0                        58                          71
  M1                         3                           4
  MX                        58                          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"
D50V7, binary
                             cls
clus                            0   1
  DEL PEAK 15(9P23) MUTATED    33  87
  DEL PEAK 15(9P23) WILD-TYPE  44 114
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(9P23) MUTATED     33   87
  DEL PEAK 15(9P23) WILD-TYPE   44  114
        clus
vv       DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  FEMALE                        33                          44
  MALE                          87                         114
[1] 2 2
[1] FALSE
D50V8, continuous
D50V9, continuous
D50V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(9P23) MUTATED      13                         7    88
  DEL PEAK 15(9P23) WILD-TYPE    18                         6   127
D50V11, multiclass
                           clus
vv                          DEL PEAK 15(9P23) MUTATED
  ASIAN                                            13
  BLACK OR AFRICAN AMERICAN                         7
  WHITE                                            88
                           clus
vv                          DEL PEAK 15(9P23) WILD-TYPE
  ASIAN                                              18
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                             127
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V12, binary
                             cls
clus                            0   1
  DEL PEAK 15(9P23) MUTATED     2 110
  DEL PEAK 15(9P23) WILD-TYPE   3 148
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 15(9P23) MUTATED      2  110
  DEL PEAK 15(9P23) WILD-TYPE    3  148
                        clus
vv                       DEL PEAK 15(9P23) MUTATED DEL PEAK 15(9P23) WILD-TYPE
  HISPANIC OR LATINO                             2                           3
  NOT HISPANIC OR LATINO                       110                         148
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 16(9P21.3) MUTATION ANALYSIS
D51V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 16(9P21.3) MUTATED   103  50
  DEL PEAK 16(9P21.3) WILD-TYPE  79  38
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                          153                           117 
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                           50                            38 
$`DEL PEAK 16(9P21.3) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
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        41.06        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         6.12        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-A6TB TCGA-FD-A6TD 
        4.83         6.28         6.38        50.66        18.81         6.71 
TCGA-FD-A6TG TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FT-A61P TCGA-G2-A2EF 
        2.66        10.85        15.19         3.48         6.48        61.94 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       35.24         7.04        20.12         0.85        52.67         6.94 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OQ 
       19.46         2.89        14.07         1.12         2.66         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
       20.98         2.20         7.36         7.59        11.31         2.04 
TCGA-GU-A763 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A3QH 
       27.09         4.73        10.65         6.41         7.63         7.79 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
        6.67         6.41        11.54         6.74        38.60         3.06 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        9.01         8.75         3.45         4.67         2.50         6.48 
TCGA-K4-A6MB TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
        4.27        11.80        12.23        16.67        14.24         0.85 
TCGA-S5-AA26 TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HI TCGA-XF-A9SW TCGA-XF-A9T0 
        3.75        97.45        56.19        17.88        11.90        26.27 
TCGA-XF-A9T5 TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN1 
       66.64        91.73         2.96         8.32         6.77        30.94 
TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39         0.66         7.96 

$`DEL PEAK 16(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        66.41 
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 
       41.56        76.60        67.36        30.67        15.35         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV 
        0.49         0.53         0.82        12.99        14.33         1.22 
TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
        0.46        12.89        15.68         6.87         4.01        12.43 
TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SO TCGA-FD-A43P TCGA-FD-A43S 
       11.93        24.30        22.45         5.52        14.93        14.96 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A6TC TCGA-FD-A6TE 
       37.15        11.01         6.84         2.66         9.30         4.11 
TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A3EE 
        2.07         2.20         4.01         7.13         4.08         3.25 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-GC-A3I6 TCGA-GC-A3OO 
       30.61         5.69        26.93        17.26         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GU-A42P 
        4.50        15.91        17.75         7.73         2.10         6.41 
TCGA-GU-A766 TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A40G 
        5.62         4.41         6.15         5.69         4.14        19.07 
TCGA-H4-A2HO TCGA-HQ-A5NE TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P 
        1.51         8.22        10.52         1.74         1.81         6.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
        6.35         3.45        13.48        45.04         6.58        88.93 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SX TCGA-XF-A9SY 
       15.35         1.87        64.80        79.66        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME 
       28.24        18.90         2.24        16.27         2.10        92.98 
TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN8 
       10.82        54.90         7.63        56.48        27.06         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YF-AA3M 
       10.36         4.83         9.04 

  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                       103.50                        140.81 
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                         9.99                          8.98 
[1] "0.1 - 103.5 (10.0)" "0.1 - 140.8 (9.0)" 
[1] "hr=" "1"  
D51V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 16(9P21.3) MUTATED          1       1       47        55       52
  DEL PEAK 16(9P21.3) WILD-TYPE        0       1       39        38       40
D51V3, multiclass
           clus
vv          DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             1                             1
  STAGE II                           47                            39
  STAGE III                          55                            38
  STAGE IV                           52                            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
  DEL PEAK 16(9P21.3) MUTATED         45 78 24
  DEL PEAK 16(9P21.3) WILD-TYPE       37 58 15
D51V4, multiclass
          clus
vv         DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE
  T0+T1+T2                          45                            37
  T3                                78                            58
  T4                                24                            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
  DEL PEAK 16(9P21.3) MUTATED   97 15 32  2
  DEL PEAK 16(9P21.3) WILD-TYPE 69 13 23  5
D51V5, multiclass
    clus
vv   DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE
  N0                          97                            69
  N1                          15                            13
  N2                          32                            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 16(9P21.3) MUTATED   75  4 79
  DEL PEAK 16(9P21.3) WILD-TYPE 54  3 62
D51V6, multiclass
    clus
vv   DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE
  M0                          75                            54
  M1                           4                             3
  MX                          79                            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"
D51V7, binary
                               cls
clus                              0   1
  DEL PEAK 16(9P21.3) MUTATED    44 115
  DEL PEAK 16(9P21.3) WILD-TYPE  33  86
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(9P21.3) MUTATED     44  115
  DEL PEAK 16(9P21.3) WILD-TYPE   33   86
        clus
vv       DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE
  FEMALE                          44                            33
  MALE                           115                            86
[1] 2 2
[1] FALSE
D51V8, continuous
D51V9, continuous
D51V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(9P21.3) MUTATED      15                         9   121
  DEL PEAK 16(9P21.3) WILD-TYPE    16                         4    94
D51V11, multiclass
                           clus
vv                          DEL PEAK 16(9P21.3) MUTATED
  ASIAN                                              15
  BLACK OR AFRICAN AMERICAN                           9
  WHITE                                             121
                           clus
vv                          DEL PEAK 16(9P21.3) WILD-TYPE
  ASIAN                                                16
  BLACK OR AFRICAN AMERICAN                             4
  WHITE                                                94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V12, binary
                               cls
clus                              0   1
  DEL PEAK 16(9P21.3) MUTATED     2 147
  DEL PEAK 16(9P21.3) WILD-TYPE   3 111
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(9P21.3) MUTATED      2  147
  DEL PEAK 16(9P21.3) WILD-TYPE    3  111
                        clus
vv                       DEL PEAK 16(9P21.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         147
                        clus
vv                       DEL PEAK 16(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           111
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 17(9Q33.2) MUTATION ANALYSIS
D52V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 17(9Q33.2) MUTATED    71  35
  DEL PEAK 17(9Q33.2) WILD-TYPE 111  53
  DEL PEAK 17(9Q33.2) MUTATED DEL PEAK 17(9Q33.2) WILD-TYPE 
                          106                           164 
  DEL PEAK 17(9Q33.2) MUTATED DEL PEAK 17(9Q33.2) WILD-TYPE 
                           35                            53 
$`DEL PEAK 17(9Q33.2) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
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        66.41        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        41.06        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 
        6.12        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-A6TB TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FJ-A3Z7 TCGA-FT-A61P 
       50.66        18.81         2.07         2.66        15.19         6.48 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3F 
        5.69        26.93        35.24         0.85        52.67        19.46 
TCGA-GC-A3BM TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 
        2.89        14.07         2.66         7.73         2.10         2.20 
TCGA-GU-A763 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3QH TCGA-GV-A40G 
       27.09         4.73        10.65         4.41         7.79        19.07 
TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
       11.54        38.60         3.06         3.45         4.67         2.50 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       11.80        13.48        16.67        14.24         0.85         3.75 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9T0 TCGA-XF-AAMR TCGA-XF-AAMW 
       56.19        15.35        17.88        26.27        91.73         8.32 
TCGA-XF-AAMX TCGA-XF-AAN1 TCGA-YF-AA3L TCGA-YF-AA3M 
        6.77        30.94         7.96         9.04 

$`DEL PEAK 17(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        41.56 
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-E7-A6ME 
        0.49         0.53         0.56         1.38         0.82        12.99 
TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 
       14.33         0.46        12.89        15.68        12.43        11.93 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SO 
       15.88        45.93        24.30        22.45        12.82         5.52 
TCGA-FD-A3SP TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BS 
       13.18        14.93        14.96        14.93        13.38        37.15 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62N 
       11.01         6.87         5.36         5.69         6.84         2.66 
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-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EF 
       10.85         7.13         3.48         4.08         3.25        61.94 
TCGA-G2-A2EJ TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3I6 
       30.61        17.26         7.04        20.12         6.94         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A3OQ 
       15.81         4.50        15.91        17.75         1.12         3.12 
TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
       20.98         7.36         6.41         7.59        11.31         2.04 
TCGA-GU-A766 TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI 
        5.62         6.41         6.15         5.69         7.63         4.14 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A5ND TCGA-HQ-A5NE 
        6.67         6.41         1.51         6.74         9.01         8.22 
TCGA-K4-A3WS TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
        8.75         6.48        10.52         1.74         1.81         4.27 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-XF-A8HB TCGA-XF-A8HC 
        6.38         6.35         3.45        12.23        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW 
       88.93        97.45         1.87        64.80        79.66        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       23.64        21.04        28.24        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML 
       66.64         2.10        92.98        10.82        54.90         7.63 
TCGA-XF-AAMT TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
        2.96        56.48        27.06        75.39         3.88        10.36 
TCGA-YC-A8S6 TCGA-YC-A9TC 
        4.83         0.66 

  DEL PEAK 17(9Q33.2) MUTATED DEL PEAK 17(9Q33.2) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK 17(9Q33.2) MUTATED DEL PEAK 17(9Q33.2) WILD-TYPE 
                       112.44                        140.81 
  DEL PEAK 17(9Q33.2) MUTATED DEL PEAK 17(9Q33.2) WILD-TYPE 
                        10.60                          8.83 
[1] "0.1 - 112.4 (10.6)" "0.1 - 140.8 (8.8)" 
[1] "hr=" "1.1"
D52V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 17(9Q33.2) MUTATED          1       0       30        39       37
  DEL PEAK 17(9Q33.2) WILD-TYPE        0       2       56        54       55
D52V3, multiclass
           clus
vv          DEL PEAK 17(9Q33.2) MUTATED DEL PEAK 17(9Q33.2) WILD-TYPE
  STAGE 0A                            1                             0
  STAGE I                             0                             2
  STAGE II                           30                            56
  STAGE III                          39                            54
  STAGE IV                           37                            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
  DEL PEAK 17(9Q33.2) MUTATED         33 56 16
  DEL PEAK 17(9Q33.2) WILD-TYPE       49 80 23
D52V4, multiclass
          clus
vv         DEL PEAK 17(9Q33.2) MUTATED DEL PEAK 17(9Q33.2) WILD-TYPE
  T0+T1+T2                          33                            49
  T3                                56                            80
  T4                                16                            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 17(9Q33.2) MUTATED   68 10 26  2
  DEL PEAK 17(9Q33.2) WILD-TYPE 98 18 29  5
D52V5, multiclass
    clus
vv   DEL PEAK 17(9Q33.2) MUTATED DEL PEAK 17(9Q33.2) WILD-TYPE
  N0                          68                            98
  N1                          10                            18
  N2                          26                            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 17(9Q33.2) MUTATED   55  2 52
  DEL PEAK 17(9Q33.2) WILD-TYPE 74  5 89
D52V6, multiclass
    clus
vv   DEL PEAK 17(9Q33.2) MUTATED DEL PEAK 17(9Q33.2) WILD-TYPE
  M0                          55                            74
  M1                           2                             5
  MX                          52                            89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                               cls
clus                              0   1
  DEL PEAK 17(9Q33.2) MUTATED    27  83
  DEL PEAK 17(9Q33.2) WILD-TYPE  50 118
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(9Q33.2) MUTATED     27   83
  DEL PEAK 17(9Q33.2) WILD-TYPE   50  118
        clus
vv       DEL PEAK 17(9Q33.2) MUTATED DEL PEAK 17(9Q33.2) WILD-TYPE
  FEMALE                          27                            50
  MALE                            83                           118
[1] 2 2
[1] FALSE
D52V8, continuous
D52V9, continuous
D52V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(9Q33.2) MUTATED      12                         4    82
  DEL PEAK 17(9Q33.2) WILD-TYPE    19                         9   133
D52V11, multiclass
                           clus
vv                          DEL PEAK 17(9Q33.2) MUTATED
  ASIAN                                              12
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              82
                           clus
vv                          DEL PEAK 17(9Q33.2) WILD-TYPE
  ASIAN                                                19
  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"
D52V12, binary
                               cls
clus                              0   1
  DEL PEAK 17(9Q33.2) MUTATED     2  99
  DEL PEAK 17(9Q33.2) WILD-TYPE   3 159
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(9Q33.2) MUTATED      2   99
  DEL PEAK 17(9Q33.2) WILD-TYPE    3  159
                        clus
vv                       DEL PEAK 17(9Q33.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          99
                        clus
vv                       DEL PEAK 17(9Q33.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           159
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 18(10P11.21) MUTATION ANALYSIS
D53V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 18(10P11.21) MUTATED    32  15
  DEL PEAK 18(10P11.21) WILD-TYPE 150  73
  DEL PEAK 18(10P11.21) MUTATED DEL PEAK 18(10P11.21) WILD-TYPE 
                             47                             223 
  DEL PEAK 18(10P11.21) MUTATED DEL PEAK 18(10P11.21) WILD-TYPE 
                             15                              73 
$`DEL PEAK 18(10P11.21) MUTATED`
TCGA-2F-A9KR TCGA-BT-A20J TCGA-BT-A20U TCGA-BT-A2LA TCGA-BT-A42C TCGA-C4-A0F0 
      103.50        19.04        14.96        17.16        28.70         1.94 
TCGA-CF-A27C TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A2HX TCGA-DK-A2I2 
        0.69         7.20         5.46         1.84         1.81         7.79 
TCGA-DK-A3IK TCGA-DK-A3IS TCGA-DK-A3IT TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A541 
        2.20        50.27        21.30        43.59        15.35         0.59 
TCGA-E7-A7DV TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SR 
        1.22        15.68         8.94         4.01        11.93        19.79 
TCGA-FD-A3SS TCGA-FD-A43Y TCGA-FD-A5BY TCGA-FD-A6TD TCGA-FJ-A3Z7 TCGA-FJ-A3ZE 
        1.97        12.13         6.84         6.71        15.19         3.48 
TCGA-FJ-A3ZF TCGA-G2-A2EL TCGA-G2-A3IB TCGA-GC-A3BM TCGA-GC-A3RC TCGA-GC-A3WC 
        4.08        26.93         7.04         2.89        15.91        17.75 
TCGA-GV-A40G TCGA-H4-A2HQ TCGA-K4-A3WU TCGA-MV-A51V TCGA-PQ-A6FI TCGA-XF-A8HC 
       19.07         6.74         3.45        13.48        12.23         6.58 
TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A9SI TCGA-XF-AAMF TCGA-XF-AAMX 
       97.45         1.87        79.66        10.82         6.77 

$`DEL PEAK 18(10P11.21) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 
       22.29        11.97        84.00        98.33         4.83        40.08 
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-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-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        5.06         8.35         8.25         5.59         3.65         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
       12.82         2.07        15.42         9.99        28.41         8.98 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       23.01         0.46         0.43         0.13         0.07         0.10 
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-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
       16.31         9.34         2.53         2.14        66.41        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-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IM 
       15.62        10.59       123.85        87.32         3.98         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
        8.22        10.49        20.02         9.67         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        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4U1 TCGA-E7-A3X6 
       67.36        15.68        41.06        30.67        26.17        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-A6ME TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B6 
        0.82        12.99        14.33         0.46        12.89         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         6.12 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43P 
       12.82         5.52        13.18        46.78        22.98        14.93 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        14.93         3.62        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-A6TB 
        2.66         4.83         6.28         6.38        50.66        18.81 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
        9.30         4.11         2.07         2.66         2.20         4.01 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.85         7.13         3.25         6.48        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
        5.69        35.24        17.26        20.12         0.85        52.67 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD 
        6.94        19.46         2.24        15.81         4.50        14.07 
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-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36         6.41         7.59        11.31         2.04 
TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW 
       27.09         5.62         4.73        10.65         4.41         6.41 
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-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
        6.41        11.54         1.51        38.60         3.06         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        8.22         8.75         4.67         2.50         6.48        10.52 
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-LT-A8JT TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB 
       11.80        16.67        14.24         0.85         3.75        45.04 
TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SW 
       88.93        56.19        15.35        17.88        64.80        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMJ TCGA-XF-AAML 
       16.27        66.64         2.10        92.98        54.90         7.63 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 
       91.73         2.96         8.32        56.48        30.94        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39         3.88        10.36         4.83         0.66         7.96 
TCGA-YF-AA3M 
        9.04 

  DEL PEAK 18(10P11.21) MUTATED DEL PEAK 18(10P11.21) WILD-TYPE 
                           0.59                            0.07 
  DEL PEAK 18(10P11.21) MUTATED DEL PEAK 18(10P11.21) WILD-TYPE 
                         103.50                          140.81 
  DEL PEAK 18(10P11.21) MUTATED DEL PEAK 18(10P11.21) WILD-TYPE 
                           8.94                            9.30 
[1] "0.6 - 103.5 (8.9)" "0.1 - 140.8 (9.3)"
[1] "hr=" "1"  
D53V2, continuous
                                 vv
clus                              STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 18(10P11.21) MUTATED          0       0       13        17       16
  DEL PEAK 18(10P11.21) WILD-TYPE        1       2       73        76       76
D53V3, multiclass
           clus
vv          DEL PEAK 18(10P11.21) MUTATED DEL PEAK 18(10P11.21) WILD-TYPE
  STAGE 0A                              0                               1
  STAGE I                               0                               2
  STAGE II                             13                              73
  STAGE III                            17                              76
  STAGE IV                             16                              76
[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(10P11.21) MUTATED         13  18  10
  DEL PEAK 18(10P11.21) WILD-TYPE       69 118  29
D53V4, multiclass
          clus
vv         DEL PEAK 18(10P11.21) MUTATED DEL PEAK 18(10P11.21) WILD-TYPE
  T0+T1+T2                            13                              69
  T3                                  18                             118
  T4                                  10                              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 18(10P11.21) MUTATED    30   2   9   4
  DEL PEAK 18(10P11.21) WILD-TYPE 136  26  46   3
D53V5, multiclass
    clus
vv   DEL PEAK 18(10P11.21) MUTATED DEL PEAK 18(10P11.21) WILD-TYPE
  N0                            30                             136
  N1                             2                              26
  N2                             9                              46
  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 18(10P11.21) MUTATED    20   2  25
  DEL PEAK 18(10P11.21) WILD-TYPE 109   5 116
D53V6, multiclass
    clus
vv   DEL PEAK 18(10P11.21) MUTATED DEL PEAK 18(10P11.21) WILD-TYPE
  M0                            20                             109
  M1                             2                               5
  MX                            25                             116
[1] 3 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 18(10P11.21) MUTATED    12  35
  DEL PEAK 18(10P11.21) WILD-TYPE  65 166
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 18(10P11.21) MUTATED     12   35
  DEL PEAK 18(10P11.21) WILD-TYPE   65  166
        clus
vv       DEL PEAK 18(10P11.21) MUTATED DEL PEAK 18(10P11.21) WILD-TYPE
  FEMALE                            12                              65
  MALE                              35                             166
[1] 2 2
[1] FALSE
D53V8, continuous
D53V9, continuous
D53V10, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(10P11.21) MUTATED       3                         7    34
  DEL PEAK 18(10P11.21) WILD-TYPE    28                         6   181
D53V11, multiclass
                           clus
vv                          DEL PEAK 18(10P11.21) MUTATED
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             7
  WHITE                                                34
                           clus
vv                          DEL PEAK 18(10P11.21) WILD-TYPE
  ASIAN                                                  28
  BLACK OR AFRICAN AMERICAN                               6
  WHITE                                                 181
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V12, binary
                                 cls
clus                                0   1
  DEL PEAK 18(10P11.21) MUTATED     0  44
  DEL PEAK 18(10P11.21) WILD-TYPE   5 214
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 18(10P11.21) MUTATED      0   44
  DEL PEAK 18(10P11.21) WILD-TYPE    5  214
                        clus
vv                       DEL PEAK 18(10P11.21) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            44
                        clus
vv                       DEL PEAK 18(10P11.21) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             214
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 19(10Q23.31) MUTATION ANALYSIS
D54V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 19(10Q23.31) MUTATED    72  38
  DEL PEAK 19(10Q23.31) WILD-TYPE 110  50
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                            110                             160 
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                             38                              50 
$`DEL PEAK 19(10Q23.31) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-BL-A0C8 TCGA-BT-A20N TCGA-BT-A20R 
       22.29        11.97       103.50        40.08        32.84         5.06 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A42B TCGA-C4-A0F0 
       14.96         5.06         8.35         3.65        15.42         1.94 
TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 
       23.01         0.69         4.90         5.46         5.19         1.84 
TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I6 
        2.14        18.41       112.44         1.81         7.79        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IV 
        2.20         3.98         7.82         8.22        50.27         9.67 
TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A541 
       67.36        30.67        43.59        24.66         0.49         0.59 
TCGA-E7-A6ME TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SJ 
       12.99         1.22         6.87         4.01        11.93        24.30 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A5BY 
       19.79         1.97        22.98        14.93        14.93         6.84 
TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FJ-A3Z7 
       27.45        49.68        50.66         6.71         2.07        15.19 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB 
        3.48         4.08         6.48         5.69        26.93         7.04 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM 
       20.12         0.85        52.67         6.94        19.46         2.89 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A76B 
       15.91        14.07        17.75         2.66         2.10         7.36 
TCGA-GU-A42P TCGA-GU-A767 TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        6.41         4.73         6.41         6.15         5.69         7.63 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OF 
        7.79         4.14        19.07        11.54         6.74         3.06 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ 
        9.01         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-A8HC 
        1.81         6.35         3.45        13.48        12.23         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A9SI TCGA-XF-A9SX 
       88.93        97.45        56.19         1.87        79.66        23.64 
TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       10.82        54.90         7.63         2.96         8.32         6.77 
TCGA-YF-AA3L TCGA-YF-AA3M 
        7.96         9.04 

$`DEL PEAK 19(10Q23.31) WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       84.00        98.33         4.83         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
       12.39         6.58        11.93        19.04        12.16        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-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-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-A47X TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A72E 
        0.10         0.10        12.92         7.20        16.31         9.34 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE 
        2.53        66.41        19.00         8.91       130.88        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IQ TCGA-DK-A3IT 
       17.62        15.62        10.59       123.85        10.49        21.30 
TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
       20.02         8.28        10.55       140.81        48.00        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A4TZ 
       64.18        41.56        76.60        15.68        41.06        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-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
        0.82        14.33         0.46        12.89        15.68         8.94 
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         6.12        12.82 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y 
        5.52        13.18        46.78        14.96         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-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB 
        6.87         2.66         4.83         6.28         6.38        18.81 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
        9.30         4.11         2.66         2.20         4.01        10.85 
TCGA-FJ-A3Z9 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A2ES 
        7.13         3.25        61.94        30.61        35.24        17.26 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OQ 
        2.24        15.81         4.50         1.12         7.73         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
       20.98         2.20         7.59        11.31         2.04        27.09 
TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HO 
        5.62        10.65         4.41         6.67         6.41         1.51 
TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A6MB TCGA-K4-A83P 
       38.60         8.22         4.67         2.50         4.27         6.38 
TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB 
       11.80        16.67        14.24         0.85         3.75        45.04 
TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9SZ 
       15.35        17.88        64.80        11.90        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-AAME TCGA-XF-AAMR TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
       92.98        91.73        56.48        30.94        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
        3.88        10.36         4.83         0.66 

  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                           0.49                            0.07 
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                         112.44                          140.81 
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                          7.805                          10.750 
[1] "0.5 - 112.4 (7.8)"  "0.1 - 140.8 (10.8)"
[1] "hr=" "1.2"
D54V2, continuous
                                 vv
clus                              STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 19(10Q23.31) MUTATED          1       1       36        28       43
  DEL PEAK 19(10Q23.31) WILD-TYPE        0       1       50        65       49
D54V3, multiclass
           clus
vv          DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE
  STAGE 0A                              1                               0
  STAGE I                               1                               1
  STAGE II                             36                              50
  STAGE III                            28                              65
  STAGE IV                             43                              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
  DEL PEAK 19(10Q23.31) MUTATED         34 51 13
  DEL PEAK 19(10Q23.31) WILD-TYPE       48 85 26
D54V4, multiclass
          clus
vv         DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE
  T0+T1+T2                            34                              48
  T3                                  51                              85
  T4                                  13                              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 19(10Q23.31) MUTATED    55  12  24   5
  DEL PEAK 19(10Q23.31) WILD-TYPE 111  16  31   2
D54V5, multiclass
    clus
vv   DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE
  N0                            55                             111
  N1                            12                              16
  N2                            24                              31
  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 19(10Q23.31) MUTATED   46  3 60
  DEL PEAK 19(10Q23.31) WILD-TYPE 83  4 81
D54V6, multiclass
    clus
vv   DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE
  M0                            46                              83
  M1                             3                               4
  MX                            60                              81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                                 cls
clus                                0   1
  DEL PEAK 19(10Q23.31) MUTATED    31  79
  DEL PEAK 19(10Q23.31) WILD-TYPE  46 122
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(10Q23.31) MUTATED     31   79
  DEL PEAK 19(10Q23.31) WILD-TYPE   46  122
        clus
vv       DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE
  FEMALE                            31                              46
  MALE                              79                             122
[1] 2 2
[1] FALSE
D54V8, continuous
D54V9, continuous
D54V10, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(10Q23.31) MUTATED       7                         7    85
  DEL PEAK 19(10Q23.31) WILD-TYPE    24                         6   130
D54V11, multiclass
                           clus
vv                          DEL PEAK 19(10Q23.31) MUTATED
  ASIAN                                                 7
  BLACK OR AFRICAN AMERICAN                             7
  WHITE                                                85
                           clus
vv                          DEL PEAK 19(10Q23.31) WILD-TYPE
  ASIAN                                                  24
  BLACK OR AFRICAN AMERICAN                               6
  WHITE                                                 130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V12, binary
                                 cls
clus                                0   1
  DEL PEAK 19(10Q23.31) MUTATED     2  99
  DEL PEAK 19(10Q23.31) WILD-TYPE   3 159
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(10Q23.31) MUTATED      2   99
  DEL PEAK 19(10Q23.31) WILD-TYPE    3  159
                        clus
vv                       DEL PEAK 19(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            99
                        clus
vv                       DEL PEAK 19(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             159
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 20(11P15.5) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 20(11P15.5) MUTATED   84 43
  DEL PEAK 20(11P15.5) WILD-TYPE 98 45
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                           127                            143 
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                            43                             45 
$`DEL PEAK 20(11P15.5) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 TCGA-BL-A13J 
       22.29       103.50        98.33         4.83        40.08         2.66 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W 
       19.04        32.84         5.06        14.89         5.06         8.35 
TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F0 
        4.67         2.07        15.42        28.70         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47X 
       23.01         0.46         0.43         0.69         0.13         0.10 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A7 
        7.20         5.46         1.84         9.34         2.14        18.41 
TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I6 
        8.91       112.44        17.62         1.81        10.59        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        2.20         3.98         7.82         8.22        10.49        50.27 
TCGA-DK-A3IT TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-E5-A4TZ TCGA-E5-A4U1 
       21.30        17.98        64.18        41.06        15.35        26.17 
TCGA-E7-A3X6 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A6ME TCGA-E7-A7DV 
       24.66         0.59         0.56         0.66        12.99         1.22 
TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SR 
        8.94         4.01        24.30        22.45        12.82        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A5C0 
        1.97        22.98        12.13         5.36        27.45         6.87 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC 
       49.68         2.66         4.83         6.28        50.66         9.30 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FT-A61P 
        2.07         2.66         2.20        15.19         3.48         6.48 
TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3BM 
       35.24        20.12         0.85        52.67        19.46         2.89 
TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 
        2.24        14.07         1.12         7.73         2.10         2.20 
TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW 
        7.36         7.59        11.31         4.73         4.41         6.41 
TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE 
        7.63         6.41        19.07        11.54         6.74        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A6MB TCGA-LT-A8JT 
        3.06         9.01         8.75         4.67         4.27        11.80 
TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HF TCGA-XF-A8HG 
       12.23        14.24         0.85         3.75        56.19        15.35 
TCGA-XF-A9SH TCGA-XF-A9SW TCGA-XF-A9SZ TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 
       64.80        11.90        28.24         2.24        66.64         2.10 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       54.90         7.63        91.73         8.32         6.77        56.48 
TCGA-YF-AA3L 
        7.96 

$`DEL PEAK 20(11P15.5) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       11.97        84.00         7.33         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20X 
       11.93        12.16        17.88        19.50        14.96         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42E TCGA-BT-A42F 
       17.16         5.59         3.65        12.82         9.99        28.41 
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-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AC 
        5.19        16.31         2.53        66.41        19.00       130.88 
TCGA-DK-A1AE TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IU TCGA-DK-A3IV 
       16.14        15.62         7.79       123.85        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        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       67.36        15.68        30.67        43.59         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B3 
        0.53         1.38         0.82        14.33         0.46        12.89 
TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       15.68         6.87        12.43        11.93        15.88        45.93 
TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A43S 
        6.12         5.52        13.18        46.78        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-A5BX TCGA-FD-A5BY TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE 
        5.69         6.84         6.38        18.81         6.71         4.11 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EF 
        4.01        10.85         7.13         4.08         3.25        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-AA3C 
       30.61         5.69        26.93        17.26         7.04         6.94 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OQ 
       15.81         4.50        15.91        17.75         2.66         3.12 
TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-AATO 
       20.98         6.41         2.04        27.09         5.62        10.65 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-H4-A2HO 
        6.15         5.69         7.79         4.14         6.67         1.51 
TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ 
        8.22         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-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI 
       45.04         6.58        88.93        97.45         1.87        17.88 
TCGA-XF-A9SI TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 
       79.66        23.64        21.04        26.27        18.90        16.27 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMT TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
       92.98        10.82         2.96        30.94        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3M 
        3.88        10.36         4.83         0.66         9.04 

  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                        112.44                         140.81 
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                          8.35                          10.65 
[1] "0.1 - 112.4 (8.3)"  "0.1 - 140.8 (10.7)"
[1] "hr=" "1.1"
D55V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 20(11P15.5) MUTATED          1       1       39        34       54
  DEL PEAK 20(11P15.5) WILD-TYPE        0       1       47        59       38
D55V3, multiclass
           clus
vv          DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE
  STAGE 0A                             1                              0
  STAGE I                              1                              1
  STAGE II                            39                             47
  STAGE III                           34                             59
  STAGE IV                            54                             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 20(11P15.5) MUTATED         42 67 17
  DEL PEAK 20(11P15.5) WILD-TYPE       40 69 22
D55V4, multiclass
          clus
vv         DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE
  T0+T1+T2                           42                             40
  T3                                 67                             69
  T4                                 17                             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 20(11P15.5) MUTATED   71 14 35  3
  DEL PEAK 20(11P15.5) WILD-TYPE 95 14 20  4
D55V5, multiclass
    clus
vv   DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE
  N0                           71                             95
  N1                           14                             14
  N2                           35                             20
  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 20(11P15.5) MUTATED   65  5 62
  DEL PEAK 20(11P15.5) WILD-TYPE 64  2 79
D55V6, multiclass
    clus
vv   DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE
  M0                           65                             64
  M1                            5                              2
  MX                           62                             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"
D55V7, binary
                                cls
clus                               0   1
  DEL PEAK 20(11P15.5) MUTATED    36  97
  DEL PEAK 20(11P15.5) WILD-TYPE  41 104
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11P15.5) MUTATED     36   97
  DEL PEAK 20(11P15.5) WILD-TYPE   41  104
        clus
vv       DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE
  FEMALE                           36                             41
  MALE                             97                            104
[1] 2 2
[1] FALSE
D55V8, continuous
D55V9, continuous
D55V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(11P15.5) MUTATED      19                         6    94
  DEL PEAK 20(11P15.5) WILD-TYPE    12                         7   121
D55V11, multiclass
                           clus
vv                          DEL PEAK 20(11P15.5) MUTATED
  ASIAN                                               19
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               94
                           clus
vv                          DEL PEAK 20(11P15.5) WILD-TYPE
  ASIAN                                                 12
  BLACK OR AFRICAN AMERICAN                              7
  WHITE                                                121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V12, binary
                                cls
clus                               0   1
  DEL PEAK 20(11P15.5) MUTATED     2 120
  DEL PEAK 20(11P15.5) WILD-TYPE   3 138
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11P15.5) MUTATED      2  120
  DEL PEAK 20(11P15.5) WILD-TYPE    3  138
                        clus
vv                       DEL PEAK 20(11P15.5) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          120
                        clus
vv                       DEL PEAK 20(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            138
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 21(11Q23.3) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 21(11Q23.3) MUTATED    62  30
  DEL PEAK 21(11Q23.3) WILD-TYPE 120  58
  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                            92                            178 
  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                            30                             58 
$`DEL PEAK 21(11Q23.3) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KT TCGA-BL-A0C8 TCGA-BT-A20J TCGA-BT-A20N 
       22.29       103.50        98.33        40.08        19.04        32.84 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B 
       14.89         8.35        17.16         5.59         4.67        15.42 
TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47X 
       28.70        28.41         8.98         0.43         0.69         0.10 
TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A1AC 
       12.92         5.46         2.14        66.41         8.91       130.88 
TCGA-DK-A1AD TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A6AV 
      112.44         7.82         8.22        10.49        50.27        64.18 
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-A5KF TCGA-E7-A6ME TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3SJ 
        0.56         0.66        12.99         8.94         4.01        24.30 
TCGA-FD-A43N TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BY 
       22.98         3.62        12.13        13.38         5.36         6.84 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA 
        6.87        49.68         2.66         4.83         6.38        50.66 
TCGA-FD-A6TC TCGA-FD-A6TH TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3IB TCGA-GC-A3BM 
        9.30         2.20         6.48        17.26         7.04         2.89 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A76B TCGA-GU-A42Q 
        1.12         2.66         7.73         2.10         7.36         7.59 
TCGA-GU-A42R TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QK TCGA-GV-A40E 
       11.31         4.73         4.41         6.41         6.67         6.41 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WV 
       19.07        11.54         6.74        38.60         3.06         4.67 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-PQ-A6FI TCGA-XF-A8HG TCGA-XF-A9SW TCGA-XF-A9T5 
        2.50         6.48        12.23        15.35        11.90        66.64 
TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMW 
        2.10        10.82        54.90         7.63         2.96         8.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 
       56.48        30.94 

$`DEL PEAK 21(11Q23.3) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       11.97        84.00         4.83         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       12.39         6.58        11.93        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LD TCGA-BT-A3PJ 
        5.06        14.96         5.06         8.25         3.65        12.82 
TCGA-BT-A3PK TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A47S 
        2.07         9.99         1.94        23.01         0.46         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-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A7 
        5.19        16.31         1.84         9.34         2.53        18.41 
TCGA-DK-A1AA TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
       19.00        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IT 
        7.79       123.85        87.32         2.20         3.98        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       20.02         9.67         8.28        10.55       140.81        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       17.98        41.56        76.60        67.36        15.68        41.06 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF 
       24.66         0.10         0.53         1.38         0.82        14.33 
TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B8 
        1.22         0.46        12.89        15.68         6.87        12.43 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       11.93        15.88        45.93        22.45         6.12        12.82 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
        5.52        13.18        46.78        19.79         1.97        14.93 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
       14.96        14.93        37.15        11.01         6.87         5.69 
TCGA-FD-A5BZ TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       27.45         6.28        18.81         6.71         4.11         2.07 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        2.66         4.01        10.85        15.19         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-A2EO TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
       35.24        20.12         0.85        52.67         6.94        19.46 
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-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A763 
        3.12        20.98         2.20         6.41         2.04        27.09 
TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        5.62        10.65         6.15         5.69         7.63         7.79 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
        4.14         1.51         9.01         8.22         8.75         3.45 
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-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
        3.45        11.80        13.48        16.67        14.24         0.85 
TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        3.75        45.04         6.58        88.93        97.45        56.19 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SX TCGA-XF-A9SY 
        1.87        17.88        64.80        79.66        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-AAME 
       28.24        26.27        18.90         2.24        16.27        92.98 
TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
       91.73         6.77        27.06        75.39         3.88        10.36 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        4.83         0.66         7.96         9.04 

  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                        130.88                         140.81 
  DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE 
                         8.630                         10.175 
[1] "0.1 - 130.9 (8.6)"  "0.1 - 140.8 (10.2)"
[1] "hr=" "1"  
D56V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 21(11Q23.3) MUTATED          1       1       32        28       30
  DEL PEAK 21(11Q23.3) WILD-TYPE        0       1       54        65       62
D56V3, multiclass
           clus
vv          DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE
  STAGE 0A                             1                              0
  STAGE I                              1                              1
  STAGE II                            32                             54
  STAGE III                           28                             65
  STAGE IV                            30                             62
[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(11Q23.3) MUTATED         34 43 12
  DEL PEAK 21(11Q23.3) WILD-TYPE       48 93 27
D56V4, multiclass
          clus
vv         DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE
  T0+T1+T2                           34                             48
  T3                                 43                             93
  T4                                 12                             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
  DEL PEAK 21(11Q23.3) MUTATED    56  11  18   0
  DEL PEAK 21(11Q23.3) WILD-TYPE 110  17  37   7
D56V5, multiclass
    clus
vv   DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE
  N0                           56                            110
  N1                           11                             17
  N2                           18                             37
  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 21(11Q23.3) MUTATED   40  2 53
  DEL PEAK 21(11Q23.3) WILD-TYPE 89  5 88
D56V6, multiclass
    clus
vv   DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE
  M0                           40                             89
  M1                            2                              5
  MX                           53                             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"
D56V7, binary
                                cls
clus                               0   1
  DEL PEAK 21(11Q23.3) MUTATED    26  69
  DEL PEAK 21(11Q23.3) WILD-TYPE  51 132
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11Q23.3) MUTATED     26   69
  DEL PEAK 21(11Q23.3) WILD-TYPE   51  132
        clus
vv       DEL PEAK 21(11Q23.3) MUTATED DEL PEAK 21(11Q23.3) WILD-TYPE
  FEMALE                           26                             51
  MALE                             69                            132
[1] 2 2
[1] FALSE
D56V8, continuous
D56V9, continuous
D56V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(11Q23.3) MUTATED      13                         5    67
  DEL PEAK 21(11Q23.3) WILD-TYPE    18                         8   148
D56V11, multiclass
                           clus
vv                          DEL PEAK 21(11Q23.3) MUTATED
  ASIAN                                               13
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               67
                           clus
vv                          DEL PEAK 21(11Q23.3) WILD-TYPE
  ASIAN                                                 18
  BLACK OR AFRICAN AMERICAN                              8
  WHITE                                                148
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V12, binary
                                cls
clus                               0   1
  DEL PEAK 21(11Q23.3) MUTATED     0  86
  DEL PEAK 21(11Q23.3) WILD-TYPE   5 172
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11Q23.3) MUTATED      0   86
  DEL PEAK 21(11Q23.3) WILD-TYPE    5  172
                        clus
vv                       DEL PEAK 21(11Q23.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           86
                        clus
vv                       DEL PEAK 21(11Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            172
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 22(11Q25) MUTATION ANALYSIS
D57V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 22(11Q25) MUTATED    59  26
  DEL PEAK 22(11Q25) WILD-TYPE 123  62
  DEL PEAK 22(11Q25) MUTATED DEL PEAK 22(11Q25) WILD-TYPE 
                          85                          185 
  DEL PEAK 22(11Q25) MUTATED DEL PEAK 22(11Q25) WILD-TYPE 
                          26                           62 
$`DEL PEAK 22(11Q25) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KT TCGA-BL-A0C8 TCGA-BT-A20W TCGA-BT-A2LA 
       22.29       103.50        98.33        40.08         8.35        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ 
        5.59         4.67        15.42        28.70         9.99         8.98 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47X TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A1A5 
        0.43         0.69         0.10        12.92         5.46         2.14 
TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
       66.41         8.91         7.82         8.22        10.49        50.27 
TCGA-DK-A6AV TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 
       64.18        30.67        43.59        15.35         0.49         0.59 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A6ME TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3SJ 
        0.56         0.66        12.99         8.94         4.01        24.30 
TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5C0 
       22.98        12.13        13.38         5.36         6.84         6.87 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TH 
       49.68         2.66         4.83         6.38         9.30         2.20 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3YS 
        6.48        17.26         7.04         0.85         2.89         1.12 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R 
        2.66         7.73         2.10         7.36         7.59        11.31 
TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A40E 
        4.73         4.41         6.41         5.69         6.67         6.41 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       19.07        11.54         6.74        38.60         3.06         9.01 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-PQ-A6FI TCGA-XF-A8HG TCGA-XF-A9SW 
        4.67         2.50         6.48        12.23        15.35        11.90 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMW 
       66.64         2.10        54.90         7.63         2.96         8.32 
TCGA-XF-AAN0 
       56.48 

$`DEL PEAK 22(11Q25) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       11.97        84.00         4.83         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
       12.39         6.58        11.93        19.04        32.84        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-A20X TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42F TCGA-C4-A0F0 
        8.25         3.65        12.82         2.07        28.41         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-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
        0.10         4.90         7.20         5.19        16.31         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AD 
        9.34         2.53        18.41        19.00       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-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-E5-A4U1 
       41.56        76.60        67.36        15.68        41.06        26.17 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF 
       24.66         0.10         0.53         1.38         0.82        14.33 
TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B8 
        1.22         0.46        12.89        15.68         6.87        12.43 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       11.93        15.88        45.93        22.45         6.12        12.82 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
        5.52        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-A5BX TCGA-FD-A5BZ TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD 
        5.69        27.45         6.28        50.66        18.81         6.71 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
        4.11         2.07         2.66         4.01        10.85        15.19 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
        7.13         3.48         4.08         3.25        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C 
        5.69        26.93        35.24        20.12        52.67         6.94 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       19.46         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A762 
       17.75         3.12        20.98         2.20         6.41         2.04 
TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH 
       27.09         5.62        10.65         6.15         7.63         7.79 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A54R 
        4.14         1.51         8.22         8.75         3.45        10.52 
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-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       11.80        13.48        16.67        14.24         0.85         3.75 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH 
       45.04         6.58        88.93        97.45        56.19         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       17.88        64.80        79.66        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMF 
       26.27        18.90         2.24        16.27        92.98        10.82 
TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
       91.73         6.77        30.94        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
       10.36         4.83         0.66         7.96         9.04 

  DEL PEAK 22(11Q25) MUTATED DEL PEAK 22(11Q25) WILD-TYPE 
                        0.10                         0.07 
  DEL PEAK 22(11Q25) MUTATED DEL PEAK 22(11Q25) WILD-TYPE 
                      103.50                       140.81 
  DEL PEAK 22(11Q25) MUTATED DEL PEAK 22(11Q25) WILD-TYPE 
                        7.73                        10.85 
[1] "0.1 - 103.5 (7.7)"  "0.1 - 140.8 (10.8)"
[1] "hr=" "1.1"
D57V2, continuous
                              vv
clus                           STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 22(11Q25) MUTATED          1       1       30        26       27
  DEL PEAK 22(11Q25) WILD-TYPE        0       1       56        67       65
D57V3, multiclass
           clus
vv          DEL PEAK 22(11Q25) MUTATED DEL PEAK 22(11Q25) WILD-TYPE
  STAGE 0A                           1                            0
  STAGE I                            1                            1
  STAGE II                          30                           56
  STAGE III                         26                           67
  STAGE IV                          27                           65
[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(11Q25) MUTATED         31 40 10
  DEL PEAK 22(11Q25) WILD-TYPE       51 96 29
D57V4, multiclass
          clus
vv         DEL PEAK 22(11Q25) MUTATED DEL PEAK 22(11Q25) WILD-TYPE
  T0+T1+T2                         31                           51
  T3                               40                           96
  T4                               10                           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 22(11Q25) MUTATED    51  10  15   1
  DEL PEAK 22(11Q25) WILD-TYPE 115  18  40   6
D57V5, multiclass
    clus
vv   DEL PEAK 22(11Q25) MUTATED DEL PEAK 22(11Q25) WILD-TYPE
  N0                         51                          115
  N1                         10                           18
  N2                         15                           40
  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 22(11Q25) MUTATED   37  2 48
  DEL PEAK 22(11Q25) WILD-TYPE 92  5 93
D57V6, multiclass
    clus
vv   DEL PEAK 22(11Q25) MUTATED DEL PEAK 22(11Q25) WILD-TYPE
  M0                         37                           92
  M1                          2                            5
  MX                         48                           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"
D57V7, binary
                              cls
clus                             0   1
  DEL PEAK 22(11Q25) MUTATED    25  63
  DEL PEAK 22(11Q25) WILD-TYPE  52 138
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 22(11Q25) MUTATED     25   63
  DEL PEAK 22(11Q25) WILD-TYPE   52  138
        clus
vv       DEL PEAK 22(11Q25) MUTATED DEL PEAK 22(11Q25) WILD-TYPE
  FEMALE                         25                           52
  MALE                           63                          138
[1] 2 2
[1] FALSE
D57V8, continuous
D57V9, continuous
D57V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(11Q25) MUTATED      14                         5    62
  DEL PEAK 22(11Q25) WILD-TYPE    17                         8   153
D57V11, multiclass
                           clus
vv                          DEL PEAK 22(11Q25) MUTATED
  ASIAN                                             14
  BLACK OR AFRICAN AMERICAN                          5
  WHITE                                             62
                           clus
vv                          DEL PEAK 22(11Q25) WILD-TYPE
  ASIAN                                               17
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                              153
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V12, binary
                              cls
clus                             0   1
  DEL PEAK 22(11Q25) MUTATED     0  81
  DEL PEAK 22(11Q25) WILD-TYPE   5 177
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 22(11Q25) MUTATED      0   81
  DEL PEAK 22(11Q25) WILD-TYPE    5  177
                        clus
vv                       DEL PEAK 22(11Q25) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                         81
                        clus
vv                       DEL PEAK 22(11Q25) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          177
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 23(12P13.1) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(12P13.1) MUTATED    26  16
  DEL PEAK 23(12P13.1) WILD-TYPE 156  72
  DEL PEAK 23(12P13.1) MUTATED DEL PEAK 23(12P13.1) WILD-TYPE 
                            42                            228 
  DEL PEAK 23(12P13.1) MUTATED DEL PEAK 23(12P13.1) WILD-TYPE 
                            16                             72 
$`DEL PEAK 23(12P13.1) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KW TCGA-BT-A20T TCGA-BT-A2LA TCGA-BT-A42C TCGA-CF-A27C 
       22.29         4.83        14.89        17.16        28.70         0.69 
TCGA-CF-A47X TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1AC TCGA-DK-A3IL TCGA-DK-A3IQ 
        0.10         5.19         1.84       130.88         3.98        10.49 
TCGA-DK-A3IV TCGA-DK-A6AV TCGA-E5-A2PC TCGA-FD-A3SL TCGA-FD-A3SQ TCGA-FD-A3SR 
        9.67        64.18        43.59        22.45        46.78        19.79 
TCGA-FD-A43N TCGA-FD-A43X TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A6TC TCGA-FD-A6TE 
       22.98         3.62         5.69         6.87         9.30         4.11 
TCGA-G2-AA3F TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A76B TCGA-GV-A3JW 
       19.46         1.12         7.73        20.98         7.36         6.41 
TCGA-K4-A6FZ TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SZ TCGA-XF-A9T3 
        1.81        56.19        15.35         1.87        28.24         2.24 
TCGA-XF-AAMF TCGA-XF-AAML TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-YF-AA3L 
       10.82         7.63         8.32         6.77        56.48         7.96 

$`DEL PEAK 23(12P13.1) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-BL-A0C8 TCGA-BL-A13I 
       11.97        84.00       103.50        98.33        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         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-A20U 
       32.84        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        5.06         8.35         8.25         5.59         3.65         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
       12.82         2.07        15.42         9.99        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T 
        1.94        23.01         0.46         0.43         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-A3KJ TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
        5.46        16.31         9.34         2.53         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       18.41        19.00         8.91       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       15.62         1.81        10.59         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        2.20         7.82         8.22        50.27        21.30        20.02 
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        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4TZ 
       76.60        67.36        15.68        41.06        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-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66         1.38         0.82        12.99        14.33 
TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
        1.22         0.46        12.89        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-A3SS TCGA-FD-A43P 
        6.12        12.82         5.52        13.18         1.97        14.93 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        14.93        12.13        13.38        37.15        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62N 
        6.87         5.36         6.84        27.45        49.68         2.66 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD 
        4.83         6.28         6.38        50.66        18.81         6.71 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
        2.07         2.66         2.20         4.01        10.85        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-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       30.61         5.69        26.93        35.24        17.26         7.04 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 
       20.12         0.85        52.67         6.94         2.89         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 
       15.81         4.50        15.91        14.07        17.75         2.66 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12         2.20         6.41         7.59        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV 
        2.04        27.09         5.62         4.73        10.65         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-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        6.41        19.07        11.54         1.51         6.74        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        3.06         9.01         8.22         8.75         3.45         4.67 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P 
        2.50         6.48        10.52         1.74         4.27         6.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        6.35         3.45        11.80        13.48        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
       14.24         0.85         3.75        45.04         6.58        88.93 
TCGA-XF-A8HE TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX 
       97.45        17.88        64.80        79.66        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       21.04        26.27        18.90        16.27        66.64         2.10 
TCGA-XF-AAME TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAN1 TCGA-XF-AAN4 
       92.98        54.90        91.73         2.96        30.94        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3M 
       75.39         3.88        10.36         4.83         0.66         9.04 

  DEL PEAK 23(12P13.1) MUTATED DEL PEAK 23(12P13.1) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 23(12P13.1) MUTATED DEL PEAK 23(12P13.1) WILD-TYPE 
                        130.88                         140.81 
  DEL PEAK 23(12P13.1) MUTATED DEL PEAK 23(12P13.1) WILD-TYPE 
                          8.81                           9.19 
[1] "0.1 - 130.9 (8.8)" "0.1 - 140.8 (9.2)"
[1] "hr=" "1.2"
D58V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 23(12P13.1) MUTATED          0       0       11        11       20
  DEL PEAK 23(12P13.1) WILD-TYPE        1       2       75        82       72
D58V3, multiclass
           clus
vv          DEL PEAK 23(12P13.1) MUTATED DEL PEAK 23(12P13.1) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              0                              2
  STAGE II                            11                             75
  STAGE III                           11                             82
  STAGE IV                            20                             72
[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(12P13.1) MUTATED         11  23   6
  DEL PEAK 23(12P13.1) WILD-TYPE       71 113  33
D58V4, multiclass
          clus
vv         DEL PEAK 23(12P13.1) MUTATED DEL PEAK 23(12P13.1) WILD-TYPE
  T0+T1+T2                           11                             71
  T3                                 23                            113
  T4                                  6                             33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 23(12P13.1) MUTATED    21   7  12   0
  DEL PEAK 23(12P13.1) WILD-TYPE 145  21  43   7
D58V5, multiclass
    clus
vv   DEL PEAK 23(12P13.1) MUTATED DEL PEAK 23(12P13.1) WILD-TYPE
  N0                           21                            145
  N1                            7                             21
  N2                           12                             43
  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 23(12P13.1) MUTATED    18   1  24
  DEL PEAK 23(12P13.1) WILD-TYPE 111   6 117
D58V6, multiclass
    clus
vv   DEL PEAK 23(12P13.1) MUTATED DEL PEAK 23(12P13.1) WILD-TYPE
  M0                           18                            111
  M1                            1                              6
  MX                           24                            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"
D58V7, binary
                                cls
clus                               0   1
  DEL PEAK 23(12P13.1) MUTATED    14  29
  DEL PEAK 23(12P13.1) WILD-TYPE  63 172
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(12P13.1) MUTATED     14   29
  DEL PEAK 23(12P13.1) WILD-TYPE   63  172
        clus
vv       DEL PEAK 23(12P13.1) MUTATED DEL PEAK 23(12P13.1) WILD-TYPE
  FEMALE                           14                             63
  MALE                             29                            172
[1] 2 2
[1] FALSE
D58V8, continuous
D58V9, continuous
D58V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(12P13.1) MUTATED       4                         1    36
  DEL PEAK 23(12P13.1) WILD-TYPE    27                        12   179
D58V11, multiclass
                           clus
vv                          DEL PEAK 23(12P13.1) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               36
                           clus
vv                          DEL PEAK 23(12P13.1) WILD-TYPE
  ASIAN                                                 27
  BLACK OR AFRICAN AMERICAN                             12
  WHITE                                                179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V12, binary
                                cls
clus                               0   1
  DEL PEAK 23(12P13.1) MUTATED     1  41
  DEL PEAK 23(12P13.1) WILD-TYPE   4 217
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(12P13.1) MUTATED      1   41
  DEL PEAK 23(12P13.1) WILD-TYPE    4  217
                        clus
vv                       DEL PEAK 23(12P13.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           41
                        clus
vv                       DEL PEAK 23(12P13.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            217
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 24(12Q24.33) MUTATION ANALYSIS
D59V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 24(12Q24.33) MUTATED    34  22
  DEL PEAK 24(12Q24.33) WILD-TYPE 148  66
  DEL PEAK 24(12Q24.33) MUTATED DEL PEAK 24(12Q24.33) WILD-TYPE 
                             56                             214 
  DEL PEAK 24(12Q24.33) MUTATED DEL PEAK 24(12Q24.33) WILD-TYPE 
                             22                              66 
$`DEL PEAK 24(12Q24.33) MUTATED`
TCGA-2F-A9KR TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A42F TCGA-C4-A0F0 
      103.50         8.35        17.16         3.65        28.41         1.94 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47X TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU 
        0.43         0.69         0.10         4.90         7.20         5.19 
TCGA-DK-A2I4 TCGA-DK-A3IQ TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-E5-A2PC TCGA-E5-A4TZ 
      123.85        10.49         9.67        17.98        43.59        15.35 
TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3SL TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SS 
        0.59         1.22        22.45         5.52        46.78         1.97 
TCGA-FD-A43X TCGA-FD-A5BZ TCGA-FD-A62P TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH 
        3.62        27.45         6.28         4.11         2.07         2.20 
TCGA-FT-A61P TCGA-G2-A3VY TCGA-G2-AA3F TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS 
        6.48         0.85        19.46        15.91        14.07         1.12 
TCGA-GD-A76B TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JW TCGA-GV-A6ZA TCGA-HQ-A5NE 
        7.36         5.62         4.73         6.41        11.54         8.22 
TCGA-K4-A4AC TCGA-K4-A5RJ TCGA-LC-A66R TCGA-PQ-A6FI TCGA-XF-A8HF TCGA-XF-A8HG 
        6.48         1.74         6.35        12.23        56.19        15.35 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SX TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML 
       64.80        79.66        23.64        10.82        54.90         7.63 
TCGA-XF-AAMW TCGA-XF-AAN0 
        8.32        56.48 

$`DEL PEAK 24(12Q24.33) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A0C8 
       22.29        11.97        84.00        98.33         4.83        40.08 
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-A20X TCGA-BT-A2LB TCGA-BT-A3PH 
       14.89        14.96         5.06         8.25         5.59         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ 
       12.82         2.07        15.42        28.70         9.99         8.98 
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-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        0.10        12.92         5.46        16.31         1.84         9.34 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
        2.53         2.14        66.41        18.41        19.00         8.91 
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-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       10.59         7.79        87.32         2.20         3.98         7.82 
TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX 
        8.22        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-A6B1 
      140.81        48.00        64.18        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       15.68        41.06        30.67        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-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.99        14.33         0.46        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-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43N 
       24.30         6.12        12.82        13.18        19.79        22.98 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       14.93        14.96        14.93        12.13        13.38        37.15 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       11.01         6.87         5.36         5.69         6.84         6.87 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
       49.68         2.66         4.83         6.38        50.66        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
        9.30         6.71         2.66         4.01        10.85        15.19 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
        7.13         3.48         4.08         3.25        61.94        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-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       52.67         6.94         2.89         2.24        15.81         4.50 
TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
       17.75         2.66         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        2.20         6.41         7.59        11.31         2.04        27.09 
TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       10.65         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-H4-A2HQ 
        4.14         6.67         6.41        19.07         1.51         6.74 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       38.60         3.06         9.01         8.75         3.45         4.67 
TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A5Z6 
        2.50        10.52         1.81         4.27         6.38         3.45 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       11.80        13.48        16.67        14.24         0.85         3.75 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI 
       45.04         6.58        88.93        97.45         1.87        17.88 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       11.90        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMR TCGA-XF-AAMT 
       16.27        66.64         2.10        92.98        91.73         2.96 
TCGA-XF-AAMX TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
        6.77        30.94        27.06        75.39         3.88        10.36 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        4.83         0.66         7.96         9.04 

  DEL PEAK 24(12Q24.33) MUTATED DEL PEAK 24(12Q24.33) WILD-TYPE 
                           0.10                            0.07 
  DEL PEAK 24(12Q24.33) MUTATED DEL PEAK 24(12Q24.33) WILD-TYPE 
                         123.85                          140.81 
  DEL PEAK 24(12Q24.33) MUTATED DEL PEAK 24(12Q24.33) WILD-TYPE 
                          7.925                          10.175 
[1] "0.1 - 123.8 (7.9)"  "0.1 - 140.8 (10.2)"
[1] "hr=" "1.3"
D59V2, continuous
                                 vv
clus                              STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 24(12Q24.33) MUTATED          1       0       20         9       26
  DEL PEAK 24(12Q24.33) WILD-TYPE        0       2       66        84       66
D59V3, multiclass
           clus
vv          DEL PEAK 24(12Q24.33) MUTATED DEL PEAK 24(12Q24.33) WILD-TYPE
  STAGE 0A                              1                               0
  STAGE I                               0                               2
  STAGE II                             20                              66
  STAGE III                             9                              84
  STAGE IV                             26                              66
[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(12Q24.33) MUTATED         23  25   8
  DEL PEAK 24(12Q24.33) WILD-TYPE       59 111  31
D59V4, multiclass
          clus
vv         DEL PEAK 24(12Q24.33) MUTATED DEL PEAK 24(12Q24.33) WILD-TYPE
  T0+T1+T2                            23                              59
  T3                                  25                             111
  T4                                   8                              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
  DEL PEAK 24(12Q24.33) MUTATED    30   8  15   2
  DEL PEAK 24(12Q24.33) WILD-TYPE 136  20  40   5
D59V5, multiclass
    clus
vv   DEL PEAK 24(12Q24.33) MUTATED DEL PEAK 24(12Q24.33) WILD-TYPE
  N0                            30                             136
  N1                             8                              20
  N2                            15                              40
  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 24(12Q24.33) MUTATED    24   2  31
  DEL PEAK 24(12Q24.33) WILD-TYPE 105   5 110
D59V6, multiclass
    clus
vv   DEL PEAK 24(12Q24.33) MUTATED DEL PEAK 24(12Q24.33) WILD-TYPE
  M0                            24                             105
  M1                             2                               5
  MX                            31                             110
[1] 3 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 24(12Q24.33) MUTATED    12  46
  DEL PEAK 24(12Q24.33) WILD-TYPE  65 155
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(12Q24.33) MUTATED     12   46
  DEL PEAK 24(12Q24.33) WILD-TYPE   65  155
        clus
vv       DEL PEAK 24(12Q24.33) MUTATED DEL PEAK 24(12Q24.33) WILD-TYPE
  FEMALE                            12                              65
  MALE                              46                             155
[1] 2 2
[1] FALSE
D59V8, continuous
D59V9, continuous
D59V10, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(12Q24.33) MUTATED       9                         0    46
  DEL PEAK 24(12Q24.33) WILD-TYPE    22                        13   169
D59V11, multiclass
                           clus
vv                          DEL PEAK 24(12Q24.33) MUTATED
  ASIAN                                                 9
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                46
                           clus
vv                          DEL PEAK 24(12Q24.33) WILD-TYPE
  ASIAN                                                  22
  BLACK OR AFRICAN AMERICAN                              13
  WHITE                                                 169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V12, binary
                                 cls
clus                                0   1
  DEL PEAK 24(12Q24.33) MUTATED     0  55
  DEL PEAK 24(12Q24.33) WILD-TYPE   5 203
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(12Q24.33) MUTATED      0   55
  DEL PEAK 24(12Q24.33) WILD-TYPE    5  203
                        clus
vv                       DEL PEAK 24(12Q24.33) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            55
                        clus
vv                       DEL PEAK 24(12Q24.33) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             203
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 25(13Q14.2) MUTATION ANALYSIS
D60V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(13Q14.2) MUTATED    69  34
  DEL PEAK 25(13Q14.2) WILD-TYPE 113  54
  DEL PEAK 25(13Q14.2) MUTATED DEL PEAK 25(13Q14.2) WILD-TYPE 
                           103                            167 
  DEL PEAK 25(13Q14.2) MUTATED DEL PEAK 25(13Q14.2) WILD-TYPE 
                            34                             54 
$`DEL PEAK 25(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-A6ME 
       43.59        24.66         0.49         0.59         0.56        12.99 
TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 
        1.22        12.89         8.94         6.87         4.01        11.93 
TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       24.30        12.82        46.78        19.79         1.97        14.93 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62N 
        6.87         5.36         6.84        27.45        49.68         2.66 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EO 
        9.30         4.11         2.20         4.08         6.48        35.24 
TCGA-G2-A2ES TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3YS 
       17.26        19.46         2.89        15.81         4.50         1.12 
TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QI 
        2.66         2.10         2.20         6.41         6.15         4.14 
TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ 
       38.60         9.01         8.22         6.48        10.52         1.74 
TCGA-K4-A6FZ TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        1.81         6.35         3.45        13.48        12.23        16.67 
TCGA-S5-AA26 TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        3.75         6.58        88.93        11.90        23.64        21.04 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMX TCGA-XF-AAN0 
        2.24        66.64        54.90         7.63         6.77        56.48 
TCGA-YF-AA3L 
        7.96 

$`DEL PEAK 25(13Q14.2) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
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 
       66.41        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        41.56        76.60        15.68 
TCGA-DK-A6B5 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KF 
       41.06        15.35        26.17         0.10         0.53         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B4 TCGA-FD-A3B8 
        1.38         0.82        14.33         0.46        15.68        12.43 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP 
       15.88        45.93        22.45         6.12         5.52        13.18 
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-A5BT TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A62O TCGA-FD-A62P 
       37.15        11.01         5.69         6.87         4.83         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG 
        6.38        50.66        18.81         6.71         2.07         2.66 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE 
        4.01        10.85        15.19         7.13         3.48         3.25 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE 
       61.94        30.61         5.69        26.93         7.04        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD 
        0.85        52.67         6.94         2.24        15.91        14.07 
TCGA-GC-A3WC TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P 
       17.75         7.73         3.12        20.98         7.36         6.41 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 
        7.59        11.31         2.04        27.09         5.62         4.73 
TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK 
       10.65         4.41         5.69         7.63         7.79         6.67 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF 
        6.41        19.07        11.54         1.51         6.74         3.06 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A6MB TCGA-K4-A83P 
        8.75         3.45         4.67         2.50         4.27         6.38 
TCGA-LT-A8JT TCGA-R3-A69X TCGA-S5-A6DX TCGA-XF-A8HB TCGA-XF-A8HE TCGA-XF-A8HF 
       11.80        14.24         0.85        45.04        97.45        56.19 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SZ 
       15.35         1.87        17.88        64.80        79.66        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF 
       26.27        18.90        16.27         2.10        92.98        10.82 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
       91.73         2.96         8.32        30.94        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3M 
        3.88        10.36         4.83         0.66         9.04 

  DEL PEAK 25(13Q14.2) MUTATED DEL PEAK 25(13Q14.2) WILD-TYPE 
                          0.43                           0.07 
  DEL PEAK 25(13Q14.2) MUTATED DEL PEAK 25(13Q14.2) WILD-TYPE 
                        130.88                         140.81 
  DEL PEAK 25(13Q14.2) MUTATED DEL PEAK 25(13Q14.2) WILD-TYPE 
                          8.22                          10.65 
[1] "0.4 - 130.9 (8.2)"  "0.1 - 140.8 (10.7)"
[1] "hr=" "1.1"
D60V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 25(13Q14.2) MUTATED          0       0       27        33       41
  DEL PEAK 25(13Q14.2) WILD-TYPE        1       2       59        60       51
D60V3, multiclass
           clus
vv          DEL PEAK 25(13Q14.2) MUTATED DEL PEAK 25(13Q14.2) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              0                              2
  STAGE II                            27                             59
  STAGE III                           33                             60
  STAGE IV                            41                             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
  DEL PEAK 25(13Q14.2) MUTATED         28 58 12
  DEL PEAK 25(13Q14.2) WILD-TYPE       54 78 27
D60V4, multiclass
          clus
vv         DEL PEAK 25(13Q14.2) MUTATED DEL PEAK 25(13Q14.2) WILD-TYPE
  T0+T1+T2                           28                             54
  T3                                 58                             78
  T4                                 12                             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
  DEL PEAK 25(13Q14.2) MUTATED    54  13  25   4
  DEL PEAK 25(13Q14.2) WILD-TYPE 112  15  30   3
D60V5, multiclass
    clus
vv   DEL PEAK 25(13Q14.2) MUTATED DEL PEAK 25(13Q14.2) WILD-TYPE
  N0                           54                            112
  N1                           13                             15
  N2                           25                             30
  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 25(13Q14.2) MUTATED   46  1 56
  DEL PEAK 25(13Q14.2) WILD-TYPE 83  6 85
D60V6, multiclass
    clus
vv   DEL PEAK 25(13Q14.2) MUTATED DEL PEAK 25(13Q14.2) WILD-TYPE
  M0                           46                             83
  M1                            1                              6
  MX                           56                             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"
D60V7, binary
                                cls
clus                               0   1
  DEL PEAK 25(13Q14.2) MUTATED    26  77
  DEL PEAK 25(13Q14.2) WILD-TYPE  51 124
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(13Q14.2) MUTATED     26   77
  DEL PEAK 25(13Q14.2) WILD-TYPE   51  124
        clus
vv       DEL PEAK 25(13Q14.2) MUTATED DEL PEAK 25(13Q14.2) WILD-TYPE
  FEMALE                           26                             51
  MALE                             77                            124
[1] 2 2
[1] FALSE
D60V8, continuous
D60V9, continuous
D60V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(13Q14.2) MUTATED       7                         8    80
  DEL PEAK 25(13Q14.2) WILD-TYPE    24                         5   135
D60V11, multiclass
                           clus
vv                          DEL PEAK 25(13Q14.2) MUTATED
  ASIAN                                                7
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                               80
                           clus
vv                          DEL PEAK 25(13Q14.2) WILD-TYPE
  ASIAN                                                 24
  BLACK OR AFRICAN AMERICAN                              5
  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"
D60V12, binary
                                cls
clus                               0   1
  DEL PEAK 25(13Q14.2) MUTATED     2  93
  DEL PEAK 25(13Q14.2) WILD-TYPE   3 165
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(13Q14.2) MUTATED      2   93
  DEL PEAK 25(13Q14.2) WILD-TYPE    3  165
                        clus
vv                       DEL PEAK 25(13Q14.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           93
                        clus
vv                       DEL PEAK 25(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            165
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 26(14Q24.1) MUTATION ANALYSIS
D61V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(14Q24.1) MUTATED    56  29
  DEL PEAK 26(14Q24.1) WILD-TYPE 126  59
  DEL PEAK 26(14Q24.1) MUTATED DEL PEAK 26(14Q24.1) WILD-TYPE 
                            85                            185 
  DEL PEAK 26(14Q24.1) MUTATED DEL PEAK 26(14Q24.1) WILD-TYPE 
                            29                             59 
$`DEL PEAK 26(14Q24.1) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BT-A20J 
       22.29        11.97       103.50        98.33         4.83        19.04 
TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A3PK TCGA-CF-A1HR 
       14.89         5.06         8.35         5.59         2.07         0.46 
TCGA-CF-A1HS TCGA-CF-A47X TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A5W6 
        0.43         0.10         4.90         7.20         5.19         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I1 
        2.53         2.14        18.41       130.88       112.44        10.59 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-E5-A4TZ 
       10.49        50.27        48.00        64.18        41.06        15.35 
TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A6ME TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SP 
       26.17         0.49        12.99        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-G2-AA3B TCGA-GC-A3RD TCGA-GD-A2C5 TCGA-GD-A76B TCGA-GU-A42Q TCGA-GV-A3JZ 
       52.67        14.07         7.73         7.36         7.59         5.69 
TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ 
        7.63         4.14         6.41        19.07        11.54         6.74 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WU TCGA-K4-A6MB TCGA-MV-A51V TCGA-PQ-A6FI 
       38.60         3.06         3.45         4.27        13.48        12.23 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A9SX TCGA-XF-A9SZ 
       14.24         0.85        56.19         1.87        23.64        28.24 
TCGA-XF-A9T0 TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       26.27        54.90         7.63         8.32         6.77        56.48 
TCGA-YF-AA3M 
        9.04 

$`DEL PEAK 26(14Q24.1) WILD-TYPE`
TCGA-2F-A9KQ TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       84.00        40.08         7.33         2.66         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.58        11.93        32.84        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH 
        5.06        14.96         8.25        17.16         3.65         4.67 
TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
       12.82        15.42        28.70         9.99        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
        1.94        23.01         0.69         0.13         0.07         0.10 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A72E 
        0.07         0.10        12.92         5.46        16.31         9.34 
TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       66.41        19.00         8.91        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
        1.81         7.79       123.85        87.32         2.20         3.98 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
        7.82         8.22        21.30        20.02         9.67         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       10.55       140.81        17.98        41.56        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       15.68        30.67        43.59        24.66         0.10         0.53 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF 
        0.59         0.56         0.66         1.38         0.82        14.33 
TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
        1.22         0.46        12.89        15.68         8.94         6.87 
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-A3SO TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X 
        6.12         5.52         1.97        14.93        14.96         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-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TB 
        6.84        27.45         2.66         4.83         6.38        18.81 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 
        6.71         4.11         2.07         4.01        10.85         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-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       17.26         7.04         6.94        19.46         2.89         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
       15.81         4.50        15.91        17.75         1.12         2.66 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42R 
        2.10         3.12        20.98         2.20         6.41        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV 
        2.04        27.09         5.62         4.73        10.65         4.41 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QK TCGA-H4-A2HO TCGA-HQ-A5ND 
        6.41         6.15         7.79         6.67         1.51         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        8.22         8.75         4.67         2.50         6.48        10.52 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
        1.74         1.81         6.38         6.35         3.45        11.80 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
       16.67         3.75        45.04         6.58        88.93        97.45 
TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SY 
       15.35        17.88        64.80        79.66        11.90        21.04 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME 
       18.90         2.24        16.27        66.64         2.10        92.98 
TCGA-XF-AAMF TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
       10.82        91.73         2.96        30.94        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
        3.88        10.36         4.83         0.66         7.96 

  DEL PEAK 26(14Q24.1) MUTATED DEL PEAK 26(14Q24.1) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 26(14Q24.1) MUTATED DEL PEAK 26(14Q24.1) WILD-TYPE 
                        130.88                         140.81 
  DEL PEAK 26(14Q24.1) MUTATED DEL PEAK 26(14Q24.1) WILD-TYPE 
                         11.54                           8.91 
[1] "0.1 - 130.9 (11.5)" "0.1 - 140.8 (8.9)" 
[1] "hr=" "1.1"
D61V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 26(14Q24.1) MUTATED          1       0       25        24       34
  DEL PEAK 26(14Q24.1) WILD-TYPE        0       2       61        69       58
D61V3, multiclass
           clus
vv          DEL PEAK 26(14Q24.1) MUTATED DEL PEAK 26(14Q24.1) WILD-TYPE
  STAGE 0A                             1                              0
  STAGE I                              0                              2
  STAGE II                            25                             61
  STAGE III                           24                             69
  STAGE IV                            34                             58
[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(14Q24.1) MUTATED         27 41 13
  DEL PEAK 26(14Q24.1) WILD-TYPE       55 95 26
D61V4, multiclass
          clus
vv         DEL PEAK 26(14Q24.1) MUTATED DEL PEAK 26(14Q24.1) WILD-TYPE
  T0+T1+T2                           27                             55
  T3                                 41                             95
  T4                                 13                             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 26(14Q24.1) MUTATED    48   4  27   1
  DEL PEAK 26(14Q24.1) WILD-TYPE 118  24  28   6
D61V5, multiclass
    clus
vv   DEL PEAK 26(14Q24.1) MUTATED DEL PEAK 26(14Q24.1) WILD-TYPE
  N0                           48                            118
  N1                            4                             24
  N2                           27                             28
  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 26(14Q24.1) MUTATED   41  1 44
  DEL PEAK 26(14Q24.1) WILD-TYPE 88  6 97
D61V6, multiclass
    clus
vv   DEL PEAK 26(14Q24.1) MUTATED DEL PEAK 26(14Q24.1) WILD-TYPE
  M0                           41                             88
  M1                            1                              6
  MX                           44                             97
[1] 3 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 26(14Q24.1) MUTATED    21  66
  DEL PEAK 26(14Q24.1) WILD-TYPE  56 135
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(14Q24.1) MUTATED     21   66
  DEL PEAK 26(14Q24.1) WILD-TYPE   56  135
        clus
vv       DEL PEAK 26(14Q24.1) MUTATED DEL PEAK 26(14Q24.1) WILD-TYPE
  FEMALE                           21                             56
  MALE                             66                            135
[1] 2 2
[1] FALSE
D61V8, continuous
D61V9, continuous
D61V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(14Q24.1) MUTATED      10                         3    66
  DEL PEAK 26(14Q24.1) WILD-TYPE    21                        10   149
D61V11, multiclass
                           clus
vv                          DEL PEAK 26(14Q24.1) MUTATED
  ASIAN                                               10
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               66
                           clus
vv                          DEL PEAK 26(14Q24.1) WILD-TYPE
  ASIAN                                                 21
  BLACK OR AFRICAN AMERICAN                             10
  WHITE                                                149
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V12, binary
                                cls
clus                               0   1
  DEL PEAK 26(14Q24.1) MUTATED     2  79
  DEL PEAK 26(14Q24.1) WILD-TYPE   3 179
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(14Q24.1) MUTATED      2   79
  DEL PEAK 26(14Q24.1) WILD-TYPE    3  179
                        clus
vv                       DEL PEAK 26(14Q24.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           79
                        clus
vv                       DEL PEAK 26(14Q24.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            179
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 27(15Q13.1) MUTATION ANALYSIS
D62V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(15Q13.1) MUTATED    78  30
  DEL PEAK 27(15Q13.1) WILD-TYPE 104  58
  DEL PEAK 27(15Q13.1) MUTATED DEL PEAK 27(15Q13.1) WILD-TYPE 
                           108                            162 
  DEL PEAK 27(15Q13.1) MUTATED DEL PEAK 27(15Q13.1) WILD-TYPE 
                            30                             58 
$`DEL PEAK 27(15Q13.1) MUTATED`
TCGA-2F-A9KW TCGA-BL-A0C8 TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20W 
        4.83        40.08         6.58        19.04        32.84         8.35 
TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        8.25         5.59         3.65        15.42        28.70         9.99 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A47X TCGA-CU-A0YR TCGA-CU-A3QU TCGA-DK-A1A6 
        8.98         1.94         0.10         7.20         5.19        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IM 
       18.41       112.44         1.81         7.79       123.85         7.82 
TCGA-DK-A3IN TCGA-DK-A3X2 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC 
        8.22        17.98        15.68        41.06        30.67        43.59 
TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A7DV TCGA-FD-A3B3 
        0.49         0.59         0.56        12.99         1.22        12.89 
TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A43N 
       11.93        45.93        24.30        12.82        13.18        22.98 
TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        5.36         6.84        27.45         6.87        49.68         2.66 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TD TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 
        4.83         6.38         6.71         2.20        10.85        15.19 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EL TCGA-G2-A3IE TCGA-G2-A3VY 
        4.08         6.48        61.94        26.93        20.12         0.85 
TCGA-G2-AA3B TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 
       52.67        15.81         4.50        14.07         1.12         2.66 
TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A766 
        2.10         2.20         7.36         6.41         2.04         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH 
        4.73        10.65         6.41         6.15         7.63         7.79 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5NE 
        6.41        19.07        11.54         6.74        38.60         8.22 
TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-LC-A66R 
        8.75         2.50         1.74         1.81         4.27         6.35 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-XF-A8HB TCGA-XF-A8HD 
        3.45        13.48        16.67        14.24        45.04        88.93 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SX TCGA-XF-A9T0 TCGA-XF-A9T3 
       56.19        15.35         1.87        23.64        26.27         2.24 
TCGA-XF-A9T5 TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT TCGA-YF-AA3L TCGA-YF-AA3M 
       66.64        54.90         7.63         2.96         7.96         9.04 

$`DEL PEAK 27(15Q13.1) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-BL-A13I 
       22.29        11.97        84.00       103.50        98.33         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P 
        2.66         6.74        12.39        11.93        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A2LA 
       19.50         5.06        14.89        14.96         5.06        17.16 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR 
        4.67        12.82         2.07        28.41        23.01         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-A47Y TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 
        0.10        12.92         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-A1AC 
        9.34         2.53         2.14        19.00         8.91       130.88 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IK 
       16.14        17.62        15.62        10.59        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        3.98        10.49        50.27        21.30        20.02         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW 
        8.28        10.55       140.81        48.00        64.18        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       76.60        67.36        15.35        26.17        24.66         0.10 
TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN 
        0.53         0.66         1.38         0.82        14.33         0.46 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 
       15.68         8.94         6.87         4.01        12.43        15.88 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       22.45         6.12         5.52        46.78        19.79         1.97 
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-A5BX TCGA-FD-A62P TCGA-FD-A6TA 
       37.15        11.01         6.87         5.69         6.28        50.66 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI 
       18.81         9.30         4.11         2.07         2.66         4.01 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO 
        7.13         3.48         3.25        30.61         5.69        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       17.26         7.04         6.94        19.46         2.89         2.24 
TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q 
       15.91        17.75         7.73         3.12        20.98         7.59 
TCGA-GU-A42R TCGA-GU-A763 TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A3QK 
       11.31        27.09         4.41         5.69         4.14         6.67 
TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC 
        1.51         3.06         9.01         3.45         4.67         6.48 
TCGA-K4-A54R TCGA-K4-A83P TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-S5-A6DX TCGA-S5-AA26 
       10.52         6.38        11.80        12.23         0.85         3.75 
TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SW 
        6.58        97.45        17.88        64.80        79.66        11.90 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME 
       21.04        28.24        18.90        16.27         2.10        92.98 
TCGA-XF-AAMF TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 
       10.82        91.73         8.32         6.77        56.48        30.94 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39         3.88        10.36         4.83         0.66 

  DEL PEAK 27(15Q13.1) MUTATED DEL PEAK 27(15Q13.1) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 27(15Q13.1) MUTATED DEL PEAK 27(15Q13.1) WILD-TYPE 
                        123.85                         140.81 
  DEL PEAK 27(15Q13.1) MUTATED DEL PEAK 27(15Q13.1) WILD-TYPE 
                         8.220                         10.535 
[1] "0.1 - 123.8 (8.2)"  "0.1 - 140.8 (10.5)"
[1] "hr=" "1.2"
D62V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 27(15Q13.1) MUTATED          1       1       31        36       39
  DEL PEAK 27(15Q13.1) WILD-TYPE        0       1       55        57       53
D62V3, multiclass
           clus
vv          DEL PEAK 27(15Q13.1) MUTATED DEL PEAK 27(15Q13.1) WILD-TYPE
  STAGE 0A                             1                              0
  STAGE I                              1                              1
  STAGE II                            31                             55
  STAGE III                           36                             57
  STAGE IV                            39                             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 27(15Q13.1) MUTATED         30 57 11
  DEL PEAK 27(15Q13.1) WILD-TYPE       52 79 28
D62V4, multiclass
          clus
vv         DEL PEAK 27(15Q13.1) MUTATED DEL PEAK 27(15Q13.1) WILD-TYPE
  T0+T1+T2                           30                             52
  T3                                 57                             79
  T4                                 11                             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
  DEL PEAK 27(15Q13.1) MUTATED    58  12  24   3
  DEL PEAK 27(15Q13.1) WILD-TYPE 108  16  31   4
D62V5, multiclass
    clus
vv   DEL PEAK 27(15Q13.1) MUTATED DEL PEAK 27(15Q13.1) WILD-TYPE
  N0                           58                            108
  N1                           12                             16
  N2                           24                             31
  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 27(15Q13.1) MUTATED   39  2 67
  DEL PEAK 27(15Q13.1) WILD-TYPE 90  5 74
D62V6, multiclass
    clus
vv   DEL PEAK 27(15Q13.1) MUTATED DEL PEAK 27(15Q13.1) WILD-TYPE
  M0                           39                             90
  M1                            2                              5
  MX                           67                             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"
D62V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(15Q13.1) MUTATED    30  79
  DEL PEAK 27(15Q13.1) WILD-TYPE  47 122
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q13.1) MUTATED     30   79
  DEL PEAK 27(15Q13.1) WILD-TYPE   47  122
        clus
vv       DEL PEAK 27(15Q13.1) MUTATED DEL PEAK 27(15Q13.1) WILD-TYPE
  FEMALE                           30                             47
  MALE                             79                            122
[1] 2 2
[1] FALSE
D62V8, continuous
D62V9, continuous
D62V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(15Q13.1) MUTATED       7                         3    90
  DEL PEAK 27(15Q13.1) WILD-TYPE    24                        10   125
D62V11, multiclass
                           clus
vv                          DEL PEAK 27(15Q13.1) MUTATED
  ASIAN                                                7
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               90
                           clus
vv                          DEL PEAK 27(15Q13.1) WILD-TYPE
  ASIAN                                                 24
  BLACK OR AFRICAN AMERICAN                             10
  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"
D62V12, binary
                                cls
clus                               0   1
  DEL PEAK 27(15Q13.1) MUTATED     4  97
  DEL PEAK 27(15Q13.1) WILD-TYPE   1 161
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(15Q13.1) MUTATED      4   97
  DEL PEAK 27(15Q13.1) WILD-TYPE    1  161
                        clus
vv                       DEL PEAK 27(15Q13.1) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           97
                        clus
vv                       DEL PEAK 27(15Q13.1) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            161
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK 28(16P13.3) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 28(16P13.3) MUTATED    76  37
  DEL PEAK 28(16P13.3) WILD-TYPE 106  51
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                           113                            157 
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                            37                             51 
$`DEL PEAK 28(16P13.3) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KW TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20N 
       22.29        11.97         4.83         2.66         6.58        32.84 
TCGA-BT-A20R TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ 
        5.06         8.35        17.16         5.59         4.67        12.82 
TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A47T TCGA-CU-A0YN 
       28.70         9.99        23.01         0.43         0.07        12.92 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A2HX 
        5.46         5.19         1.84         2.53        18.41         1.81 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT 
      123.85        87.32         2.20         7.82         8.22        21.30 
TCGA-DK-A3IV TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A4TZ 
        9.67        10.55        17.98        67.36        30.67        15.35 
TCGA-E5-A4U1 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6ME TCGA-FD-A3B3 TCGA-FD-A3B6 
       26.17         0.59         0.56        12.99        12.89         6.87 
TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BR 
       13.18        19.79        22.98        14.93        12.13        13.38 
TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
        5.36         6.84        27.45         2.66         4.83         6.38 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 
        6.71         4.11         2.07         2.20        10.85        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-GU-A762 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JW 
       11.31         2.04         5.62         4.73        10.65         6.41 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE 
        6.15         5.69         7.79        11.54         6.74        38.60 
TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ 
        3.06         8.75         6.48        10.52         1.74         1.81 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-S5-A6DX TCGA-XF-A8HC 
        6.35         3.45        13.48        16.67         0.85         6.58 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SI TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
       56.19        15.35        79.66        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-AAML TCGA-XF-AAMT 
       28.24        26.27         2.24         2.10         7.63         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-YF-AA3L TCGA-YF-AA3M 
        8.32         6.77        56.48         7.96         9.04 

$`DEL PEAK 28(16P13.3) WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM 
       84.00       103.50        98.33        40.08         7.33         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       12.39        11.93        19.04        12.16        17.88        19.50 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LD TCGA-BT-A3PK 
       14.89        14.96         5.06         8.25         3.65         2.07 
TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A27C 
       15.42        28.41         8.98         1.94         0.46         0.69 
TCGA-CF-A47S TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YO 
        0.13         0.10         0.07         0.10         0.10         4.90 
TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA 
        7.20        16.31         9.34         2.14        66.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
        8.91       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU 
       10.59         7.79         3.98        10.49        50.27        20.02 
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        41.56        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       15.68        41.06        43.59        24.66         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV 
        0.53         0.66         1.38         0.82        14.33         1.22 
TCGA-E7-A7XN TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
        0.46        15.68         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-A3SN 
       15.88        45.93        24.30        22.45         6.12        12.82 
TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X 
        5.52        46.78         1.97        14.93        14.96         3.62 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A5C1 
       37.15        11.01         6.87         5.69         6.87        49.68 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TI 
        6.28        50.66        18.81         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-G2-AA3B 
        5.69        35.24        17.26         7.04         0.85        52.67 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3WC 
        6.94        19.46         2.89         2.24        15.81        17.75 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A763 TCGA-GV-A3JV 
        3.12        20.98         7.36         7.59        27.09         4.41 
TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO 
        7.63         4.14         6.67         6.41        19.07         1.51 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A6MB 
        9.01         8.22         3.45         4.67         2.50         4.27 
TCGA-K4-A83P TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-AA26 TCGA-XF-A8HB 
        6.38        11.80        12.23        14.24         3.75        45.04 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9T2 
       88.93        97.45         1.87        17.88        64.80        18.90 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMR 
       16.27        66.64        92.98        10.82        54.90        91.73 
TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       30.94        27.06        75.39         3.88        10.36         4.83 
TCGA-YC-A9TC 
        0.66 

  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                        123.85                         140.81 
  DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE 
                          8.22                          10.59 
[1] "0.1 - 123.8 (8.2)"  "0.1 - 140.8 (10.6)"
[1] "hr=" "1.2"
D63V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 28(16P13.3) MUTATED          1       0       29        41       40
  DEL PEAK 28(16P13.3) WILD-TYPE        0       2       57        52       52
D63V3, multiclass
           clus
vv          DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE
  STAGE 0A                             1                              0
  STAGE I                              0                              2
  STAGE II                            29                             57
  STAGE III                           41                             52
  STAGE IV                            40                             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
  DEL PEAK 28(16P13.3) MUTATED         25 62 16
  DEL PEAK 28(16P13.3) WILD-TYPE       57 74 23
D63V4, multiclass
          clus
vv         DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE
  T0+T1+T2                           25                             57
  T3                                 62                             74
  T4                                 16                             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 28(16P13.3) MUTATED    62   7  32   2
  DEL PEAK 28(16P13.3) WILD-TYPE 104  21  23   5
D63V5, multiclass
    clus
vv   DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE
  N0                           62                            104
  N1                            7                             21
  N2                           32                             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 28(16P13.3) MUTATED   42  2 69
  DEL PEAK 28(16P13.3) WILD-TYPE 87  5 72
D63V6, multiclass
    clus
vv   DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE
  M0                           42                             87
  M1                            2                              5
  MX                           69                             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"
D63V7, binary
                                cls
clus                               0   1
  DEL PEAK 28(16P13.3) MUTATED    33  80
  DEL PEAK 28(16P13.3) WILD-TYPE  44 121
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(16P13.3) MUTATED     33   80
  DEL PEAK 28(16P13.3) WILD-TYPE   44  121
        clus
vv       DEL PEAK 28(16P13.3) MUTATED DEL PEAK 28(16P13.3) WILD-TYPE
  FEMALE                           33                             44
  MALE                             80                            121
[1] 2 2
[1] FALSE
D63V8, continuous
D63V9, continuous
D63V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(16P13.3) MUTATED       7                         3    95
  DEL PEAK 28(16P13.3) WILD-TYPE    24                        10   120
D63V11, multiclass
                           clus
vv                          DEL PEAK 28(16P13.3) MUTATED
  ASIAN                                                7
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               95
                           clus
vv                          DEL PEAK 28(16P13.3) WILD-TYPE
  ASIAN                                                 24
  BLACK OR AFRICAN AMERICAN                             10
  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"
D63V12, binary
                                cls
clus                               0   1
  DEL PEAK 28(16P13.3) MUTATED     2 106
  DEL PEAK 28(16P13.3) WILD-TYPE   3 152
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(16P13.3) MUTATED      2  106
  DEL PEAK 28(16P13.3) WILD-TYPE    3  152
                        clus
vv                       DEL PEAK 28(16P13.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          106
                        clus
vv                       DEL PEAK 28(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            152
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK 29(16Q23.1) MUTATION ANALYSIS
D64V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(16Q23.1) MUTATED    51  26
  DEL PEAK 29(16Q23.1) WILD-TYPE 131  62
  DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE 
                            77                            193 
  DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE 
                            26                             62 
$`DEL PEAK 29(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-E7-A6ME TCGA-FD-A3B5 TCGA-FD-A3N5 
        0.49         0.59         1.38        12.99         8.94        11.93 
TCGA-FD-A3SO TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A62N TCGA-FD-A62O 
        5.52         1.97        22.98        14.93         2.66         4.83 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2EF 
        9.30         6.71         4.11        15.19         6.48        61.94 
TCGA-G2-A2EJ TCGA-G2-A3IE TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GD-A3OP TCGA-GD-A6C6 
       30.61        20.12        15.91        14.07         2.10         2.20 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A766 TCGA-GV-A3JV TCGA-GV-A3JX 
        6.41         7.59         2.04         5.62         4.41         6.15 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HQ TCGA-HQ-A2OE 
        5.69         7.63         7.79         4.14         6.74        38.60 
TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-MV-A51V 
        4.67         6.48         1.74         1.81         3.45        13.48 
TCGA-PQ-A6FI TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SI 
       12.23         6.58        97.45        56.19        15.35        79.66 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T6 TCGA-XF-AAMF 
       11.90        23.64        21.04        26.27         2.10        10.82 
TCGA-XF-AAML TCGA-XF-AAN0 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        7.63        56.48         0.66         7.96         9.04 

$`DEL PEAK 29(16Q23.1) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        84.00       103.50        98.33         4.83 
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        66.41        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        41.56        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       15.68        41.06        43.59        26.17        24.66         0.10 
TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV 
        0.53         0.56         0.66         0.82        14.33         1.22 
TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
        0.46        12.89        15.68         6.87         4.01        12.43 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       15.88        45.93        24.30        22.45         6.12        12.82 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X 
       13.18        46.78        19.79        14.93        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-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P 
        5.69         6.84        27.45         6.87        49.68         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        6.38        50.66        18.81         2.07         2.66         2.20 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
        4.01        10.85         7.13         3.48         4.08         3.25 
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-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
       52.67         6.94        19.46         2.89         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ 
        4.50        17.75         1.12         2.66         7.73         3.12 
TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A767 TCGA-GU-AATO 
       20.98         7.36        11.31        27.09         4.73        10.65 
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-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
        3.06         9.01         8.22         8.75         3.45         2.50 
TCGA-K4-A54R TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FN 
       10.52         4.27         6.38         6.35        11.80        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HH 
       14.24         0.85         3.75        45.04        88.93         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       17.88        64.80        28.24        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-AAME TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       66.64        92.98        54.90        91.73         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
        6.77        30.94        27.06        75.39         3.88        10.36 
TCGA-YC-A8S6 
        4.83 

  DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE 
                          0.49                           0.07 
  DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE 
                        130.88                         140.81 
  DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE 
                          8.22                          10.49 
[1] "0.5 - 130.9 (8.2)"  "0.1 - 140.8 (10.5)"
[1] "hr=" "1.1"
D64V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 29(16Q23.1) MUTATED          0       1       24        23       28
  DEL PEAK 29(16Q23.1) WILD-TYPE        1       1       62        70       64
D64V3, multiclass
           clus
vv          DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              1                              1
  STAGE II                            24                             62
  STAGE III                           23                             70
  STAGE IV                            28                             64
[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(16Q23.1) MUTATED         22  34  12
  DEL PEAK 29(16Q23.1) WILD-TYPE       60 102  27
D64V4, multiclass
          clus
vv         DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE
  T0+T1+T2                           22                             60
  T3                                 34                            102
  T4                                 12                             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
  DEL PEAK 29(16Q23.1) MUTATED    38   6  19   3
  DEL PEAK 29(16Q23.1) WILD-TYPE 128  22  36   4
D64V5, multiclass
    clus
vv   DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE
  N0                           38                            128
  N1                            6                             22
  N2                           19                             36
  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(16Q23.1) MUTATED    28   2  47
  DEL PEAK 29(16Q23.1) WILD-TYPE 101   5  94
D64V6, multiclass
    clus
vv   DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE
  M0                           28                            101
  M1                            2                              5
  MX                           47                             94
[1] 3 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 29(16Q23.1) MUTATED    15  62
  DEL PEAK 29(16Q23.1) WILD-TYPE  62 139
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q23.1) MUTATED     15   62
  DEL PEAK 29(16Q23.1) WILD-TYPE   62  139
        clus
vv       DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE
  FEMALE                           15                             62
  MALE                             62                            139
[1] 2 2
[1] FALSE
D64V8, continuous
D64V9, continuous
D64V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(16Q23.1) MUTATED       6                         3    63
  DEL PEAK 29(16Q23.1) WILD-TYPE    25                        10   152
D64V11, multiclass
                           clus
vv                          DEL PEAK 29(16Q23.1) MUTATED
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               63
                           clus
vv                          DEL PEAK 29(16Q23.1) WILD-TYPE
  ASIAN                                                 25
  BLACK OR AFRICAN AMERICAN                             10
  WHITE                                                152
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V12, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q23.1) MUTATED     2  72
  DEL PEAK 29(16Q23.1) WILD-TYPE   3 186
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q23.1) MUTATED      2   72
  DEL PEAK 29(16Q23.1) WILD-TYPE    3  186
                        clus
vv                       DEL PEAK 29(16Q23.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           72
                        clus
vv                       DEL PEAK 29(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            186
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK 30(17P12) MUTATION ANALYSIS
D65V1, survival
                              sevent
clus2                           0  1
  DEL PEAK 30(17P12) MUTATED   88 47
  DEL PEAK 30(17P12) WILD-TYPE 94 41
  DEL PEAK 30(17P12) MUTATED DEL PEAK 30(17P12) WILD-TYPE 
                         135                          135 
  DEL PEAK 30(17P12) MUTATED DEL PEAK 30(17P12) WILD-TYPE 
                          47                           41 
$`DEL PEAK 30(17P12) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KT TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A5ZZ 
       22.29       103.50        98.33        40.08         2.66        12.39 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20X 
       19.04        32.84        17.88        19.50        14.89         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42E TCGA-C4-A0EZ 
       17.16         5.59         4.67         2.07         9.99         8.98 
TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47X TCGA-CU-A3KJ 
        1.94         0.46         0.43         0.69         0.10         5.46 
TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A1AC 
        1.84         2.14        66.41        18.41         8.91       130.88 
TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
      112.44         1.81        10.59        87.32         2.20         3.98 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X1 
        8.22        10.49        50.27        21.30         9.67        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-E5-A2PC TCGA-E5-A4TZ 
       17.98        64.18        41.06        30.67        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A6ME 
       26.17         0.49         0.59         0.56         1.38        12.99 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SO 
       15.68         8.94        45.93        24.30        12.82         5.52 
TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43X 
       46.78         1.97        22.98        14.93        14.93         3.62 
TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       13.38         5.36         6.84         4.83         6.28         6.38 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TK 
       50.66        18.81         9.30         6.71         2.66        10.85 
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-G2-AA3B TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3RD 
       20.12         0.85        52.67         2.89         4.50        14.07 
TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        1.12         7.73         2.10         2.20         7.36         6.41 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A767 TCGA-GV-A3JZ TCGA-GV-A3QF 
        7.59        11.31         2.04         4.73         5.69         7.63 
TCGA-GV-A3QH TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
        7.79         6.41        19.07         6.74        38.60         3.06 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A4AC TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-PQ-A6FI 
        9.01         8.22         6.48         1.74         4.27        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       16.67        14.24         0.85        88.93        97.45        56.19 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SI TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T3 
       15.35         1.87        79.66        23.64        28.24         2.24 
TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 
       10.82        54.90        91.73         2.96         8.32        56.48 
TCGA-XF-AAN1 TCGA-YF-AA3L TCGA-YF-AA3M 
       30.94         7.96         9.04 

$`DEL PEAK 30(17P12) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 
       11.97        84.00         4.83         7.33         6.74         6.58 
TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       11.93        12.16         5.06        14.96         5.06         8.35 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0F6 
        3.65        12.82        15.42        28.70        28.41        23.01 
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-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 
        4.90         7.20         5.19        16.31         9.34         2.53 
TCGA-DK-A1AA TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 
       19.00        16.14        17.62        15.62         7.79       123.85 
TCGA-DK-A3IM TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW 
        7.82        20.02         8.28        10.55       140.81        41.56 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       76.60        67.36        15.68        24.66         0.10         0.53 
TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 
        0.66         0.82        14.33         1.22         0.46        12.89 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SL 
        6.87         4.01        12.43        11.93        15.88        22.45 
TCGA-FD-A3SM TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BS 
        6.12        13.18        19.79        14.96        12.13        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-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z9 
        2.66         4.11         2.07         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-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3WC 
        6.94        19.46         2.24        15.81        15.91        17.75 
TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-AATO 
        2.66         3.12        20.98        27.09         5.62        10.65 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A6ZA 
        4.41         6.41         6.15         4.14         6.67        11.54 
TCGA-H4-A2HO TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R 
        1.51         8.75         3.45         4.67         2.50        10.52 
TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
        1.81         6.38         6.35         3.45        11.80        13.48 
TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SW 
        3.75        45.04         6.58        17.88        64.80        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       21.04        26.27        18.90        16.27        66.64         2.10 
TCGA-XF-AAME TCGA-XF-AAML TCGA-XF-AAMX TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
       92.98         7.63         6.77        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       10.36         4.83         0.66 

  DEL PEAK 30(17P12) MUTATED DEL PEAK 30(17P12) WILD-TYPE 
                        0.10                         0.07 
  DEL PEAK 30(17P12) MUTATED DEL PEAK 30(17P12) WILD-TYPE 
                      130.88                       140.81 
  DEL PEAK 30(17P12) MUTATED DEL PEAK 30(17P12) WILD-TYPE 
                        9.99                         8.28 
[1] "0.1 - 130.9 (10.0)" "0.1 - 140.8 (8.3)" 
[1] "hr=" "1"  
D65V2, continuous
                              vv
clus                           STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 30(17P12) MUTATED          0       1       43        40       50
  DEL PEAK 30(17P12) WILD-TYPE        1       1       43        53       42
D65V3, multiclass
           clus
vv          DEL PEAK 30(17P12) MUTATED DEL PEAK 30(17P12) WILD-TYPE
  STAGE 0A                           0                            1
  STAGE I                            1                            1
  STAGE II                          43                           43
  STAGE III                         40                           53
  STAGE IV                          50                           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
  DEL PEAK 30(17P12) MUTATED         41 65 20
  DEL PEAK 30(17P12) WILD-TYPE       41 71 19
D65V4, multiclass
          clus
vv         DEL PEAK 30(17P12) MUTATED DEL PEAK 30(17P12) WILD-TYPE
  T0+T1+T2                         41                           41
  T3                               65                           71
  T4                               20                           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 30(17P12) MUTATED   77 12 33  3
  DEL PEAK 30(17P12) WILD-TYPE 89 16 22  4
D65V5, multiclass
    clus
vv   DEL PEAK 30(17P12) MUTATED DEL PEAK 30(17P12) WILD-TYPE
  N0                         77                           89
  N1                         12                           16
  N2                         33                           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
  DEL PEAK 30(17P12) MUTATED   66  3 68
  DEL PEAK 30(17P12) WILD-TYPE 63  4 73
D65V6, multiclass
    clus
vv   DEL PEAK 30(17P12) MUTATED DEL PEAK 30(17P12) WILD-TYPE
  M0                         66                           63
  M1                          3                            4
  MX                         68                           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"
D65V7, binary
                              cls
clus                             0   1
  DEL PEAK 30(17P12) MUTATED    37 101
  DEL PEAK 30(17P12) WILD-TYPE  40 100
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 30(17P12) MUTATED     37  101
  DEL PEAK 30(17P12) WILD-TYPE   40  100
        clus
vv       DEL PEAK 30(17P12) MUTATED DEL PEAK 30(17P12) WILD-TYPE
  FEMALE                         37                           40
  MALE                          101                          100
[1] 2 2
[1] FALSE
D65V8, continuous
D65V9, continuous
D65V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(17P12) MUTATED      15                         5   104
  DEL PEAK 30(17P12) WILD-TYPE    16                         8   111
D65V11, multiclass
                           clus
vv                          DEL PEAK 30(17P12) MUTATED
  ASIAN                                             15
  BLACK OR AFRICAN AMERICAN                          5
  WHITE                                            104
                           clus
vv                          DEL PEAK 30(17P12) WILD-TYPE
  ASIAN                                               16
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V12, binary
                              cls
clus                             0   1
  DEL PEAK 30(17P12) MUTATED     3 124
  DEL PEAK 30(17P12) WILD-TYPE   2 134
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 30(17P12) MUTATED      3  124
  DEL PEAK 30(17P12) WILD-TYPE    2  134
                        clus
vv                       DEL PEAK 30(17P12) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                        124
                        clus
vv                       DEL PEAK 30(17P12) WILD-TYPE
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          134
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK 31(18Q23) MUTATION ANALYSIS
D66V1, survival
                              sevent
clus2                           0  1
  DEL PEAK 31(18Q23) MUTATED   84 27
  DEL PEAK 31(18Q23) WILD-TYPE 98 61
  DEL PEAK 31(18Q23) MUTATED DEL PEAK 31(18Q23) WILD-TYPE 
                         111                          159 
  DEL PEAK 31(18Q23) MUTATED DEL PEAK 31(18Q23) WILD-TYPE 
                          27                           61 
$`DEL PEAK 31(18Q23) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-BT-A0YX TCGA-BT-A20J 
       22.29        84.00       103.50         4.83        11.93        19.04 
TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A42B TCGA-BT-A42C 
       32.84         5.06         8.35        17.16        15.42        28.70 
TCGA-BT-A42E TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T TCGA-CU-A0YN 
        9.99         0.46         0.43         0.13         0.07        12.92 
TCGA-CU-A0YR TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AB 
        7.20         1.84         9.34         2.14        18.41         8.91 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 
      130.88       112.44        16.14        17.62         1.81        10.59 
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-A3X1 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC 
       21.30        48.00        64.18        15.68        41.06        43.59 
TCGA-E7-A3X6 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A7DV TCGA-FD-A3B4 
       24.66         0.59         0.56         1.38         1.22        15.68 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
        4.01        45.93        24.30        12.82         5.52        13.18 
TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A62N TCGA-FD-A62O 
       46.78         1.97        22.98        12.13         2.66         4.83 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3ZF 
        6.38        50.66         6.71         2.66         2.20         4.08 
TCGA-G2-A2EF TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3RC 
       61.94        20.12        52.67        19.46         2.89        15.91 
TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A6C6 
       14.07         1.12         2.66         2.10        20.98         2.20 
TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JW 
        6.41         2.04         5.62         4.73        10.65         6.41 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE 
        6.15         5.69        19.07        11.54         6.74        38.60 
TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A5RJ TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI 
        3.06         8.75         1.74         6.35        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A9SW TCGA-XF-A9SX 
       16.67        14.24         6.58        56.19        11.90        23.64 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT 
       66.64         2.10        54.90         7.63        91.73         2.96 
TCGA-XF-AAMX TCGA-YF-AA3L TCGA-YF-AA3M 
        6.77         7.96         9.04 

$`DEL PEAK 31(18Q23) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KT TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       11.97        98.33        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T 
       12.39         6.58        12.16        17.88        19.50        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
       14.96         5.06         8.25         5.59         3.65         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
       12.82         2.07        28.41         8.98         1.94        23.01 
TCGA-CF-A27C TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CU-A0YO 
        0.69         0.10         0.07         0.10         0.10         4.90 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AA 
        5.46         5.19        16.31         2.53        66.41        19.00 
TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3IV 
       15.62         7.79       123.85        10.49        20.02         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 
        8.28        10.55       140.81        17.98        41.56        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       67.36        30.67        15.35        26.17         0.10         0.49 
TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN 
        0.53         0.66         0.82        12.99        14.33         0.46 
TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       12.89         8.94         6.87        12.43        11.93        15.88 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       22.45         6.12        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-A5BV 
        3.62        13.38        37.15        11.01         6.87         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P 
        5.69         6.84        27.45         6.87        49.68         6.28 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TI TCGA-FD-A6TK 
       18.81         9.30         4.11         2.07         4.01        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ 
       15.19         7.13         3.48         3.25         6.48        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-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GD-A2C5 
        6.94         2.24        15.81         4.50        17.75         7.73 
TCGA-GD-A3OQ TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GV-A3JV 
        3.12         7.36         7.59        11.31        27.09         4.41 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HO 
        7.63         7.79         4.14         6.67         6.41         1.51 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        9.01         8.22         3.45         4.67         2.50         6.48 
TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-LT-A8JT 
       10.52         1.81         4.27         6.38         3.45        11.80 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG 
        0.85         3.75        45.04        88.93        97.45        15.35 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SY TCGA-XF-A9SZ 
        1.87        17.88        64.80        79.66        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMF 
       26.27        18.90         2.24        16.27        92.98        10.82 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
        8.32        56.48        30.94        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       10.36         4.83         0.66 

  DEL PEAK 31(18Q23) MUTATED DEL PEAK 31(18Q23) WILD-TYPE 
                        0.07                         0.07 
  DEL PEAK 31(18Q23) MUTATED DEL PEAK 31(18Q23) WILD-TYPE 
                      130.88                       140.81 
  DEL PEAK 31(18Q23) MUTATED DEL PEAK 31(18Q23) WILD-TYPE 
                        9.99                         8.98 
[1] "0.1 - 130.9 (10.0)" "0.1 - 140.8 (9.0)" 
[1] "hr=" "1.7"
D66V2, continuous
                              vv
clus                           STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 31(18Q23) MUTATED          1       0       32        38       40
  DEL PEAK 31(18Q23) WILD-TYPE        0       2       54        55       52
D66V3, multiclass
           clus
vv          DEL PEAK 31(18Q23) MUTATED DEL PEAK 31(18Q23) WILD-TYPE
  STAGE 0A                           1                            0
  STAGE I                            0                            2
  STAGE II                          32                           54
  STAGE III                         38                           55
  STAGE IV                          40                           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
  DEL PEAK 31(18Q23) MUTATED         34 61 13
  DEL PEAK 31(18Q23) WILD-TYPE       48 75 26
D66V4, multiclass
          clus
vv         DEL PEAK 31(18Q23) MUTATED DEL PEAK 31(18Q23) WILD-TYPE
  T0+T1+T2                         34                           48
  T3                               61                           75
  T4                               13                           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 31(18Q23) MUTATED   68 11 25  3
  DEL PEAK 31(18Q23) WILD-TYPE 98 17 30  4
D66V5, multiclass
    clus
vv   DEL PEAK 31(18Q23) MUTATED DEL PEAK 31(18Q23) WILD-TYPE
  N0                         68                           98
  N1                         11                           17
  N2                         25                           30
  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(18Q23) MUTATED   56  1 57
  DEL PEAK 31(18Q23) WILD-TYPE 73  6 84
D66V6, multiclass
    clus
vv   DEL PEAK 31(18Q23) MUTATED DEL PEAK 31(18Q23) WILD-TYPE
  M0                         56                           73
  M1                          1                            6
  MX                         57                           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"
D66V7, binary
                              cls
clus                             0   1
  DEL PEAK 31(18Q23) MUTATED    32  82
  DEL PEAK 31(18Q23) WILD-TYPE  45 119
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(18Q23) MUTATED     32   82
  DEL PEAK 31(18Q23) WILD-TYPE   45  119
        clus
vv       DEL PEAK 31(18Q23) MUTATED DEL PEAK 31(18Q23) WILD-TYPE
  FEMALE                         32                           45
  MALE                           82                          119
[1] 2 2
[1] FALSE
D66V8, continuous
D66V9, continuous
D66V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(18Q23) MUTATED      13                         5    88
  DEL PEAK 31(18Q23) WILD-TYPE    18                         8   127
D66V11, multiclass
                           clus
vv                          DEL PEAK 31(18Q23) MUTATED
  ASIAN                                             13
  BLACK OR AFRICAN AMERICAN                          5
  WHITE                                             88
                           clus
vv                          DEL PEAK 31(18Q23) WILD-TYPE
  ASIAN                                               18
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                              127
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V12, binary
                              cls
clus                             0   1
  DEL PEAK 31(18Q23) MUTATED     3 104
  DEL PEAK 31(18Q23) WILD-TYPE   2 154
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(18Q23) MUTATED      3  104
  DEL PEAK 31(18Q23) WILD-TYPE    2  154
                        clus
vv                       DEL PEAK 31(18Q23) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                        104
                        clus
vv                       DEL PEAK 31(18Q23) WILD-TYPE
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          154
[1] 2 2
[1] FALSE

Clustering(67) Variable = DEL PEAK 32(19P13.3) MUTATION ANALYSIS
D67V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 32(19P13.3) MUTATED    63  34
  DEL PEAK 32(19P13.3) WILD-TYPE 119  54
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                            97                            173 
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                            34                             54 
$`DEL PEAK 32(19P13.3) MUTATED`
TCGA-2F-A9KW TCGA-BL-A5ZZ TCGA-BT-A20J TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V 
        4.83        12.39        19.04         5.06        14.89         5.06 
TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B 
        8.35         5.59         3.65         4.67         2.07        15.42 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
        9.99        28.41         8.98        23.01         0.46         0.43 
TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A2I6 TCGA-DK-A3IL 
        2.14        18.41         8.91       112.44        87.32         3.98 
TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B5 TCGA-E5-A2PC 
       10.49        21.30        48.00        17.98        41.06        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         6.12        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-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FJ-A3ZE 
       18.81         9.30         4.11         2.07         2.20         3.48 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
        4.08         6.48        61.94        17.26         7.04        20.12 
TCGA-G2-A3VY TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GC-A6I1 
        0.85        19.46         2.24         4.50         1.12         2.66 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-AATO TCGA-GV-A3JW 
        6.41         7.59        11.31         2.04        10.65         6.41 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A5ND 
        6.15         5.69        19.07         1.51         6.74         9.01 
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 TCGA-R3-A69X TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HF TCGA-XF-A9SH 
       16.67        14.24         3.75        45.04        56.19        64.80 
TCGA-XF-A9SW TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMJ TCGA-XF-AAMT TCGA-XF-AAMX 
       11.90        66.64         2.10        54.90         2.96         6.77 
TCGA-YF-AA3M 
        9.04 

$`DEL PEAK 32(19P13.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-BL-A0C8 
       22.29        11.97        84.00       103.50        98.33        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N 
        7.33         2.66         6.74         6.58        11.93        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA 
       12.16        17.88        19.50        14.96         8.25        17.16 
TCGA-BT-A3PJ TCGA-BT-A42C TCGA-C4-A0F0 TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
       12.82        28.70         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-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        7.20         5.46         5.19        16.31         1.84         9.34 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF 
        2.53        66.41        19.00       130.88        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       15.62         1.81        10.59         7.79       123.85         2.20 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
        7.82         8.22        50.27        20.02         9.67         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        41.56        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-E7-A6ME 
        0.59         0.56         0.66         1.38         0.82        12.99 
TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 
       14.33         0.46        12.89         8.94         4.01        12.43 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       11.93        15.88        45.93        13.18        46.78        19.79 
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-A62N TCGA-FD-A62O TCGA-FD-A62P 
       11.01         6.87         5.69         2.66         4.83         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK 
        6.38        50.66         6.71         2.66         4.01        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
       15.19         7.13         3.25        30.61         5.69        26.93 
TCGA-G2-A2EO TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RC 
       35.24        52.67         6.94         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-GD-A76B TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JV 
        2.20         7.36        27.09         5.62         4.73         4.41 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA 
        7.63         7.79         4.14         6.67         6.41        11.54 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
       38.60         3.06         8.22         3.45         4.67         2.50 
TCGA-K4-A4AC TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
        6.48         1.81         6.38         6.35         3.45        11.80 
TCGA-S5-A6DX TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HH 
        0.85         6.58        88.93        97.45        15.35         1.87 
TCGA-XF-A8HI TCGA-XF-A9SI TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       17.88        79.66        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAML 
       18.90         2.24        16.27        92.98        10.82         7.63 
TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
       91.73         8.32        56.48        30.94        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
        3.88        10.36         4.83         0.66         7.96 

  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                          0.43                           0.07 
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                        112.44                         140.81 
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                          8.91                          10.55 
[1] "0.4 - 112.4 (8.9)"  "0.1 - 140.8 (10.6)"
[1] "hr=" "1.3"
D67V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 32(19P13.3) MUTATED          0       0       22        31       43
  DEL PEAK 32(19P13.3) WILD-TYPE        1       2       64        62       49
D67V3, multiclass
           clus
vv          DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              0                              2
  STAGE II                            22                             64
  STAGE III                           31                             62
  STAGE IV                            43                             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
  DEL PEAK 32(19P13.3) MUTATED         19 55 16
  DEL PEAK 32(19P13.3) WILD-TYPE       63 81 23
D67V4, multiclass
          clus
vv         DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE
  T0+T1+T2                           19                             63
  T3                                 55                             81
  T4                                 16                             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 32(19P13.3) MUTATED    49  16  20   4
  DEL PEAK 32(19P13.3) WILD-TYPE 117  12  35   3
D67V5, multiclass
    clus
vv   DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE
  N0                           49                            117
  N1                           16                             12
  N2                           20                             35
  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 32(19P13.3) MUTATED   37  6 54
  DEL PEAK 32(19P13.3) WILD-TYPE 92  1 87
D67V6, multiclass
    clus
vv   DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE
  M0                           37                             92
  M1                            6                              1
  MX                           54                             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                                cls
clus                               0   1
  DEL PEAK 32(19P13.3) MUTATED    30  68
  DEL PEAK 32(19P13.3) WILD-TYPE  47 133
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(19P13.3) MUTATED     30   68
  DEL PEAK 32(19P13.3) WILD-TYPE   47  133
        clus
vv       DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE
  FEMALE                           30                             47
  MALE                             68                            133
[1] 2 2
[1] FALSE
D67V8, continuous
D67V9, continuous
D67V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(19P13.3) MUTATED       7                         6    78
  DEL PEAK 32(19P13.3) WILD-TYPE    24                         7   137
D67V11, multiclass
                           clus
vv                          DEL PEAK 32(19P13.3) MUTATED
  ASIAN                                                7
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               78
                           clus
vv                          DEL PEAK 32(19P13.3) WILD-TYPE
  ASIAN                                                 24
  BLACK OR AFRICAN AMERICAN                              7
  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"
D67V12, binary
                                cls
clus                               0   1
  DEL PEAK 32(19P13.3) MUTATED     3  90
  DEL PEAK 32(19P13.3) WILD-TYPE   2 168
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(19P13.3) MUTATED      3   90
  DEL PEAK 32(19P13.3) WILD-TYPE    2  168
                        clus
vv                       DEL PEAK 32(19P13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           90
                        clus
vv                       DEL PEAK 32(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            168
[1] 2 2
[1] FALSE

Clustering(68) Variable = DEL PEAK 33(22Q13.32) MUTATION ANALYSIS
D68V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 33(22Q13.32) MUTATED    80  40
  DEL PEAK 33(22Q13.32) WILD-TYPE 102  48
  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE 
                            120                             150 
  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE 
                             40                              48 
$`DEL PEAK 33(22Q13.32) MUTATED`
TCGA-2F-A9KP TCGA-2F-A9KW TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20R TCGA-BT-A20V 
       11.97         4.83         2.66        19.04         5.06         5.06 
TCGA-BT-A20W TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ 
        8.35        12.82        15.42        28.70         9.99         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A47X TCGA-CU-A0YN TCGA-CU-A3QU TCGA-DK-A1A7 
        1.94        23.01         0.10        12.92         5.19        18.41 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL 
      130.88         1.81        10.59         7.79       123.85         3.98 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3X2 TCGA-DK-A6B1 
        7.82         8.22        10.49        21.30        17.98        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 
       15.68        41.06        43.59        15.35         0.49         0.59 
TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A7DV TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
        0.56        12.99         1.22        12.89        15.68         8.94 
TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN 
        6.87        11.93        45.93        24.30        22.45        12.82 
TCGA-FD-A3SO TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43U 
        5.52        19.79         1.97        22.98        14.93        14.93 
TCGA-FD-A43Y TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       12.13        11.01         5.36         6.84        27.45         6.87 
TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        2.66         6.28        18.81         9.30         6.71         4.11 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF 
        2.07        10.85        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-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R 
        7.73         2.10         2.20         7.36         7.59        11.31 
TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JX TCGA-GV-A40E TCGA-GV-A40G 
        2.04         5.62        10.65         6.15         6.41        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A5RJ 
       11.54         6.74         8.22         8.75         3.45         1.74 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
        1.81         4.27         6.35         3.45        13.48        12.23 
TCGA-PQ-A6FN TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SW TCGA-XF-A9SX 
       16.67         6.58        56.19        15.35        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-AAMF 
       21.04        28.24        26.27         2.24         2.10        10.82 
TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-YF-AA3L TCGA-YF-AA3M 
        7.63         2.96         6.77        56.48         7.96         9.04 

$`DEL PEAK 33(22Q13.32) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-BL-A0C8 TCGA-BL-A13I 
       22.29        84.00       103.50        98.33        40.08         7.33 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O 
        6.74        12.39         6.58        11.93        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA 
       17.88        19.50        14.89        14.96         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42F TCGA-CF-A1HR 
        5.59         3.65         4.67         2.07        28.41         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-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-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB 
        9.34         2.53         2.14        66.41        19.00         8.91 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I6 TCGA-DK-A3IK 
      112.44        16.14        17.62        15.62        87.32         2.20 
TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       50.27        20.02         9.67         8.28        10.55       140.81 
TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B6 TCGA-E5-A4U1 
       48.00        64.18        41.56        76.60        30.67        26.17 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       24.66         0.10         0.53         0.66         1.38         0.82 
TCGA-E7-A6MF TCGA-E7-A7XN TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SM 
       14.33         0.46         4.01        12.43        15.88         6.12 
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-G2-AA3B 
       30.61         5.69        26.93        35.24        17.26        52.67 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
        6.94        19.46         2.89         2.24        15.81         4.50 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A763 
       14.07        17.75         3.12        20.98         6.41        27.09 
TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        4.73         4.41         6.41         5.69         7.63         7.79 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
        4.14         6.67         1.51        38.60         3.06         9.01 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A83P TCGA-LT-A8JT 
        4.67         2.50         6.48        10.52         6.38        11.80 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE 
       14.24         0.85         3.75        45.04        88.93        97.45 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9T2 TCGA-XF-A9T4 
        1.87        17.88        64.80        79.66        18.90        16.27 
TCGA-XF-A9T5 TCGA-XF-AAME TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAN1 
       66.64        92.98        54.90        91.73         8.32        30.94 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39         3.88        10.36         4.83         0.66 

  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE 
                           0.10                            0.07 
  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE 
                         130.88                          140.81 
  DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE 
                          8.960                          10.015 
[1] "0.1 - 130.9 (9.0)"  "0.1 - 140.8 (10.0)"
[1] "hr=" "1.3"
D68V2, continuous
                                 vv
clus                              STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 33(22Q13.32) MUTATED          1       0       34        38       48
  DEL PEAK 33(22Q13.32) WILD-TYPE        0       2       52        55       44
D68V3, multiclass
           clus
vv          DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  STAGE 0A                              1                               0
  STAGE I                               0                               2
  STAGE II                             34                              52
  STAGE III                            38                              55
  STAGE IV                             48                              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 33(22Q13.32) MUTATED         31 59 21
  DEL PEAK 33(22Q13.32) WILD-TYPE       51 77 18
D68V4, multiclass
          clus
vv         DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  T0+T1+T2                            31                              51
  T3                                  59                              77
  T4                                  21                              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 33(22Q13.32) MUTATED    64  11  32   4
  DEL PEAK 33(22Q13.32) WILD-TYPE 102  17  23   3
D68V5, multiclass
    clus
vv   DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  N0                            64                             102
  N1                            11                              17
  N2                            32                              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 33(22Q13.32) MUTATED   39  4 77
  DEL PEAK 33(22Q13.32) WILD-TYPE 90  3 64
D68V6, multiclass
    clus
vv   DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  M0                            39                              90
  M1                             4                               3
  MX                            77                              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"
D68V7, binary
                                 cls
clus                                0   1
  DEL PEAK 33(22Q13.32) MUTATED    33  88
  DEL PEAK 33(22Q13.32) WILD-TYPE  44 113
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(22Q13.32) MUTATED     33   88
  DEL PEAK 33(22Q13.32) WILD-TYPE   44  113
        clus
vv       DEL PEAK 33(22Q13.32) MUTATED DEL PEAK 33(22Q13.32) WILD-TYPE
  FEMALE                            33                              44
  MALE                              88                             113
[1] 2 2
[1] FALSE
D68V8, continuous
D68V9, continuous
D68V10, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(22Q13.32) MUTATED       8                         8    96
  DEL PEAK 33(22Q13.32) WILD-TYPE    23                         5   119
D68V11, multiclass
                           clus
vv                          DEL PEAK 33(22Q13.32) MUTATED
  ASIAN                                                 8
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                                96
                           clus
vv                          DEL PEAK 33(22Q13.32) WILD-TYPE
  ASIAN                                                  23
  BLACK OR AFRICAN AMERICAN                               5
  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"
D68V12, binary
                                 cls
clus                                0   1
  DEL PEAK 33(22Q13.32) MUTATED     3 111
  DEL PEAK 33(22Q13.32) WILD-TYPE   2 147
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(22Q13.32) MUTATED      3  111
  DEL PEAK 33(22Q13.32) WILD-TYPE    2  147
                        clus
vv                       DEL PEAK 33(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           111
                        clus
vv                       DEL PEAK 33(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   2
  NOT HISPANIC OR LATINO                             147
[1] 2 2
[1] FALSE

Clustering(69) Variable = DEL PEAK 34(XP11.3) MUTATION ANALYSIS
D69V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 34(XP11.3) MUTATED    42  19
  DEL PEAK 34(XP11.3) WILD-TYPE 140  69
  DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE 
                           61                           209 
  DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE 
                           19                            69 
$`DEL PEAK 34(XP11.3) MUTATED`
TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-BL-A13J TCGA-BT-A20P TCGA-BT-A20T 
       84.00        98.33         4.83         2.66        17.88        14.89 
TCGA-BT-A20V TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-CF-A27C TCGA-CF-A47X 
        5.06         4.67        15.42         9.99         0.69         0.10 
TCGA-CU-A0YN TCGA-CU-A3QU TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD 
       12.92         5.19         2.14        19.00         8.91       112.44 
TCGA-DK-A1AG TCGA-DK-A2I6 TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A6B2 
       15.62        87.32        50.27        21.30         9.67        15.68 
TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A7DV TCGA-FD-A3B4 TCGA-FD-A3B6 
       41.06        43.59        24.66         1.22        15.68         6.87 
TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43Y TCGA-FD-A5BY TCGA-FD-A62N 
       12.82        19.79         1.97        12.13         6.84         2.66 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TF TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3VY 
       50.66         9.30         2.07        26.93         7.04         0.85 
TCGA-G2-AA3F TCGA-GD-A3OS TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-HQ-A2OF 
       19.46        20.98         6.15         7.79         4.14         3.06 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-PQ-A6FI 
        9.01         8.75         1.74         1.81         3.45        12.23 
TCGA-S5-AA26 TCGA-XF-A8HF TCGA-XF-A9SZ TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMW 
        3.75        56.19        28.24         7.63         2.96         8.32 
TCGA-XF-AAN1 
       30.94 

$`DEL PEAK 34(XP11.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM 
       22.29        11.97       103.50        40.08         7.33         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
       12.39         6.58        11.93        19.04        32.84        12.16 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
       19.50         5.06        14.96         8.35         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42F 
        5.59         3.65        12.82         2.07        28.70        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-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-A1A6 
        5.46        16.31         1.84         9.34         2.53        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 
       18.41       130.88        16.14        17.62         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
        7.79       123.85         2.20         3.98         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       10.49        20.02         8.28        10.55       140.81        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 
       17.98        64.18        41.56        76.60        67.36        30.67 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 
       15.35        26.17         0.10         0.49         0.53         0.59 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66         1.38         0.82        12.99        14.33 
TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
        0.46        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         6.12         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-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
        6.38        18.81         6.71         4.11         2.66         2.20 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        4.01        10.85        15.19         7.13         3.48         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-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 
       17.26        20.12        52.67         6.94         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-A6C6 TCGA-GD-A76B 
        2.66         7.73         2.10         3.12         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 
        6.41         7.59        11.31         2.04        27.09         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF 
        4.73        10.65         4.41         6.41         5.69         7.63 
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-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
       38.60         8.22         3.45         4.67         2.50         6.48 
TCGA-K4-A54R TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A8JT TCGA-MV-A51V 
       10.52         4.27         6.38         6.35        11.80        13.48 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
       16.67        14.24         0.85        45.04         6.58        88.93 
TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI 
       97.45        15.35         1.87        17.88        64.80        79.66 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       11.90        23.64        21.04        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ 
       16.27        66.64         2.10        92.98        10.82        54.90 
TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
       91.73         6.77        56.48        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
       10.36         4.83         0.66         7.96         9.04 

  DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE 
                       112.44                        140.81 
  DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE 
                         9.30                          9.04 
[1] "0.1 - 112.4 (9.3)" "0.1 - 140.8 (9.0)"
[1] "hr=" "1.1"
D69V2, continuous
                               vv
clus                            STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 34(XP11.3) MUTATED          0       0       18        21       23
  DEL PEAK 34(XP11.3) WILD-TYPE        1       2       68        72       69
D69V3, multiclass
           clus
vv          DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  STAGE 0A                            0                             1
  STAGE I                             0                             2
  STAGE II                           18                            68
  STAGE III                          21                            72
  STAGE IV                           23                            69
[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(XP11.3) MUTATED         15  30  11
  DEL PEAK 34(XP11.3) WILD-TYPE       67 106  28
D69V4, multiclass
          clus
vv         DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  T0+T1+T2                          15                            67
  T3                                30                           106
  T4                                11                            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
  DEL PEAK 34(XP11.3) MUTATED    35   8  10   2
  DEL PEAK 34(XP11.3) WILD-TYPE 131  20  45   5
D69V5, multiclass
    clus
vv   DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  N0                          35                           131
  N1                           8                            20
  N2                          10                            45
  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 34(XP11.3) MUTATED    31   1  30
  DEL PEAK 34(XP11.3) WILD-TYPE  98   6 111
D69V6, multiclass
    clus
vv   DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  M0                          31                            98
  M1                           1                             6
  MX                          30                           111
[1] 3 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 34(XP11.3) MUTATED    15  48
  DEL PEAK 34(XP11.3) WILD-TYPE  62 153
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XP11.3) MUTATED     15   48
  DEL PEAK 34(XP11.3) WILD-TYPE   62  153
        clus
vv       DEL PEAK 34(XP11.3) MUTATED DEL PEAK 34(XP11.3) WILD-TYPE
  FEMALE                          15                            62
  MALE                            48                           153
[1] 2 2
[1] FALSE
D69V8, continuous
D69V9, continuous
D69V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(XP11.3) MUTATED       6                         4    47
  DEL PEAK 34(XP11.3) WILD-TYPE    25                         9   168
D69V11, multiclass
                           clus
vv                          DEL PEAK 34(XP11.3) MUTATED
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              47
                           clus
vv                          DEL PEAK 34(XP11.3) WILD-TYPE
  ASIAN                                                25
  BLACK OR AFRICAN AMERICAN                             9
  WHITE                                               168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V12, binary
                               cls
clus                              0   1
  DEL PEAK 34(XP11.3) MUTATED     1  58
  DEL PEAK 34(XP11.3) WILD-TYPE   4 200
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 34(XP11.3) MUTATED      1   58
  DEL PEAK 34(XP11.3) WILD-TYPE    4  200
                        clus
vv                       DEL PEAK 34(XP11.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          58
                        clus
vv                       DEL PEAK 34(XP11.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           200
[1] 2 2
[1] FALSE

Clustering(70) Variable = DEL PEAK 35(XQ21.33) MUTATION ANALYSIS
D70V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 35(XQ21.33) MUTATED    40  15
  DEL PEAK 35(XQ21.33) WILD-TYPE 142  73
  DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE 
                            55                            215 
  DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE 
                            15                             73 
$`DEL PEAK 35(XQ21.33) MUTATED`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20X 
       84.00       103.50        98.33        14.89         5.06         8.25 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C TCGA-CF-A1HS TCGA-CF-A27C 
        5.59         4.67        15.42        28.70         0.43         0.69 
TCGA-CF-A47X TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A3IS 
        0.10         5.46         5.19         8.91       130.88        50.27 
TCGA-DK-A3IT TCGA-DK-A6B5 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-FD-A3B4 TCGA-FD-A3SN 
       21.30        41.06        43.59        24.66        15.68        12.82 
TCGA-FD-A3SS TCGA-FD-A5BY TCGA-FD-A6TA TCGA-FJ-A3Z7 TCGA-FT-A3EE TCGA-G2-A2EL 
        1.97         6.84        50.66        15.19         3.25        26.93 
TCGA-G2-A3IB TCGA-G2-AA3B TCGA-GC-A6I1 TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GV-A3JW 
        7.04        52.67         2.66         2.20         6.41         6.41 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40G TCGA-HQ-A2OE TCGA-K4-A3WV 
        6.15         7.79         4.14        19.07        38.60         4.67 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-S5-A6DX 
       10.52         1.74         3.45        13.48        12.23         0.85 
TCGA-S5-AA26 TCGA-XF-A8HI TCGA-XF-A9SZ TCGA-XF-A9T5 TCGA-XF-AAMT TCGA-XF-AAMX 
        3.75        17.88        28.24        66.64         2.96         6.77 
TCGA-YF-AA3L 
        7.96 

$`DEL PEAK 35(XQ21.33) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KW TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       22.29        11.97         4.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        11.93        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20W 
       12.16        17.88        19.50         5.06        14.96         8.35 
TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42E TCGA-BT-A42F 
       17.16         3.65        12.82         2.07         9.99        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A47S TCGA-CF-A47T 
        8.98         1.94        23.01         0.46         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-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       16.31         1.84         9.34         2.53         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       18.41        19.00       112.44        16.14        17.62        15.62 
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-A3IU TCGA-DK-A3IV 
        3.98         7.82         8.22        10.49        20.02         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
        8.28        10.55       140.81        48.00        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-E5-A4TZ 
       41.56        76.60        67.36        15.68        30.67        15.35 
TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 TCGA-E7-A5KE 
       26.17         0.10         0.49         0.53         0.59         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV 
        0.66         1.38         0.82        12.99        14.33         1.22 
TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
        0.46        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         6.12 
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-A6TB 
       49.68         2.66         4.83         6.28         6.38        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        9.30         6.71         4.11         2.07         2.66         2.20 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A61P 
        4.01        10.85         7.13         3.48         4.08         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-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        0.85         6.94        19.46         2.89         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 
        4.50        15.91        14.07        17.75         1.12         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12        20.98         7.36         7.59        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV 
        2.04        27.09         5.62         4.73        10.65         4.41 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO 
        5.69         7.63         6.67         6.41        11.54         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
        6.74         3.06         9.01         8.22         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-LT-A8JT TCGA-PQ-A6FN TCGA-R3-A69X TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
       11.80        16.67        14.24        45.04         6.58        88.93 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SH TCGA-XF-A9SI 
       97.45        56.19        15.35         1.87        64.80        79.66 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       11.90        23.64        21.04        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML 
       16.27         2.10        92.98        10.82        54.90         7.63 
TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
       91.73         8.32        56.48        30.94        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3M 
        3.88        10.36         4.83         0.66         9.04 

  DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE 
                        130.88                         140.81 
  DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE 
                          8.25                           9.34 
[1] "0.1 - 130.9 (8.2)" "0.1 - 140.8 (9.3)"
[1] "hr=" "1.3"
D70V2, continuous
                                vv
clus                             STAGE 0A STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 35(XQ21.33) MUTATED          0       0       18        15       19
  DEL PEAK 35(XQ21.33) WILD-TYPE        1       2       68        78       73
D70V3, multiclass
           clus
vv          DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  STAGE 0A                             0                              1
  STAGE I                              0                              2
  STAGE II                            18                             68
  STAGE III                           15                             78
  STAGE IV                            19                             73
[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(XQ21.33) MUTATED         17  24   9
  DEL PEAK 35(XQ21.33) WILD-TYPE       65 112  30
D70V4, multiclass
          clus
vv         DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  T0+T1+T2                           17                             65
  T3                                 24                            112
  T4                                  9                             30
[1] 3 2
[1] 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(XQ21.33) MUTATED    31   6  11   1
  DEL PEAK 35(XQ21.33) WILD-TYPE 135  22  44   6
D70V5, multiclass
    clus
vv   DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  N0                           31                            135
  N1                            6                             22
  N2                           11                             44
  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 35(XQ21.33) MUTATED    23   0  32
  DEL PEAK 35(XQ21.33) WILD-TYPE 106   7 109
D70V6, multiclass
    clus
vv   DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  M0                           23                            106
  M1                            0                              7
  MX                           32                            109
[1] 3 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 35(XQ21.33) MUTATED    17  38
  DEL PEAK 35(XQ21.33) WILD-TYPE  60 163
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(XQ21.33) MUTATED     17   38
  DEL PEAK 35(XQ21.33) WILD-TYPE   60  163
        clus
vv       DEL PEAK 35(XQ21.33) MUTATED DEL PEAK 35(XQ21.33) WILD-TYPE
  FEMALE                           17                             60
  MALE                             38                            163
[1] 2 2
[1] FALSE
D70V8, continuous
D70V9, continuous
D70V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(XQ21.33) MUTATED       3                         5    42
  DEL PEAK 35(XQ21.33) WILD-TYPE    28                         8   173
D70V11, multiclass
                           clus
vv                          DEL PEAK 35(XQ21.33) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               42
                           clus
vv                          DEL PEAK 35(XQ21.33) WILD-TYPE
  ASIAN                                                 28
  BLACK OR AFRICAN AMERICAN                              8
  WHITE                                                173
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V12, binary
                                cls
clus                               0   1
  DEL PEAK 35(XQ21.33) MUTATED     2  49
  DEL PEAK 35(XQ21.33) WILD-TYPE   3 209
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(XQ21.33) MUTATED      2   49
  DEL PEAK 35(XQ21.33) WILD-TYPE    3  209
                        clus
vv                       DEL PEAK 35(XQ21.33) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           49
                        clus
vv                       DEL PEAK 35(XQ21.33) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            209
[1] 2 2
[1] FALSE
